sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | kmer 0~20150903+r2013-9 (amd64) Mon, 30 Jun 2025 18:42:11 +0000 | +==============================================================================+ Package: kmer Version: 0~20150903+r2013-9 Source Version: 0~20150903+r2013-9 Distribution: perl-5.40-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 Mon, 30 Jun 2025 18:42:12 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup kmer_0~20150903+r2013-9 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup kmer_0~20150903+r2013-9 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 30 Jun 2025 18:42:13 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/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 Mon, 30 Jun 2025 18:42:19 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/kmer_0~20150903+r2013-9.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 30 Jun 2025 18:42:19 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive ./ InRelease Get:2 copy:/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive ./ Release [609 B] Ign:3 copy:/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive ./ Release.gpg Get:4 copy:/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive ./ Sources [643 B] Get:5 copy:/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive ./ Packages [682 B] Fetched 1934 B in 0s (0 B/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-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libjs-jquery libjs-sphinxdoc libjs-underscore libmagic-mgc libmagic1t64 libpipeline1 libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libtool libuchardet0 libxml2 m4 man-db media-types netbase po-debconf python3 python3-dev python3-minimal python3.13 python3.13-dev python3.13-minimal sensible-utils tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libjs-jquery libjs-sphinxdoc libjs-underscore libmagic-mgc libmagic1t64 libpipeline1 libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libtool libuchardet0 libxml2 m4 man-db media-types netbase po-debconf python3 python3-dev python3-minimal python3.13 python3.13-dev python3.13-minimal sbuild-build-depends-main-dummy sensible-utils tzdata zlib1g-dev 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. Need to get 26.7 MB of archives. After this operation, 105 MB of additional disk space will be used. Get:1 copy:/build/kmer-GRpvsw/resolver-tFzIZS/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-4 [260 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:34 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.30 [25.6 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.1-1 [161 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.5-2 [2160 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.5-2 [5291 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.5-1 [10.4 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.5-2 [504 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.5-1 [26.1 kB] Preconfiguring packages ... Fetched 26.7 MB in 0s (166 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... 23091 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 23425 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jun 30 18:42:25 UTC 2025. Universal Time is now: Mon Jun 30 18:42:25 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:amd64 (2.7.1-1) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpython3.13:amd64 (3.13.5-2) ... 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 (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up python3.13 (3.13.5-2) ... Setting up python3 (3.13.5-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libpython3.13-dev:amd64 (3.13.5-2) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up dh-python (6.20250414) ... Setting up libpython3-dev:amd64 (3.13.5-1) ... Setting up python3.13-dev (3.13.5-2) ... 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 python3-dev (3.13.5-1) ... Setting up debhelper (13.24.2) ... Setting up dh-exec (0.30) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 30 Jun 2025 18:42:26 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 30 Jun 2025 18:42:26 +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_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-exec_0.30 dh-python_6.20250414 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.44-3 libblkid1_2.41-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libexpat1_2.7.1-1 libexpat1-dev_2.7.1-1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libhogweed6t64_3.10.1-1 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_8.1.3-5 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap2_2.6.10+dfsg-1+b1 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 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_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libpython3-dev_3.13.5-1 libpython3-stdlib_3.13.5-1 libpython3.13_3.13.5-2 libpython3.13-dev_3.13.5-2 libpython3.13-minimal_3.13.5-2 libpython3.13-stdlib_3.13.5-2 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 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 libsframe1_2.44-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 media-types_13.0.0 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.5 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 po-debconf_1.0.21+nmu1 python3_3.13.5-1 python3-dev_3.13.5-1 python3-minimal_3.13.5-1 python3.13_3.13.5-2 python3.13-dev_3.13.5-2 python3.13-minimal_3.13.5-2 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 tzdata_2025b-4 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 30 Jun 2025 18:42:26 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kmer Binary: kmer, libkmer-dev, meryl, libmeryl-dev, leaff, sim4db, atac, kmer-examples Architecture: any all Version: 0~20150903+r2013-9 Maintainer: Debian Med Packaging Team Uploaders: Afif Elghraoui Homepage: http://kmer.sourceforge.net Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kmer Vcs-Git: https://salsa.debian.org/med-team/kmer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev Package-List: atac deb science optional arch=any kmer deb science optional arch=all kmer-examples deb science optional arch=all leaff deb science optional arch=any libkmer-dev deb libdevel optional arch=any libmeryl-dev deb libdevel optional arch=any meryl deb science optional arch=any sim4db deb science optional arch=any Checksums-Sha1: 6da7324491e761437f27207f0b9135d767452e7a 1251653 kmer_0~20150903+r2013.orig.tar.gz bff8b0b6f815807795d55bf9adb33c18dee8cf94 2380056 kmer_0~20150903+r2013-9.debian.tar.xz Checksums-Sha256: 8fd9c289244e69e38bb7709f3523d39edf1c2ced2cbcc687fcf00ecfca78ea47 1251653 kmer_0~20150903+r2013.orig.tar.gz 27e69d0ec3c9f716d2a81a0aedd9c0d48c9807abf17815db0327f0f8901a0758 2380056 kmer_0~20150903+r2013-9.debian.tar.xz Files: 30b66a10ddc64022509dd8b85425880f 1251653 kmer_0~20150903+r2013.orig.tar.gz 5fb535fd2ba7759f38b418f0008eb2d5 2380056 kmer_0~20150903+r2013-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbgD4MACgkQPCZ2P2xn 5uKZKA/+ItZCQH6KTrqdKHP/e+NVJ89S9hoixlgaKwxFxp+4xlJNQAxK22CN7mWe QFzs2miUWNDtrs1LwEjvCCcubEvwdsqy8w524udkZ8cXcOIPpbiamvFVT9CBH9mv GhYquR3pLIsNvJP4V2Wg0YpI4VO+AnLObpxhfAPw3YXFFV3yEsxV10XuoEwRJlSb DENV12lmnUlT2SmErXD+rwv/xBAIEsTBc5Jh6S0AJetqScE5d0uoBtpy0/bfShkj ebBCJYH2ufELcXm5ujgoHTBx1O+vjwtitHvYTdR7KIOFjNFTJeTBIBrTXNW4gxYg uXo+iS14JrHDDDLW01a8utkiVJaJfNRmNKUhSKAgBCHY2uQKVVZZhqfr93gzcNM+ GesWALfRz2kMmBP88GRV9Q2QyP7xmunAC/sLCS3r1eBOp5eM5W7ntkiM7hgdyvaI tMsXOC7rvN73pCd2PHu++mF1VbGM3vMR0lhQ8k+uDkFFCtqmbOBEurnW/HJvtHLa nm3yhWD3VjEjqHwr6QOKumfBPKdSdeMAnPX6FTrJnEyhEWLajKmDoGCXcZ9yDY5z tuQGDtx5+iYEvxl1Nyj9VpOVEfZtFq4CWBOak5GnCmzlL97IE66OaXGrDtLvb70p McpVXmtFKDvfVq/bhXYs3WNP3Y3snHh1p2DO8ee/71n4hE3rX0Y= =hXe+ -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./kmer_0~20150903+r2013-9.dsc: no acceptable signature found dpkg-source: info: extracting kmer in /build/kmer-GRpvsw/kmer-0~20150903+r2013 dpkg-source: info: unpacking kmer_0~20150903+r2013.orig.tar.gz dpkg-source: info: unpacking kmer_0~20150903+r2013-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying allow-freebsd-build.patch dpkg-source: info: applying atac-helper-script-paths.patch dpkg-source: info: applying atac-readme.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying linux-cflags.patch dpkg-source: info: applying fix_wrong_evaluation_order.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying drop_distutils Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 30 Jun 2025 18:42:27 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network kmer_0~20150903+r2013-9 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network kmer_0~20150903+r2013-9 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en 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/kmer-GRpvsw/kmer-0~20150903+r2013 SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-c50df9d4-c93b-4f3a-a583-10172f4df144 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 kmer dpkg-buildpackage: info: source version 0~20150903+r2013-9 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 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' /usr/bin/make real-clean make[2]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' rm -f ESTmapper/*.o ESTmapper/mergeCounts ESTmapper/terminate ESTmapper/Make.depends ESTmapper/mergeCounts.C.d ESTmapper/terminate.C.d ESTmapper/mergeCounts ESTmapper/terminate rm -f atac-driver/libatac/*.o atac-driver/libatac/*~ atac-driver/libatac/libatac.a atac-driver/libatac/Make.depends atac-driver/libatac/atacFeature.C.d atac-driver/libatac/atacFeatureList.C.d atac-driver/libatac/atacFile.C.d atac-driver/libatac/atacFileStreamMerge.C.d atac-driver/libatac/atacMatch.C.d atac-driver/libatac/atacMatchList.C.d atac-driver/libatac/atacMatchOrder.C.d rm -f atac-driver/alignOverlap/*.o atac-driver/alignOverlap/*~ atac-driver/alignOverlap/core atac-driver/alignOverlap/overlap-process1.C atac-driver/alignOverlap/overlap-process2.C atac-driver/alignOverlap/overlap atac-driver/alignOverlap/Make.depends atac-driver/alignOverlap/overlap.C.d atac-driver/alignOverlap/overlap-sort.C.d atac-driver/alignOverlap/overlap-printAnno.C.d atac-driver/alignOverlap/overlap-find.C.d rm -f atac-driver/gapShifter/*.o atac-driver/gapShifter/*~ atac-driver/gapShifter/core atac-driver/gapShifter/gapShifter atac-driver/gapShifter/extractSequence atac-driver/gapShifter/extractUnmapped atac-driver/gapShifter/coalesceMatches atac-driver/gapShifter/correctGaps atac-driver/gapShifter/testAtac atac-driver/gapShifter/cleanAtac atac-driver/gapShifter/projectFeatures atac-driver/gapShifter/Make.depends atac-driver/gapShifter/gapShifter.C.d atac-driver/gapShifter/extractSequence.C.d atac-driver/gapShifter/extractUnmapped.C.d atac-driver/gapShifter/coalesceMatches.C.d atac-driver/gapShifter/correctGaps.C.d atac-driver/gapShifter/testAtac.C.d atac-driver/gapShifter/cleanAtac.C.d atac-driver/gapShifter/projectFeatures.C.d rm -f atac-driver/lengthFilter/*.o atac-driver/lengthFilter/*~ atac-driver/lengthFilter/core atac-driver/lengthFilter/lengthFilter atac-driver/lengthFilter/Make.depends atac-driver/lengthFilter/lengthFilter.C.d rm -f atac-driver/matchExtender/*.o atac-driver/matchExtender/*~ atac-driver/matchExtender/core atac-driver/matchExtender/matchExtender atac-driver/matchExtender/Make.depends atac-driver/matchExtender/matchExtender.C.d atac-driver/matchExtender/matchExtender-dump.C.d atac-driver/matchExtender/matchExtender-func.C.d rm -f atac-driver/mismatchCounter/*.o atac-driver/mismatchCounter/*~ atac-driver/mismatchCounter/core atac-driver/mismatchCounter/mismatchCounter atac-driver/mismatchCounter/Make.depends atac-driver/mismatchCounter/mismatchCounter.C.d rm -f atac-driver/statsGenerator/*.o atac-driver/statsGenerator/*~ atac-driver/statsGenerator/core atac-driver/statsGenerator/statsGenerator atac-driver/statsGenerator/Make.depends atac-driver/statsGenerator/statsGenerator.C.d rm -f atac-driver/uniqueFilter/*.o atac-driver/uniqueFilter/*~ atac-driver/uniqueFilter/core atac-driver/uniqueFilter/uniqueFilter atac-driver/uniqueFilter/Make.depends atac-driver/uniqueFilter/uniqueFilter.C.d rm -f atac-driver/clumpMaker/*.o atac-driver/clumpMaker/*~ atac-driver/clumpMaker/core atac-driver/clumpMaker/clumpMaker atac-driver/clumpMaker/Make.depends atac-driver/clumpMaker/clumpMaker.C.d rm -f atac-driver/chainer/*.o atac-driver/chainer/*/*.o atac-driver/chainer/*.so atac-driver/chainer/python/*.pyc atac-driver/chainer/localAlignerInterfacemodule.so atac-driver/chainer/halignmodule.so atac-driver/chainer/Make.depends atac-driver/chainer/localalign/GF_ALN_dpaligner.C.d atac-driver/chainer/localalign/GF_ALN_local.C.d atac-driver/chainer/localalign/GF_ALN_overlap.C.d atac-driver/chainer/localalign/GF_ALN_loverlapper.C.d atac-driver/chainer/localalign/GF_ALN_pieceOlap.C.d atac-driver/chainer/localalign/localAlignerInterfacemodule.C.d atac-driver/chainer/halign/halign.C.d atac-driver/chainer/halign/halignmodule.C.d rm -f atac-driver/chimera/*.o atac-driver/chimera/*~ atac-driver/chimera/core atac-driver/chimera/happy-clones-span-clumps atac-driver/chimera/Make.depends atac-driver/chimera/happy-clones-span-clumps.C.d rm -f atac-driver/Make.depends rm -f seatac/*.o seatac/seatac seatac/heavychains seatac/filter-nop.so seatac/filter-heavychains.so seatac/Make.depends seatac/seatac.C.d seatac/configuration.C.d seatac/encodedQuery.C.d seatac/hitMatrix.C.d seatac/thr-search.C.d seatac/thr-loader.C.d seatac/thr-deadlock.C.d seatac/hitMatrix-sort.C.d rm -f leaff/*.o leaff/leaff leaff/Make.depends leaff/leaff.C.d leaff/blocks.C.d leaff/dups.C.d leaff/gc.C.d leaff/partition.C.d leaff/simseq.C.d leaff/stats.C.d rm -f meryl/*.o meryl/meryl meryl/simple meryl/mapMers meryl/mapMers-depth meryl/kmer-mask meryl/libmerylguts.a meryl/Make.depends meryl/args.C.d meryl/binaryOp.C.d meryl/build.C.d meryl/build-threads.C.d meryl/dump.C.d meryl/estimate.C.d meryl/merge.C.d meryl/unaryOp.C.d meryl/meryl.C.d meryl/simple.C.d meryl/mapMers.C.d meryl/mapMers-depth.C.d meryl/kmer-mask.C.d rm -f seagen/*.o seagen/seagen seagen/hitConverter seagen/filterEST seagen/filterMRNA seagen/filterNULL seagen/filtertest seagen/sortHits seagen/filterESTsimple seagen/Make.depends seagen/searchGENOME.C.d seagen/configuration.C.d seagen/encodedQuery.C.d seagen/thr-deadlock.C.d seagen/thr-loader.C.d seagen/thr-search.C.d seagen/thr-output.C.d seagen/hitMatrix-sort.C.d seagen/aHit.C.d seagen/hitConverter.C.d seagen/filterEST.C.d seagen/filterEST-complicated.C.d seagen/filterMRNA.C.d seagen/filterNULL.C.d seagen/sortHits.C.d seagen/filtertest.C.d seagen/hitReader.C.d seagen/hitMatrix.C.d rm -f sim4dbutils/*.o sim4dbutils/cleanPolishes sim4dbutils/fixPolishesIID sim4dbutils/comparePolishes sim4dbutils/convertToAtac sim4dbutils/convertToExtent sim4dbutils/convertPolishes sim4dbutils/detectChimera sim4dbutils/depthOfPolishes sim4dbutils/filterPolishes sim4dbutils/headPolishes sim4dbutils/mappedCoverage sim4dbutils/mergePolishes sim4dbutils/parseSNP sim4dbutils/pickBestPolish sim4dbutils/pickBestPair sim4dbutils/pickUniquePolish sim4dbutils/plotCoverageVsIdentity sim4dbutils/removeDuplicate sim4dbutils/sortPolishes sim4dbutils/summarizePolishes sim4dbutils/uniqPolishes sim4dbutils/vennPolishes sim4dbutils/realignPolishes sim4dbutils/removeRedundant sim4dbutils/reportAlignmentDifferences sim4dbutils/Make.depends sim4dbutils/cleanPolishes.C.d sim4dbutils/fixPolishesIID.C.d sim4dbutils/comparePolishes.C.d sim4dbutils/convertToAtac.C.d sim4dbutils/convertToExtent.C.d sim4dbutils/convertPolishes.C.d sim4dbutils/detectChimera.C.d sim4dbutils/depthOfPolishes.C.d sim4dbutils/filterPolishes.C.d sim4dbutils/headPolishes.C.d sim4dbutils/mappedCoverage.C.d sim4dbutils/mergePolishes.C.d sim4dbutils/parseSNP.C.d sim4dbutils/pickBestPolish.C.d sim4dbutils/pickBestPair.C.d sim4dbutils/pickUniquePolish.C.d sim4dbutils/plotCoverageVsIdentity.C.d sim4dbutils/removeDuplicate.C.d sim4dbutils/sortPolishes.C.d sim4dbutils/summarizePolishes.C.d sim4dbutils/uniqPolishes.C.d sim4dbutils/vennPolishes.C.d sim4dbutils/realignPolishes.C.d sim4dbutils/removeRedundant.C.d sim4dbutils/reportAlignmentDifferences.C.d sim4dbutils/s4p_overlap.C.d rm -f sim4db/*.o sim4db/sim4db sim4db/Make.depends sim4db/sim4th.C.d rm -f snapper/*.o snapper/snapper2 snapper/Make.depends snapper/snapper2.C.d snapper/configuration.C.d snapper/thr-search.C.d snapper/thr-filter.C.d snapper/thr-polish.C.d snapper/thr-polish-dp.C.d snapper/hitMatrix.C.d snapper/hitMatrix-sort.C.d rm -f tapper/*.o tapper/tagger tapper/tapper tapper/tapperconvert tapper/tappermerge tapper/tappersort tapper/tappererrorcorrect tapper/Make.depends tapper/tagger.C.d tapper/tapper.C.d tapper/tapperconvert.C.d tapper/tappermerge.C.d tapper/tappersort.C.d tapper/tappererrorcorrect.C.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/reversecomplement.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.C.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/diffs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/diffs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.c.d rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/*.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/Make.depends /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/md5.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/palloc.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.c.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.C.d /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C.d rm -f Make.depends Make.compilers make[2]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' rm -rf installdir make[1]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building kmer using existing ./kmer_0~20150903+r2013.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building kmer in kmer_0~20150903+r2013-9.debian.tar.xz dpkg-source: info: building kmer in kmer_0~20150903+r2013-9.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' # The Makefile apparently doesn't use regular LDFLAGS. # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's # use them here. /usr/bin/make install \ CLDFLAGS="-Wl,-z,relro -Wl,-z,now" \ CXXLDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' making ESTmapper/mergeCounts.C.d making ESTmapper/terminate.C.d making atac-driver/libatac/atacFeature.C.d making atac-driver/libatac/atacFeatureList.C.d making atac-driver/libatac/atacFile.C.d making atac-driver/libatac/atacFileStreamMerge.C.d making atac-driver/libatac/atacMatch.C.d making atac-driver/libatac/atacMatchList.C.d making atac-driver/libatac/atacMatchOrder.C.d making atac-driver/alignOverlap/overlap.C.d making atac-driver/alignOverlap/overlap-sort.C.d making atac-driver/alignOverlap/overlap-printAnno.C.d making atac-driver/alignOverlap/overlap-find.C.d making atac-driver/gapShifter/gapShifter.C.d making atac-driver/gapShifter/extractSequence.C.d making atac-driver/gapShifter/extractUnmapped.C.d making atac-driver/gapShifter/coalesceMatches.C.d making atac-driver/gapShifter/correctGaps.C.d making atac-driver/gapShifter/testAtac.C.d making atac-driver/gapShifter/cleanAtac.C.d making atac-driver/gapShifter/projectFeatures.C.d making atac-driver/lengthFilter/lengthFilter.C.d making atac-driver/matchExtender/matchExtender.C.d making atac-driver/matchExtender/matchExtender-dump.C.d making atac-driver/matchExtender/matchExtender-func.C.d making atac-driver/mismatchCounter/mismatchCounter.C.d making atac-driver/statsGenerator/statsGenerator.C.d making atac-driver/uniqueFilter/uniqueFilter.C.d making atac-driver/clumpMaker/clumpMaker.C.d making atac-driver/chainer/localalign/GF_ALN_dpaligner.C.d making atac-driver/chainer/localalign/GF_ALN_local.C.d making atac-driver/chainer/localalign/GF_ALN_overlap.C.d making atac-driver/chainer/localalign/GF_ALN_loverlapper.C.d making atac-driver/chainer/localalign/GF_ALN_pieceOlap.C.d making atac-driver/chainer/localalign/localAlignerInterfacemodule.C.d making atac-driver/chainer/halign/halign.C.d making atac-driver/chainer/halign/halignmodule.C.d making atac-driver/chimera/happy-clones-span-clumps.C.d making seatac/seatac.C.d making seatac/configuration.C.d making seatac/encodedQuery.C.d making seatac/hitMatrix.C.d making seatac/thr-search.C.d making seatac/thr-loader.C.d making seatac/thr-deadlock.C.d making seatac/hitMatrix-sort.C.d making leaff/leaff.C.d making leaff/blocks.C.d making leaff/dups.C.d making leaff/gc.C.d making leaff/partition.C.d making leaff/simseq.C.d making leaff/stats.C.d making meryl/args.C.d making meryl/binaryOp.C.d making meryl/build.C.d making meryl/build-threads.C.d making meryl/dump.C.d making meryl/estimate.C.d making meryl/merge.C.d making meryl/unaryOp.C.d making meryl/meryl.C.d making meryl/simple.C.d making meryl/mapMers.C.d making meryl/mapMers-depth.C.d making meryl/kmer-mask.C.d making seagen/searchGENOME.C.d making seagen/configuration.C.d making seagen/encodedQuery.C.d making seagen/thr-deadlock.C.d making seagen/thr-loader.C.d making seagen/thr-search.C.d making seagen/thr-output.C.d making seagen/hitMatrix-sort.C.d making seagen/aHit.C.d making seagen/hitConverter.C.d making seagen/filterEST.C.d making seagen/filterEST-complicated.C.d making seagen/filterMRNA.C.d making seagen/filterNULL.C.d making seagen/sortHits.C.d making seagen/filtertest.C.d making seagen/hitReader.C.d making seagen/hitMatrix.C.d making sim4dbutils/cleanPolishes.C.d making sim4dbutils/fixPolishesIID.C.d making sim4dbutils/comparePolishes.C.d making sim4dbutils/convertToAtac.C.d making sim4dbutils/convertToExtent.C.d making sim4dbutils/convertPolishes.C.d making sim4dbutils/detectChimera.C.d making sim4dbutils/depthOfPolishes.C.d making sim4dbutils/filterPolishes.C.d making sim4dbutils/headPolishes.C.d making sim4dbutils/mappedCoverage.C.d making sim4dbutils/mergePolishes.C.d making sim4dbutils/parseSNP.C.d making sim4dbutils/pickBestPolish.C.d making sim4dbutils/pickBestPair.C.d making sim4dbutils/pickUniquePolish.C.d making sim4dbutils/plotCoverageVsIdentity.C.d making sim4dbutils/removeDuplicate.C.d making sim4dbutils/sortPolishes.C.d making sim4dbutils/summarizePolishes.C.d making sim4dbutils/uniqPolishes.C.d making sim4dbutils/vennPolishes.C.d making sim4dbutils/realignPolishes.C.d making sim4dbutils/removeRedundant.C.d making sim4dbutils/reportAlignmentDifferences.C.d making sim4dbutils/s4p_overlap.C.d making sim4db/sim4th.C.d making snapper/snapper2.C.d making snapper/configuration.C.d making snapper/thr-search.C.d making snapper/thr-filter.C.d making snapper/thr-polish.C.d making snapper/thr-polish-dp.C.d making snapper/hitMatrix.C.d making snapper/hitMatrix-sort.C.d making tapper/tagger.C.d making tapper/tapper.C.d making tapper/tapperconvert.C.d making tapper/tappermerge.C.d making tapper/tappersort.C.d making tapper/tappererrorcorrect.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/reversecomplement.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/md5.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/palloc.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c.d gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c: In function ‘mtRandomGaussian’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c:166:34: warning: variable ‘y2’ set but not used [-Wunused-but-set-variable] 166 | double x1=0, x2=0, w=0, y1=0, y2=0; | ^~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.c gcc -Wl,-z,relro -Wl,-z,now -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.o -pthread -ldl -lm /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test | diff - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.out > /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/diffs 2>&1 if test -s /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/diffs ; then echo 'MT19937: TEST FAILED'; else echo 'MT19937: Test Passed'; fi MT19937: Test Passed touch /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test | diff - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.out making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.c.d making /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.c.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ESTmapper/mergeCounts.o -c ESTmapper/mergeCounts.C ESTmapper/mergeCounts.C: In function ‘int main(int, char**)’: ESTmapper/mergeCounts.C:33:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 33 | fgets(buf, 256, Fs[i]); | ~~~~~^~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o ESTmapper/mergeCounts ESTmapper/mergeCounts.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ESTmapper/terminate.o -c ESTmapper/terminate.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from ESTmapper/terminate.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ ESTmapper/terminate.C: In member function ‘void iidReaderWriter::load(uint32)’: ESTmapper/terminate.C:82:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fscanf(inFile, uint32FMT, &iid); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ESTmapper/terminate.C:85:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(inFile, uint32FMT, &iid); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function ‘void sim4command::finalize()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:147:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 147 | if (_genLo > _genHi) | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function ‘char* sim4command::getESTheader()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:184:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 184 | static char *xxx = "anonymous cDNA sequence"; | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function ‘char* sim4command::getGENheader()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:222:15: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 222 | char *xxx = "anonymous genomic sequence"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.H:8, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C: In member function ‘void Sim4::IDISPLAY(sim4polishBuilder&, char*, char*, char*, char*, int, int, int*, int, int, int, Exon*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:681:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 681 | builder.addExonAlignment("Empty exon list; no alignment possible!", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:682:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 682 | "Empty exon list; no alignment possible!"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:694:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 694 | builder.addExonAlignment("Alignment fragment not found; no alignment possible!", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:695:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 695 | "Alignment fragment not found; no alignment possible!"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C: In member function ‘void Sim4::path(int, int, char, int, int, char, int, edit_script**, edit_script**)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C:777:13: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 777 | if (head2) *tail = tail2; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.C:557:38: note: ‘head2’ declared here 557 | edit_script *head1, *tail1, *head2, *tail2; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C: In function ‘void readModel(Fixed_Length_ICM_t*, const char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:53:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 53 | fread (line, sizeof (char), ID_STRING_LEN, fp); // skip the text header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:84:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fread ((*fixed).permutation, sizeof (int), (*fixed).length, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C: In function ‘int readtree(Sim4*, char*, tree*, int)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:452:6: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 452 | int len; | ^~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C: In function ‘int Is_Cod_NonCod(const int*, double*, int)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:751:12: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized] 751 | double *scores; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C: In member function ‘void Sim4::bld_table(char*, int, mss_t, int)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C:112:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 112 | if (emer < 0) | ^~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.C:115:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 115 | ecode <<= 2; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:249:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 249 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:249:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 249 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:365:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:365:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:58:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:68:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:80:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 80 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:91:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | sprintf(gpp, "%c"uint32FMT"", gaptyp, gapcnt); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:163:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 163 | fprintf(stderr, "sim4reader: Unknown matchOrientation '"uint32FMT"' in printPolish()\n", _matchOrientation); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:176:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stderr, "sim4reader: Unknown strandOrientation '"uint32FMT"' in printPolish()\n", _matchOrientation); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:100: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:323:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 323 | fprintf(stderr, "sim4reader: Unknown strandOrientation '"uint32FMT"' in printPolishGFF3()\n", _matchOrientation); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:46:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "sim4reader: Got '%s', expecting 'sim4begin' at byte "uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:65:2: warning: #warning LAZY PROGRAMMER did not extend an array [-Wcpp] 65 | #warning LAZY PROGRAMMER did not extend an array | ^~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:126:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "sim4reader: Got '%s', expecting GFF3 mRNA line at byte "uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:150:2: warning: #warning LAZY PROGRAMMER did not extend an array [-Wcpp] 150 | #warning LAZY PROGRAMMER did not extend an array | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:55:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:72:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 72 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:169:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:246:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 246 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:275:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | r = sscanf(crttok, "ID=sim4db"uint32FMT"", &matchID); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:280:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 280 | r = sscanf(crttok, "Name="uint32FMT":%s", &_estID, _estDefLine); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:293:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 293 | r = sscanf(crttok, "targetLen="uint32FMT"", &_estLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:296:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | r = sscanf(crttok, "pA="uint32FMT"", &_estPolyA); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:299:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | r = sscanf(crttok, "pT="uint32FMT"", &_estPolyT); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:302:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | r = sscanf(crttok, "genRegion="uint32FMT"-"uint32FMT"", &_genRegionOffset, &dummy1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:302:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | r = sscanf(crttok, "genRegion="uint32FMT"-"uint32FMT"", &_genRegionOffset, &dummy1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:313:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 313 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:342:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 342 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:366:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 366 | r = sscanf(crttok, "Parent=sim4db"uint32FMT"", &dummy1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:377:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 377 | r = sscanf(crttok, "nMatches="uint32FMT"", &exon._numMatches); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:403:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 403 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:437:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 437 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C: In member function ‘void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:140:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 140 | memcpy(nnn, _exons, sizeof(sim4polishExon) * _numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C: In member function ‘void sim4polish::s4p_linesToPolishGFF3(uint32, uint32, char**, uint32*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:261:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 261 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:261:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 261 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:262:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 262 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:262:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 262 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:263:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 263 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:263:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 263 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:264:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 264 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:264:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 264 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:265:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 265 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:265:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 265 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:266:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 266 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:266:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 266 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:267:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 267 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:267:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 267 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:268:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 268 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:268:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 268 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:346:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32’ {aka ‘unsigned int’} [-Wsign-compare] 346 | if ((dummy1 != _genID) || strcmp(dummybuf, _genDefLine) || | ~~~~~~~^~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:347:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 347 | (sOri != '+') && (sOri != '-') && (sOri != '.')) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:352:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 352 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:352:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 352 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:353:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 353 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:353:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 353 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:354:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 354 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:354:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 354 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:355:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 355 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:355:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 355 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:356:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 356 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:356:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 356 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:357:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 357 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:357:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 357 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:358:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 358 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:358:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 358 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:359:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 359 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:359:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 359 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:30: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[1000]’ [-Wformat=] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ | | | char (*)[1000] /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:383:39: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[1000]’ [-Wformat=] 383 | r = sscanf(crttok, "intron=%s", &dummybuf); | ~^ ~~~~~~~~~ | | | | | char (*)[1000] | char* /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:414:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 414 | memcpy(nnn, _exons, sizeof(sim4polishExon) * _numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C: In member function ‘sim4polish* sim4polishBuilder::release()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:246:11: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 246 | memcpy(it->_exons + i, ex[i], sizeof(sim4polishExon)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Failed to reposition %s to record "uint32FMT", only "uint32FMT" records\n", _path, ordinal, _polishRecordLen), exit(1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:120:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Failed to reposition %s to record "uint32FMT", only "uint32FMT" records\n", _path, ordinal, _polishRecordLen), exit(1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:248:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "polishes: "uint32FMT"\r", _polishRecordLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C: In member function ‘void sim4polishFile::loadIndex()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:141:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 141 | fread(&magic, sizeof(char), 8, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:145:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 145 | fread(&_polishRecordLen, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:151:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fread( _polishRecord, sizeof(polishRecord), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:152:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | fread( _polishRecordEST, sizeof(uint32), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:153:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | fread( _polishRecordGEN, sizeof(uint32), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:155:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fread(&_maxEST, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:156:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fread(&_maxGEN, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:161:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 161 | fread( _ESTiidLocation, sizeof(uint32), _maxEST, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:162:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fread( _GENiidLocation, sizeof(uint32), _maxGEN, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/align.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/extend.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/poly.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/splice.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/table.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4core/util.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:151:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "fastaFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:151:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "fastaFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:252:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 252 | fprintf(stderr, "fastaFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:252:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 252 | fprintf(stderr, "fastaFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C: In member function ‘void fastaFile::loadIndex(char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:357:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 357 | fread(&_header, sizeof(fastaFileHeader), 1, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:379:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 379 | fread(_index, sizeof(fastaFileIndex), _header._numberOfSequences, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.C:380:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(_names, sizeof(char), _header._namesLength, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.C: In member function ‘virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.C:110:9: warning: unused variable ‘ret’ [-Wunused-variable] 110 | bool ret = true; | ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:141:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 141 | fprintf(stderr, "fastqFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:141:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 141 | fprintf(stderr, "fastqFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:253:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 253 | fprintf(stderr, "fastqFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:253:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 253 | fprintf(stderr, "fastqFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:533:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:533:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:533:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C: In member function ‘void fastqFile::loadIndex(char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:354:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 354 | fread(&_header, sizeof(fastqFileHeader), 1, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:374:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 374 | fread(_index, sizeof(fastqFileIndex), _header._numberOfSequences, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.C:375:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 375 | fread(_names, sizeof(char), _header._namesLength, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.C: In member function ‘virtual bool fastqStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.C:110:9: warning: unused variable ‘ret’ [-Wunused-variable] 110 | bool ret = true; | ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:129:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "seqStore::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:129:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "seqStore::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:197:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "seqStore::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:197:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "seqStore::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:203:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:203:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:203:96: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:203:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:463:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 463 | fprintf(stderr, "constructSeqStore()-- sequence %s too long, must be shorter than "uint64FMT" Gbp.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:467:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 467 | fprintf(stderr, "constructSeqStore()-- too many sequences, must be fewer than "uint64FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:620:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:620:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:620:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:620:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C: In function ‘void constructSeqStore(char*, seqCache*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:410:9: warning: ‘memset’ used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 410 | memset(&HEAD, sizeof(seqStoreHeader), 0); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C: In constructor ‘seqStore::seqStore(const char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:21:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 21 | fread(&_header, sizeof(seqStoreHeader), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C: In member function ‘virtual seqFile* seqStore::openFile(const char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:73:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | fread(&magic1, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:74:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 74 | fread(&magic2, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C: In member function ‘void seqStore::loadIndex()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:318:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 318 | fread(&_header, sizeof(seqStoreHeader), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:329:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 329 | fread( _index, sizeof(seqStoreIndex), _header._numberOfSequences, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:343:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 343 | fread( _block, sizeof(seqStoreBlock), _header._numberOfBlocks, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.C:347:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 347 | fread( _names, sizeof(char), _header._namesLength, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.C:171:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stderr, "seqCache::loadAllSequences()-- Failed to load iid "uint32FMT".\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:236:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:236:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:236:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:268:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="uint64FMT" too big; only "uint64FMT" positions.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:268:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="uint64FMT" too big; only "uint64FMT" positions.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:340:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:340:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:340:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:386:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:386:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.C:386:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:15:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 15 | fprintf(stderr, "testID:"uint32FMT" - empty sequence\n", testID); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:22:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 22 | fprintf(stderr, "testID:"uint32FMT" - header differs '%s' vs '%s'\n", testID, S->header(), correctSequence[sid].header); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:30:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 30 | fprintf(stderr, "testID:"uint32FMT" - sequence differs\n", testID); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:17:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stderr, "testIndexing()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:17:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stderr, "testIndexing()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:95:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 95 | fprintf(stderr, "wrong separator at sep "uint32FMT" got %d expected %d\n", x, s, sep); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:145:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 145 | fprintf(stderr, "iterated length wrong; sib="uint32FMT" sie="uint32FMT"\n", sib, sie); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:145:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 145 | fprintf(stderr, "iterated length wrong; sib="uint32FMT" sie="uint32FMT"\n", sib, sie); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:159:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 159 | fprintf(stderr, "testChaining()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.C:159:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 159 | fprintf(stderr, "testChaining()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:11:2: warning: #warning HOW DO WE TEST IF WE GET ALL THE MERS? [-Wcpp] 11 | #warning HOW DO WE TEST IF WE GET ALL THE MERS? | ^~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:33:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:33:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:33:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:33:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:39:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(stdout, "MS pos="uint32FMT" failed '%s' != '%s'.\n", pos, testmer, seq + pos); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:124:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:124:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:124:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C: In function ‘int main(int, char**)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:223:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 223 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:225:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 225 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:228:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 228 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:243:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 243 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:245:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 245 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.C:248:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 248 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaFile.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastaStdin.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqFile.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/fastqStdin.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStore.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/sffFile.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqFactory.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqCache.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/seqStream.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/merStream.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.c: In function ‘align_path’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.c:385:7: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 385 | if (head2) *tail = tail2; | ^~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.c:163:32: note: ‘head2’ declared here 163 | edit_script *head1, *tail1, *head2, *tail2; | ^~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/reversecomplement.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/reversecomplement.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.H:28, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.H:29: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/reversecomplement.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/halign.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/reversecomplement.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/kmer.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.c: In function ‘openFile’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.c:382:9: warning: variable ‘isRW’ set but not used [-Wunused-but-set-variable] 382 | int isRW = 1; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/md5.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/md5.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/palloc.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/palloc.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function ‘qsort_algo’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c:264:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 264 | pthread_t id; | ^~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function ‘qsort_thread’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.c:370:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 370 | pthread_t id; | ^~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C: In member function ‘void bigQueue::mergeTemporaryFiles()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C:204:16: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 204 | fread(thing, _objectSize, 1, _temporaryFiles[i]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C:255:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 255 | fread(thing, _objectSize, 1, _temporaryFiles[fileid]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C: In member function ‘bool bigQueue::next()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.C:302:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 302 | fread(_thingBuffer, _objectSize, 1, _temporaryFiles[0]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.C:8: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.C:35:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stderr, "bitPackedArray::get()-- element index "uint64FMT" is out of range, only "uint64FMT" elements.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.C:35:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stderr, "bitPackedArray::get()-- element index "uint64FMT" is out of range, only "uint64FMT" elements.\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:168:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 168 | fprintf(stderr, " at position "uint64HEX"\n", file_offset); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:367:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 367 | fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos="uint64FMT" failed: %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:376:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 376 | fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of "uint64FMT" bytes failed': %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C: In constructor ‘bitPackedFile::bitPackedFile(const char*, uint64, bool)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:109:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | write(_file, t, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:110:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 110 | write(_file, &at, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:111:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | write(_file, &bt, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C: In member function ‘void bitPackedFile::flushDirty()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.C:232:8: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | write(_file, _bfr, sizeof(uint64) * _bfrmax); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C:132:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "readBuffer::fillBuffer()-- only read "uint64FMT" bytes, couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C:132:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "readBuffer::fillBuffer()-- only read "uint64FMT" bytes, couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C:165:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position "int64FMT": %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.C:228:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(stderr, "readBuffer()-- couldn't read "uint64FMT" bytes from '%s': n%s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:227:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 227 | fprintf(stderr, "recordFile::seek() '%s' seek to record="uint64FMT" at fileposition="uint64FMT" failed: %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:227:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 227 | fprintf(stderr, "recordFile::seek() '%s' seek to record="uint64FMT" at fileposition="uint64FMT" failed: %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:233:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:233:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:233:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C: In constructor ‘recordFile::recordFile(const char*, uint32, uint32, char)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:68:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 68 | write(_file, &recordFileMagic1, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:69:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | write(_file, &recordFileMagic2, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:70:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | write(_file, &_numRecords, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:71:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | write(_file, &_recordSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:72:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | write(_file, &_headerSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:73:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | write(_file, _header, sizeof(char) * _headerSize); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:112:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 112 | read(_file, &m1, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:113:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 113 | read(_file, &m2, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:114:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | read(_file, &_numRecords, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:115:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | read(_file, &_recordSize, sizeof(uint32)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:116:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 116 | read(_file, &_headerSize, sizeof(uint32)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:117:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | read(_file, _header, sizeof(char) * _headerSize); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C: In destructor ‘recordFile::~recordFile()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:151:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | write(_file, &recordFileMagic1, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:152:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | write(_file, &recordFileMagic2, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:153:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | write(_file, &_numRecords, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:154:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 154 | write(_file, &_recordSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:155:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | write(_file, &_headerSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:156:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | write(_file, _header, sizeof(char) * _headerSize); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C: In member function ‘void recordFile::flushDirty()’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:197:8: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 197 | write(_file, _bfr, _recordSize * _rec); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C: In member function ‘void recordFile::seek(uint64, bool)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.C:231:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 231 | read(_file, _bfr, _recordSize * _bfrmax); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.H:7, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:127:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "sweatShop::setThreadData()-- worker ID "uint32FMT" more than number of workers="uint32FMT"\n", t, _numberOfWorkers), exit(1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:127:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "sweatShop::setThreadData()-- worker ID "uint32FMT" more than number of workers="uint32FMT"\n", t, _numberOfWorkers), exit(1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:390:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:390:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:390:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:390:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:390:135: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:425:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:425:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:425:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:560:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 560 | fprintf(stderr, "sweatShop::run()-- Failed to launch worker thread "uint32FMT": %s.\n", i, strerror(err)), exit(1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.C:580:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 580 | fprintf(stderr, "sweatShop::run()-- Failed to join worker thread "uint32FMT": %s.\n", i, strerror(err)), exit(1); | ^ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.c rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/md5.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/palloc.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/file.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/md5.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/palloc.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/qsort_mt.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bigQueue.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/readBuffer.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/speedCounter.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/sweatShop.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.o g++ -Wl,-z,relro -Wl,-z,now -o ESTmapper/terminate ESTmapper/terminate.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFeature.o -c atac-driver/libatac/atacFeature.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFeature.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFeature.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.C:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "Feature longer than sequence (by "uint32FMT"bp): seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacFeature.C:109:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "Feature longer than sequence (by "uint32FMT"bp): seqLen="uint32FMTW(8)" %s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFeatureList.o -c atac-driver/libatac/atacFeatureList.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFeatureList.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFeatureList.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFeatureList.C: In member function ‘void atacFeatureList::add(atacFeature&)’: atac-driver/libatac/atacFeatureList.C:50:52: warning: operation on ‘((atacFeatureList*)this)->atacFeatureList::_featuresLen’ may be undefined [-Wsequence-point] 50 | _features[_featuresLen].featureiid = _featuresLen++; | ~~~~~~~~~~~~^~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFile.o -c atac-driver/libatac/atacFile.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFile.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFile.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFile.C: In member function ‘void atacFileBase::readHeader(char*, FILE*)’: atac-driver/libatac/atacFile.C:255:7: warning: the address of ‘atacFileBase::_fileA’ will never be NULL [-Waddress] 255 | if (_fileA && _fileA[0]) { | ^~~~~~ atac-driver/libatac/atac.H:59:22: note: ‘atacFileBase::_fileA’ declared here 59 | char _fileA[1024]; // The name of our genome files | ^~~~~~ atac-driver/libatac/atacFile.C:262:7: warning: the address of ‘atacFileBase::_fileB’ will never be NULL [-Waddress] 262 | if (_fileB && _fileB[0]) { | ^~~~~~ atac-driver/libatac/atac.H:60:22: note: ‘atacFileBase::_fileB’ declared here 60 | char _fileB[1024]; | ^~~~~~ atac-driver/libatac/atacFile.C: In member function ‘atacMatch* atacFileStream::nextMatch(char)’: atac-driver/libatac/atacFile.C:76:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fgets(_inLine, 1024, _inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In member function ‘atacFeature* atacFileStream::nextFeature(char*)’: atac-driver/libatac/atacFile.C:105:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fgets(_inLine, 1024, _inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In constructor ‘atacFile::atacFile(const char*)’: atac-driver/libatac/atacFile.C:171:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 171 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In member function ‘void atacFileBase::readHeader(char*, FILE*)’: atac-driver/libatac/atacFile.C:206:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 206 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C:245:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 245 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFileStreamMerge.o -c atac-driver/libatac/atacFileStreamMerge.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFileStreamMerge.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFileStreamMerge.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFileStreamMerge.C: In member function ‘void atacFileStreamMerge::addFile(const char*)’: atac-driver/libatac/atacFileStreamMerge.C:86:11: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class afsm’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 86 | memcpy(F, _files, sizeof(afsm) * _filesLen); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFileStreamMerge.C:27:7: note: ‘class afsm’ declared here 27 | class afsm { | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatch.o -c atac-driver/libatac/atacMatch.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atac.H:26, from atac-driver/libatac/atacMatch.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacMatch.C:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 1: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:131:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 1: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 2: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:139:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 2: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C: In constructor ‘atacMatch::atacMatch(char*, char*, uint32, char*, uint32, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: atac-driver/libatac/atacMatch.C:50:10: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 16 equals destination size [-Wstringop-truncation] 50 | strncpy(matchuid, muid, 16); | ^ atac-driver/libatac/atacMatch.C: In member function ‘void atacMatch::decode(char*)’: atac-driver/libatac/atacMatch.C:100:10: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 16 equals destination size [-Wstringop-truncation] 100 | strncpy(matchuid, S[2], 16); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatchList.o -c atac-driver/libatac/atacMatchList.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacMatchList.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacMatchList.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatchOrder.o -c atac-driver/libatac/atacMatchOrder.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacMatchOrder.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacMatchOrder.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacMatchOrder.C:38:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | sprintf(n.matchuid, "merge"uint32FMT, mergeuid); | ^ rm -f atac-driver/libatac/libatac.a && ar ruvs atac-driver/libatac/libatac.a atac-driver/libatac/atacFeature.o atac-driver/libatac/atacFeatureList.o atac-driver/libatac/atacFile.o atac-driver/libatac/atacFileStreamMerge.o atac-driver/libatac/atacMatch.o atac-driver/libatac/atacMatchList.o atac-driver/libatac/atacMatchOrder.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating atac-driver/libatac/libatac.a a - atac-driver/libatac/atacFeature.o a - atac-driver/libatac/atacFeatureList.o a - atac-driver/libatac/atacFile.o a - atac-driver/libatac/atacFileStreamMerge.o a - atac-driver/libatac/atacMatch.o a - atac-driver/libatac/atacMatchList.o a - atac-driver/libatac/atacMatchOrder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap.o -c atac-driver/alignOverlap/overlap.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap.C:123:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 123 | fprintf(stderr, "unmapped: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.unmapped.getSum(), statsB.unmapped.getSum()); | ^ atac-driver/alignOverlap/overlap.C:123:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 123 | fprintf(stderr, "unmapped: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.unmapped.getSum(), statsB.unmapped.getSum()); | ^ atac-driver/alignOverlap/overlap.C:124:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "unique mapping 1: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map1unique.getSum(), statsB.map1unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:124:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "unique mapping 1: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map1unique.getSum(), statsB.map1unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:125:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 125 | fprintf(stderr, "unique mapping 2: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map2unique.getSum(), statsB.map2unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:125:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 125 | fprintf(stderr, "unique mapping 2: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map2unique.getSum(), statsB.map2unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:126:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "different: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.different.getSum(), statsB.different.getSum()); | ^ atac-driver/alignOverlap/overlap.C:126:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "different: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.different.getSum(), statsB.different.getSum()); | ^ atac-driver/alignOverlap/overlap.C:127:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "wild diff: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.wilddiff.getSum(), statsB.wilddiff.getSum()); | ^ atac-driver/alignOverlap/overlap.C:127:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "wild diff: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.wilddiff.getSum(), statsB.wilddiff.getSum()); | ^ atac-driver/alignOverlap/overlap.C:128:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "same: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.same.getSum(), statsB.same.getSum()); | ^ atac-driver/alignOverlap/overlap.C:128:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "same: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.same.getSum(), statsB.same.getSum()); | ^ atac-driver/alignOverlap/overlap.C:129:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "inconsistent: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.inconsistent.getSum(), statsB.inconsistent.getSum()); | ^ atac-driver/alignOverlap/overlap.C:129:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "inconsistent: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.inconsistent.getSum(), statsB.inconsistent.getSum()); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-find.o -c atac-driver/alignOverlap/overlap-find.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-find.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap-find.C:45:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 45 | fprintf(stderr, "isolated Unique: map1: "uint32FMT" map2: "uint32FMT"\n", sumA, sumB); | ^ atac-driver/alignOverlap/overlap-find.C:45:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 45 | fprintf(stderr, "isolated Unique: map1: "uint32FMT" map2: "uint32FMT"\n", sumA, sumB); | ^ atac-driver/alignOverlap/overlap-find.C:59:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(stderr, "got invalid type; "uint32FMT" -- %c\n", type, (char)type), exit(1); | ^ atac-driver/alignOverlap/overlap-find.C:91:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "%s: "uint32FMT" len:"uint32FMT"\n", msg, count, len); | ^ atac-driver/alignOverlap/overlap-find.C:91:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "%s: "uint32FMT" len:"uint32FMT"\n", msg, count, len); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-matchTree.o -c atac-driver/alignOverlap/overlap-matchTree.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-matchTree.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-printAnno.o -c atac-driver/alignOverlap/overlap-printAnno.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-printAnno.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:14: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-sort.o -c atac-driver/alignOverlap/overlap-sort.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-sort.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ ln -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process.C /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process1.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -DINDEX=1 -DNAME=process1 -DPOS1=pos1 -DPOS2=pos2 -DLEN2=len2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-process1.o -c atac-driver/alignOverlap/overlap-process1.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-process1.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ ln -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process.C /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process2.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -DINDEX=2 -DNAME=process2 -DPOS1=pos2 -DPOS2=pos1 -DLEN2=len1 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-process2.o -c atac-driver/alignOverlap/overlap-process2.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-process2.C:19: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/alignOverlap/overlap atac-driver/alignOverlap/overlap.o atac-driver/alignOverlap/overlap-find.o atac-driver/alignOverlap/overlap-matchTree.o atac-driver/alignOverlap/overlap-printAnno.o atac-driver/alignOverlap/overlap-sort.o atac-driver/alignOverlap/overlap-process1.o atac-driver/alignOverlap/overlap-process2.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/gapShifter.o -c atac-driver/gapShifter/gapShifter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/gapShifter/gapShifter.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:203:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:203:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:223:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 223 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:223:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 223 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:510:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:515:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:523:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:528:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:738:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 738 | fprintf(stderr, "Shifting gaps of length at most "uint32FMT" bases, to the %s.\n", gapLimit, (shiftRight) ? "right" : "left"); | ^ atac-driver/gapShifter/gapShifter.C:750:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 750 | fprintf(stderr, "numShifted = "uint32FMT"\n", numShifted); | ^ atac-driver/gapShifter/gapShifter.C:751:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 751 | fprintf(stderr, "numNotShifted = "uint32FMT"\n", numNotShifted); | ^ atac-driver/gapShifter/gapShifter.C:752:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 752 | fprintf(stderr, "numDiffSeq = "uint32FMT"\n", numDiffSeq); | ^ atac-driver/gapShifter/gapShifter.C:753:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 753 | fprintf(stderr, "numDiffOri = "uint32FMT"\n", numDiffOri); | ^ atac-driver/gapShifter/gapShifter.C:754:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 754 | fprintf(stderr, "numZeroLen = "uint32FMT"\n", numZeroLen); | ^ atac-driver/gapShifter/gapShifter.C:755:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 755 | fprintf(stderr, "numOutOfOrder = "uint32FMT"\n", numOutOfOrder); | ^ atac-driver/gapShifter/gapShifter.C:756:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 756 | fprintf(stderr, "numNotAdjacent = "uint32FMT"\n", numNotAdjacent); | ^ atac-driver/gapShifter/gapShifter.C:757:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 757 | fprintf(stderr, "numNoGap = "uint32FMT"\n", numNoGap); | ^ atac-driver/gapShifter/gapShifter.C:758:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 758 | fprintf(stderr, "numGapTooBig = "uint32FMT"\n", numGapTooBig); | ^ atac-driver/gapShifter/gapShifter.C:759:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 759 | fprintf(stderr, "numOverlapping = "uint32FMT"\n", numOverlapping); | ^ atac-driver/gapShifter/gapShifter.C:762:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "amountShifted["uint32FMT"] = "uint32FMT" (number of gaps shifted by [number of bases])\n", x, amountShifted[x]); | ^ atac-driver/gapShifter/gapShifter.C:762:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "amountShifted["uint32FMT"] = "uint32FMT" (number of gaps shifted by [number of bases])\n", x, amountShifted[x]); | ^ atac-driver/gapShifter/gapShifter.C:764:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 764 | fprintf(stderr, "shifted "uint32FMT" out of "uint32FMT" (%6.2f%%)\n", gapsShifted, ML.numMatches(), (double)gapsShifted / (double)ML.numMatches() * 100.0); | ^ atac-driver/gapShifter/gapShifter.C:764:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 764 | fprintf(stderr, "shifted "uint32FMT" out of "uint32FMT" (%6.2f%%)\n", gapsShifted, ML.numMatches(), (double)gapsShifted / (double)ML.numMatches() * 100.0); | ^ atac-driver/gapShifter/gapShifter.C:780:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/gapShifter atac-driver/gapShifter/gapShifter.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/extractSequence.o -c atac-driver/gapShifter/extractSequence.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/gapShifter/extractSequence.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/extractSequence.C:110:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:110:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:110:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/extractSequence atac-driver/gapShifter/extractSequence.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/extractUnmapped.o -c atac-driver/gapShifter/extractUnmapped.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/extractUnmapped.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/extractUnmapped.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:583:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 583 | fprintf(stderr, "Done masking. "uint32FMT" in A, "uint32FMT" in B.\n", stats[0], stats[1]); | ^ atac-driver/gapShifter/extractUnmapped.C:583:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 583 | fprintf(stderr, "Done masking. "uint32FMT" in A, "uint32FMT" in B.\n", stats[0], stats[1]); | ^ atac-driver/gapShifter/extractUnmapped.C: In function ‘int main(int, char**)’: atac-driver/gapShifter/extractUnmapped.C:541:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/extractUnmapped atac-driver/gapShifter/extractUnmapped.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/coalesceMatches.o -c atac-driver/gapShifter/coalesceMatches.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/coalesceMatches.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/coalesceMatches.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/coalesceMatches atac-driver/gapShifter/coalesceMatches.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/correctGaps.o -c atac-driver/gapShifter/correctGaps.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/correctGaps.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/correctGaps.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/correctGaps.C:138:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 138 | fprintf(logFile, "HEY! F gap of size "uint32FMT" not in a run?\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:200:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(logFile, "HEY! R gap of size "uint32FMT" not in a run?\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:222:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(logFile, "CLOSE "uint32FMT"----------------------------------------\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:235:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ atac-driver/gapShifter/correctGaps.C:235:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ atac-driver/gapShifter/correctGaps.C:235:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/correctGaps atac-driver/gapShifter/correctGaps.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/testAtac.o -c atac-driver/gapShifter/testAtac.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/testAtac.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/testAtac.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/testAtac.C:89:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity: ", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/testAtac atac-driver/gapShifter/testAtac.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/cleanAtac.o -c atac-driver/gapShifter/cleanAtac.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/cleanAtac.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/cleanAtac.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/cleanAtac.C:149:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 149 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity and "uint32FMT" long: ", | ^ atac-driver/gapShifter/cleanAtac.C:149:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 149 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity and "uint32FMT" long: ", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/cleanAtac atac-driver/gapShifter/cleanAtac.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/projectFeatures.o -c atac-driver/gapShifter/projectFeatures.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/projectFeatures.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/projectFeatures.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/projectFeatures.C:72:2: warning: #warning BROKEN [-Wcpp] 72 | #warning BROKEN | ^~~~~~~ atac-driver/gapShifter/projectFeatures.C:132:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/projectFeatures atac-driver/gapShifter/projectFeatures.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/lengthFilter/lengthFilter.o -c atac-driver/lengthFilter/lengthFilter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/lengthFilter/lengthFilter.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ atac-driver/lengthFilter/lengthFilter.C:46:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | sprintf(inLine, "/globalMatchMinSize="uint32FMT"\n", minLength); | ^ atac-driver/lengthFilter/lengthFilter.C:57:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 57 | fprintf(stdout, "/globalMatchMinSize="uint32FMT"\n", minLength); | ^ atac-driver/lengthFilter/lengthFilter.C:114:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stderr, "lengthFilter: Discarded "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:114:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stderr, "lengthFilter: Discarded "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:116:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "lengthFilter: Saved "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:116:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "lengthFilter: Saved "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C: In function ‘void readHeader(char*, FILE*, uint32&, FILE*)’: atac-driver/lengthFilter/lengthFilter.C:34:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 34 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/lengthFilter/lengthFilter.C:53:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 53 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/lengthFilter/lengthFilter.C: In function ‘int main(int, char**)’: atac-driver/lengthFilter/lengthFilter.C:111:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fgets(inLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/lengthFilter/lengthFilter atac-driver/lengthFilter/lengthFilter.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender.o -c atac-driver/matchExtender/matchExtender.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/matchExtender/matchExtender.C:27: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/matchExtender/matchExtender.C:192:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender-dump.o -c atac-driver/matchExtender/matchExtender-dump.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/matchExtender/matchExtender-dump.C:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/matchExtender/match.H:8, from atac-driver/matchExtender/matchExtender-dump.C:26: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender-func.o -c atac-driver/matchExtender/matchExtender-func.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/matchExtender/matchExtender-func.C:26: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/matchExtender/matchExtender-func.C:27: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/matchExtender/matchExtender atac-driver/matchExtender/matchExtender.o atac-driver/matchExtender/matchExtender-dump.o atac-driver/matchExtender/matchExtender-func.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/mismatchCounter/mismatchCounter.o -c atac-driver/mismatchCounter/mismatchCounter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/mismatchCounter/mismatchCounter.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/mismatchCounter/mismatchCounter.C:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/mismatchCounter/mismatchCounter.C:197:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "globalSequence = "uint32FMT"\n", globalSequence); | ^ atac-driver/mismatchCounter/mismatchCounter.C:198:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 198 | fprintf(stderr, "globalMismatches = "uint32FMT"\n", globalMismatches); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/mismatchCounter/mismatchCounter atac-driver/mismatchCounter/mismatchCounter.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/statsGenerator/statsGenerator.o -c atac-driver/statsGenerator/statsGenerator.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/statsGenerator/statsGenerator.C:26: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/statsGenerator/statsGenerator.C:91:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stdout, "histogram %s "uint32FMT" items %8.3f average %8.3f std.dev.\n", | ^ atac-driver/statsGenerator/statsGenerator.C:102:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 102 | fprintf(out, uint64FMT" "uint32FMT"\n", i * _b, _h[i]); | ^ atac-driver/statsGenerator/statsGenerator.C:103:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(out, ">"uint64FMT" "uint32FMT"\n", _m, _l); | ^ atac-driver/statsGenerator/statsGenerator.C:103:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(out, ">"uint64FMT" "uint32FMT"\n", _m, _l); | ^ atac-driver/statsGenerator/statsGenerator.C:133:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 133 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:133:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 133 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:136:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:136:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:172:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # all letters, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:172:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # all letters, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:193:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:193:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:282:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 282 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifa.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:283:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 283 | fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifa.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:285:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifa.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:286:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifa.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:287:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 287 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifa, offset1, A)); | ^ atac-driver/statsGenerator/statsGenerator.C:289:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 289 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mma.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:290:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 290 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mma.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:291:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 291 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mma, offset1, A)); | ^ atac-driver/statsGenerator/statsGenerator.C:295:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:296:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:298:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 298 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:299:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:300:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 300 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifb, offset2, B)); | ^ atac-driver/statsGenerator/statsGenerator.C:302:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mmb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:303:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 303 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mmb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:304:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 304 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mmb, offset2, B)); | ^ atac-driver/statsGenerator/statsGenerator.C:335:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 335 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)matches.numberOfMatches()); | ^ atac-driver/statsGenerator/statsGenerator.C:337:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 337 | fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n", | ^ atac-driver/statsGenerator/statsGenerator.C:337:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 337 | fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n", | ^ atac-driver/statsGenerator/statsGenerator.C:349:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 349 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:349:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 349 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:353:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 353 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n", | ^ atac-driver/statsGenerator/statsGenerator.C:353:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 353 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n", | ^ atac-driver/statsGenerator/statsGenerator.C:409:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 409 | fprintf(out, uint64FMT" "uint32FMT"\n", n, n50[iter-1]); | ^ atac-driver/statsGenerator/statsGenerator.C:507:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:516:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 516 | sprintf(label, "chr"uint32FMTW(02)"full", c); | ^ atac-driver/statsGenerator/statsGenerator.C:520:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | sprintf(label, "chr"uint32FMTW(02)"acgt", c); | ^ atac-driver/statsGenerator/statsGenerator.C:628:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 628 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:628:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 628 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:631:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 631 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:631:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 631 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C: In function ‘void tandemRepeatStats(atacFileStream&, atacFileStream&, atacFile&, seqCache*, seqCache*)’: atac-driver/statsGenerator/statsGenerator.C:267:37: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 267 | while ((f = featuresA.nextFeature("tr")) != 0L) | ^~~~ atac-driver/statsGenerator/statsGenerator.C:269:37: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 269 | while ((f = featuresB.nextFeature("tr")) != 0L) | ^~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:99:29: warning: ‘.histogramdat’ directive writing 13 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 99 | sprintf(filename, "%s.%s.histogramdat", prefix, label); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from atac-driver/statsGenerator/statsGenerator.C:21: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:99:12, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:95:14, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:517:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 15 or more bytes (assuming 1038) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:127:29: warning: ‘.histogram.gnuplot’ directive writing 18 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 127 | sprintf(filename, "%s.%s.histogram.gnuplot", prefix, label); | ^~~~~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:127:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:518:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 20 or more bytes (assuming 1043) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:140:37: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 140 | sprintf(filename, "gnuplot < %s.%s.histogram.gnuplot", prefix, label); | ^~ ...... 518 | hist1full[c]->plot(prefix, label); | ~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:140:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:518:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 1053) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:99:29: warning: ‘.histogramdat’ directive writing 13 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 99 | sprintf(filename, "%s.%s.histogramdat", prefix, label); | ^~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:99:12, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:95:14, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:521:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 15 or more bytes (assuming 1038) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:127:29: warning: ‘.histogram.gnuplot’ directive writing 18 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 127 | sprintf(filename, "%s.%s.histogram.gnuplot", prefix, label); | ^~~~~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:127:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:522:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 20 or more bytes (assuming 1043) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:140:37: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 140 | sprintf(filename, "gnuplot < %s.%s.histogram.gnuplot", prefix, label); | ^~ ...... 522 | hist1acgt[c]->plot(prefix, label); | ~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:140:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:522:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 1053) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/statsGenerator/statsGenerator atac-driver/statsGenerator/statsGenerator.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/uniqueFilter/uniqueFilter.o -c atac-driver/uniqueFilter/uniqueFilter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/uniqueFilter/uniqueFilter.C:23: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/uniqueFilter/uniqueFilter.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:226:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 226 | fprintf(stderr, "Sorting error -- have negative coverage (axis="uint32FMT" position="uint32FMT")!\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:226:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 226 | fprintf(stderr, "Sorting error -- have negative coverage (axis="uint32FMT" position="uint32FMT")!\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:236:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "offsetsToCoverage()-- Found "uint64FMT" bases at coverage "uint32FMT" or greater.\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:236:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "offsetsToCoverage()-- Found "uint64FMT" bases at coverage "uint32FMT" or greater.\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:370:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | fprintf(stderr, "Got fwd intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:370:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | fprintf(stderr, "Got fwd intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:374:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 374 | fprintf(stdout, "--key1 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:374:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 374 | fprintf(stdout, "--key1 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:379:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 379 | fprintf(stderr, "Got rev intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:379:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 379 | fprintf(stderr, "Got rev intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:383:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 383 | fprintf(stdout, "--key2 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:383:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 383 | fprintf(stdout, "--key2 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:418:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 418 | #define D08D2 uint32FMTW(8)" "uint32FMTW(8) | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:818:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 818 | fprintf(stderr, "match "uint32FMT" is outside the extent!\n", i); | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/uniqueFilter/uniqueFilter atac-driver/uniqueFilter/uniqueFilter.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/clumpMaker/clumpMaker.o -c atac-driver/clumpMaker/clumpMaker.C In file included from atac-driver/clumpMaker/clumpMaker.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/clumpMaker/clumpMaker.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/clumpMaker/clumpMaker.C:341:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 341 | sprintf(C.matchuid, "clump"int32FMTW(06), cc); | ^ atac-driver/clumpMaker/clumpMaker.C:377:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 377 | sprintf(hits[mm].match.parentuid, "clump"int32FMTW(06), cc); | ^ atac-driver/clumpMaker/clumpMaker.C: In function ‘int main(int, char**)’: atac-driver/clumpMaker/clumpMaker.C:220:12: warning: variable ‘isSorted’ set but not used [-Wunused-but-set-variable] 220 | bool isSorted = false; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/clumpMaker/clumpMaker atac-driver/clumpMaker/clumpMaker.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_dpaligner.o -c atac-driver/chainer/localalign/GF_ALN_dpaligner.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_local.o -c atac-driver/chainer/localalign/GF_ALN_local.C atac-driver/chainer/localalign/GF_ALN_local.C: In function ‘void Align_Recursion(const char*, int, const char*, int, const Trapezoid*, int, int, int, double, int)’: atac-driver/chainer/localalign/GF_ALN_local.C:872:15: warning: variable ‘indel’ set but not used [-Wunused-but-set-variable] 872 | int j, mid, indel; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_overlap.o -c atac-driver/chainer/localalign/GF_ALN_overlap.C atac-driver/chainer/localalign/GF_ALN_overlap.C: In function ‘void AVLinit()’: atac-driver/chainer/localalign/GF_ALN_overlap.C:93:17: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 93 | OutOfMemory("Candidate list"); | ^~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C: In function ‘AVLnode* NEW(AVLnode*, Candidate*, AVLnode*)’: atac-driver/chainer/localalign/GF_ALN_overlap.C:125:21: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 125 | OutOfMemory("Candidate list"); | ^~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C: In function ‘Local_Overlap* Find_Local_Overlap(int, int, int, int, Local_Segment*, int, int, double)’: atac-driver/chainer/localalign/GF_ALN_overlap.C:396:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 396 | OutOfMemory("Overlap Trace Array"); | ^~~~~~~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C:662:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 662 | OutOfMemory("Overlap descriptor"); | ^~~~~~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C:614:20: warning: variable ‘beg’ set but not used [-Wunused-but-set-variable] 614 | int best, end, beg; | ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_loverlapper.o -c atac-driver/chainer/localalign/GF_ALN_loverlapper.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_pieceOlap.o -c atac-driver/chainer/localalign/GF_ALN_pieceOlap.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -I/usr/include/python3.13 -o atac-driver/chainer/localalign/localAlignerInterfacemodule.o -c atac-driver/chainer/localalign/localAlignerInterfacemodule.C atac-driver/chainer/localalign/localAlignerInterfacemodule.C: In function ‘PyObject* spam_syntenicSegments(PyObject*, PyObject*)’: atac-driver/chainer/localalign/localAlignerInterfacemodule.C:176:18: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 176 | char *Aseq = "undefined"; | ^~~~~~~~~~~ atac-driver/chainer/localalign/localAlignerInterfacemodule.C:179:18: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 179 | char *Bseq = "undefined"; | ^~~~~~~~~~~ rm -f atac-driver/chainer/localAlignerInterfacemodule.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o atac-driver/chainer/localAlignerInterfacemodule.so atac-driver/chainer/localalign/GF_ALN_dpaligner.o atac-driver/chainer/localalign/GF_ALN_local.o atac-driver/chainer/localalign/GF_ALN_overlap.o atac-driver/chainer/localalign/GF_ALN_loverlapper.o atac-driver/chainer/localalign/GF_ALN_pieceOlap.o atac-driver/chainer/localalign/localAlignerInterfacemodule.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/halign/halign.o -c atac-driver/chainer/halign/halign.C atac-driver/chainer/halign/halign.C: In function ‘int diff(const char*, const char*, int, int, int*, int*, int*, int*, int, int, int, int, int, int, int, int, int, EditScript**, EditScript**)’: atac-driver/chainer/halign/halign.C:295:9: warning: variable ‘cost1’ set but not used [-Wunused-but-set-variable] 295 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:295:16: warning: variable ‘cost2’ set but not used [-Wunused-but-set-variable] 295 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:345:9: warning: variable ‘cost1’ set but not used [-Wunused-but-set-variable] 345 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:345:16: warning: variable ‘cost2’ set but not used [-Wunused-but-set-variable] 345 | int cost1, cost2; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -I/usr/include/python3.13 -o atac-driver/chainer/halign/halignmodule.o -c atac-driver/chainer/halign/halignmodule.C rm -f atac-driver/chainer/halignmodule.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o atac-driver/chainer/halignmodule.so atac-driver/chainer/halign/halign.o atac-driver/chainer/halign/halignmodule.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chimera/happy-clones-span-clumps.o -c atac-driver/chimera/happy-clones-span-clumps.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/chimera/happy-clones-span-clumps.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ atac-driver/chimera/happy-clones-span-clumps.C:202:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "ERROR: increase scaffoldsMax "uint32FMT"\n", scaffoldid); | ^ atac-driver/chimera/happy-clones-span-clumps.C:229:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(stderr, "Deleted "uint32FMT" scaffolds with less than 2 clumps.\n", deleted); | ^ atac-driver/chimera/happy-clones-span-clumps.C:230:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 230 | fprintf(stderr, "Remain "uint32FMT" scaffolds with more than 2 clumps.\n", remain); | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:85: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:449:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 449 | fprintf(stdout, "%s spans clump in scaffold %s,"uint32FMT"\n", ina, A[7], scfa); | ^ atac-driver/chimera/happy-clones-span-clumps.C:453:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 453 | fprintf(stdout, "%s spans clump in scaffold %s,"uint32FMT" \n", inb, B[7], scfb); | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C: In function ‘int main(int, char**)’: atac-driver/chimera/happy-clones-span-clumps.C:393:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 393 | char *uidmapName = "/project/huref6/assembly/fasta/HUREF6A.info"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C: In function ‘atacClumpCoordTree* buildCoordTree(char*)’: atac-driver/chimera/happy-clones-span-clumps.C:313:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fgets(inl, 1024, inf); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:340:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 340 | fgets(inl, 1024, inf); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C: In function ‘int main(int, char**)’: atac-driver/chimera/happy-clones-span-clumps.C:402:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 402 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:409:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 409 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:426:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 426 | fgets(ina, 1024, inf); chomp(ina); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:427:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 427 | fgets(inb, 1024, inf); chomp(inb); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:473:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 473 | fgets(ina, 1024, inf); chomp(ina); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:474:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 474 | fgets(inb, 1024, inf); chomp(inb); | ~~~~~^~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/chimera/happy-clones-span-clumps atac-driver/chimera/happy-clones-span-clumps.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/seatac.o -c seatac/seatac.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/seatac.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/seatac.C:201:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "\n"uint32FMTW(7)" sequences (%5.1f%%; %8.3f/sec) %5.2f seconds.\n", | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/configuration.o -c seatac/configuration.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/configuration.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/configuration.C:259:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(out, "/seatacNumSearchThreads="uint32FMT"\n", _numSearchThreads); | ^ seatac/configuration.C:260:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(out, "/seatacLoaderHighWaterMark="uint32FMT"\n", _loaderHighWaterMark); | ^ seatac/configuration.C:264:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 264 | fprintf(out, "/seatacWriterHighWaterMark="uint32FMT"\n", _writerHighWaterMark); | ^ seatac/configuration.C:267:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 267 | fprintf(out, "/seatacMaxDiagonal="uint32FMT"\n", _maxDiagonal); | ^ seatac/configuration.C:268:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(out, "/seatacMaxGap="uint32FMT"\n", _maxGap); | ^ seatac/configuration.C:269:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(out, "/seatacQsOverlap="uint32FMT"\n", _qsOverlap); | ^ seatac/configuration.C:270:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 270 | fprintf(out, "/seatacDsOverlap="uint32FMT"\n", _dsOverlap); | ^ seatac/configuration.C:271:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 271 | fprintf(out, "/seatacMinLength="uint32FMT"\n", _minLength + _merSize); | ^ seatac/configuration.C:272:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 272 | fprintf(out, "/seatacMerSize="uint32FMT"\n", _merSize); | ^ seatac/configuration.C:273:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 273 | fprintf(out, "/seatacMerSkip="uint32FMT"\n", _merSkip); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/encodedQuery.o -c seatac/encodedQuery.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/encodedQuery.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/hitMatrix.o -c seatac/hitMatrix.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/hitMatrix.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-search.o -c seatac/thr-search.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-search.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/thr-search.C:3:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:3:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:3:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:130:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^ seatac/thr-search.C:130:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-loader.o -c seatac/thr-loader.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-loader.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/thr-loader.C: In function ‘void* loaderThread(void*)’: seatac/thr-loader.C:68:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 68 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-deadlock.o -c seatac/thr-deadlock.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-deadlock.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/hitMatrix-sort.o -c seatac/hitMatrix-sort.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/hitMatrix.H:8, from seatac/hitMatrix-sort.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/hitMatrix.H:9: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromFastA()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:137:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | fprintf(stderr, "existDB::createFromFastA()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "existDB::createFromFastA()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:27:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 27 | fprintf(stderr, "createFromMeryl()-- ERROR: requested merSize ("uint32FMT") is different than merSize in meryl database ("uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:27:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 27 | fprintf(stderr, "createFromMeryl()-- ERROR: requested merSize ("uint32FMT") is different than merSize in meryl database ("uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:54:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stderr, "createFromMeryl()-- tableSizeInEntries "uint64FMT"\n", tableSizeInEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:55:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "createFromMeryl()-- count range "uint32FMT"-"uint32FMT"\n", lo, hi); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:55:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "createFromMeryl()-- count range "uint32FMT"-"uint32FMT"\n", lo, hi); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:104:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 104 | fprintf(stderr, "createFromMeryl()-- numberOfMers "uint64FMT"\n", numberOfMers); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:135:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | fprintf(stderr, "existDB::createFromMeryl()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromMeryl()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:138:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 138 | fprintf(stderr, "existDB::createFromMeryl()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromSequence()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:137:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | fprintf(stderr, "existDB::createFromSequence()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "existDB::createFromSequence()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:169:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stream, "merSizeInBases: "uint32FMT"\n", _merSizeInBases); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:170:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 170 | fprintf(stream, "tableBits "uint32FMT"\n", 2 * _merSizeInBases - _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:172:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stream, "_hashTableWords "uint64FMT" ("uint64FMT" KB)\n", _hashTableWords, _hashTableWords >> 7); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:172:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stream, "_hashTableWords "uint64FMT" ("uint64FMT" KB)\n", _hashTableWords, _hashTableWords >> 7); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:173:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stream, "_bucketsWords "uint64FMT" ("uint64FMT" KB)\n", _bucketsWords, _bucketsWords >> 7); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:173:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stream, "_bucketsWords "uint64FMT" ("uint64FMT" KB)\n", _bucketsWords, _bucketsWords >> 7); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:174:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(stream, "_countsWords "uint64FMT" ("uint64FMT" KB)\n", _countsWords, _countsWords >> 7); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:174:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(stream, "_countsWords "uint64FMT" ("uint64FMT" KB)\n", _countsWords, _countsWords >> 7); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:176:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stream, "_shift1: "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:177:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 177 | fprintf(stream, "_shift2 "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:178:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stream, "_mask1 "uint64HEX"\n", _mask1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:179:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 179 | fprintf(stream, "_mask2 "uint64HEX"\n", _mask2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:183:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stream, "_hshWidth "uint32FMT"\n", _hshWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:191:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stream, "_chkWidth "uint32FMT"\n", _chkWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:199:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 199 | fprintf(stream, "_cntWidth "uint32FMT"\n", _cntWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C: In member function ‘bool existDB::loadState(const char*, bool, bool)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:80:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | fread(cigam, sizeof(char), 16, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:124:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 124 | fread(&_merSizeInBases, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:125:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fread(&_shift1, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:126:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 126 | fread(&_shift2, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:127:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 127 | fread(&_mask1, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:128:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fread(&_mask2, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:129:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fread(&_hshWidth, sizeof(uint32), 1, F); // only valid if _compressedHash | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:130:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | fread(&_chkWidth, sizeof(uint32), 1, F); // only valid if _compressedBucket | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:131:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fread(&_cntWidth, sizeof(uint32), 1, F); // only valid if _compressedCounts | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:133:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fread(&_hashTableWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:134:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 134 | fread(&_bucketsWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:135:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 135 | fread(&_countsWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:148:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 148 | fread(_hashTable, sizeof(uint64), _hashTableWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:149:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fread(_buckets, sizeof(uint64), _bucketsWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:152:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | fread(_counts, sizeof(uint64), _countsWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C: In member function ‘void existDB::saveState(const char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.C:24:10: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 24 | strncpy(cigam, magic, 16); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.C:44:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "existDB::existDB()-- Got "uint32FMT", expected "uint32FMT"\n", _merSizeInBases, merSize); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.C:44:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "existDB::existDB()-- Got "uint32FMT", expected "uint32FMT"\n", _merSizeInBases, merSize); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:2: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:22:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 22 | fprintf(stderr, "positionDB::get()-- Can't allocate space for more positions, requested "uint64FMT" uint64's.\n", posnMax); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:215:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 215 | fprintf(stderr, "positionDB::filter()-- Filtering out kmers less than "uint64FMT" and more than "uint64FMT"\n", lo, hi); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:215:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 215 | fprintf(stderr, "positionDB::filter()-- Filtering out kmers less than "uint64FMT" and more than "uint64FMT"\n", lo, hi); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:339:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers less than "uint64FMT"\n", loCount, lo); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:339:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers less than "uint64FMT"\n", loCount, lo); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:340:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers more than "uint64FMT"\n", hiCount, hi); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:340:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers more than "uint64FMT"\n", hiCount, hi); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:341:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 341 | fprintf(stderr, "positionDB::filter()-- Saved "uint64FMT" kmers with acceptable count\n", okCount); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C: In member function ‘void positionDB::filter(uint64, uint64)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.C:204:11: warning: unused variable ‘vv’ [-Wunused-variable] 204 | uint64 vv; | ^~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:40:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(F, " "uint64FMT, getDecodedValue(_positions, pos, _posnWidth)); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:197:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stream, "merSizeInBases: "uint32FMT"\n", _merSizeInBases); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:198:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 198 | fprintf(stream, "merSkipInBases: "uint32FMT"\n", _merSkipInBases); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:199:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 199 | fprintf(stream, "tableSizeInBits: "uint32FMT"\n", _tableSizeInBits); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:200:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stream, "tableSizeInEntries: "uint64FMT"\n", _tableSizeInEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:201:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stream, "hashWidth: "uint32FMT"\n", _hashWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:202:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stream, "chckWidth: "uint32FMT"\n", _chckWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:203:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stream, "posnWidth: "uint32FMT"\n", _posnWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:204:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stream, "numberOfMers: "uint64FMT"\n", _numberOfMers); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:205:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 205 | fprintf(stream, "numberOfPositions: "uint64FMT"\n", _numberOfPositions); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:206:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 206 | fprintf(stream, "numberOfDistinct: "uint64FMT"\n", _numberOfDistinct); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:207:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 207 | fprintf(stream, "numberOfUnique: "uint64FMT"\n", _numberOfUnique); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:208:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 208 | fprintf(stream, "numberOfEntries: "uint64FMT"\n", _numberOfEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:209:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stream, "maximumEntries: "uint64FMT"\n", _maximumEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C: In member function ‘void positionDB::saveState(const char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:63:22: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 63 | _hashTable_FW = (uint32 *)((_hashTable_FW) ? uint32ONE : uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:37:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | write(F, magic, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:39:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | write(F, faild, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.C:95:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 95 | write(F, magic, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C:324:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 324 | fprintf(stderr, "positionDB::getUpToNMismatches()-- Can't allocate space for initial positions, requested "uint64FMT" uint64's.\n", posnMax); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:86:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 86 | fprintf(stdout, uint32FMTW(4)"] chck="uint64HEX" posn="uint64FMT"\n", t, _sortedChck[t], _sortedPosn[t]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:86:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 86 | fprintf(stdout, uint32FMTW(4)"] chck="uint64HEX" posn="uint64FMT"\n", t, _sortedChck[t], _sortedPosn[t]); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:46:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer size is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:46:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer size is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:52:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer skip is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:52:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer skip is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:58:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but max number of mismatches is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:58:123: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but max number of mismatches is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:127:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, " sm = "uint64FMT"\n", sm); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:128:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, " lg = "uint64FMT"\n", lg); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:129:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, " merSize = "uint32FMT" bits\n", 2 * merSize); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:130:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, " approxMers = "uint64FMT" mers\n", approxMers); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:131:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, " posnWidth = "uint64FMT" bits\n", posnWidth); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:142:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:142:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:142:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:200:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:200:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:200:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:217:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:217:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:217:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:217:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:217:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:217:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:326:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 326 | fprintf(stderr, "positionDB()-- bktAlloc = new uint64 ["uint64FMT"]\n", _tableSizeInEntries / 2 + 4); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:348:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 348 | fprintf(stderr, " Allocated bucket size counting space with total size "uint64FMT" KB\n", _tableSizeInEntries >> 8); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:392:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 392 | fprintf(stderr, " Found "uint64FMT" mers (max position = "uint64FMT")\n", _numberOfMers, _numberOfPositions); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:392:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 392 | fprintf(stderr, " Found "uint64FMT" mers (max position = "uint64FMT")\n", _numberOfMers, _numberOfPositions); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:430:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 430 | fprintf(stderr, " Allocated "uint64FMT"KB for buckets ("uint64FMT" 64-bit words)\n", bucketsSpace >> 7, bucketsSpace); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:430:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 430 | fprintf(stderr, " Allocated "uint64FMT"KB for buckets ("uint64FMT" 64-bit words)\n", bucketsSpace >> 7, bucketsSpace); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:435:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 435 | fprintf(stderr, "positionDB()-- _countingBuckets = new uint64 ["uint64FMT"]\n", bucketsSpace); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:553:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, " Sorting and repacking buckets ("uint64FMT" buckets).\n", _tableSizeInEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:565:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 565 | " Found "uint64FMTW(12)" total mers\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:566:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 566 | " Found "uint64FMTW(12)" distinct mers\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:567:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 567 | " Found "uint64FMTW(12)" unique mers\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:568:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 568 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:568:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 568 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:637:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 637 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for hash table ("uint64FMT" 64-bit words)\n", hs >> 7, hs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:637:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 637 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for hash table ("uint64FMT" 64-bit words)\n", hs >> 7, hs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:643:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 643 | fprintf(stderr, "positionDB()-- _hashTable_BP = new uint64 ["uint64FMT"]\n", hs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:662:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 662 | fprintf(stderr, " Reusing bucket space; Have: "uint64FMT" Need: "uint64FMT" (64-bit words)\n", bucketsSpace, bs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:662:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 662 | fprintf(stderr, " Reusing bucket space; Have: "uint64FMT" Need: "uint64FMT" (64-bit words)\n", bucketsSpace, bs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:669:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 669 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for buckets ("uint64FMT" 64-bit words)\n", bs >> 7, bs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:669:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 669 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for buckets ("uint64FMT" 64-bit words)\n", bs >> 7, bs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:674:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 674 | fprintf(stderr, "positionDB()-- _buckets = new uint64 ["uint64FMT"]\n", bs); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:680:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 680 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for positions ("uint64FMT" 64-bit words)\n", ps >> 7, ps); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:680:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 680 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for positions ("uint64FMT" 64-bit words)\n", ps >> 7, ps); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:685:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 685 | fprintf(stderr, "positionDB()-- _positions = new uint64 ["uint64FMT"\n", ps); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:695:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 695 | fprintf(stderr, " Transferring to final structure ("uint64FMT" buckets).\n", _tableSizeInEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:878:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 878 | fprintf(stderr, "positionDB()-- ERROR: Got position "uint64FMT", but only "uint64FMT" available!\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:878:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 878 | fprintf(stderr, "positionDB()-- ERROR: Got position "uint64FMT", but only "uint64FMT" available!\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:916:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 916 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", bs, ps); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:916:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 916 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", bs, ps); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:917:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 917 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:917:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 917 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:918:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 918 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", currentBbit / 64, currentPbit / 64); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:918:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 918 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", currentBbit / 64, currentPbit / 64); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:928:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 928 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:928:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 928 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:930:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 930 | " Found "uint64FMTW(12)" total mers\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:931:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 931 | " Found "uint64FMTW(12)" distinct mers\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:932:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 932 | " Found "uint64FMTW(12)" unique mers\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:933:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 933 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:933:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 933 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:955:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 955 | fprintf(stderr, " Rebuilding the hash table, from "uint32FMT" bits wide to "uint32FMT" bits wide.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:955:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 955 | fprintf(stderr, " Rebuilding the hash table, from "uint32FMT" bits wide to "uint32FMT" bits wide.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:990:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 990 | fprintf(stderr, " Loading "uint64FMT" mercounts.\n", counts->numberOfDistinctMers()); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:1013:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1013 | fprintf(stderr, " Loaded "uint64FMT" mercounts; largest is "uint64FMT".\n", countsLoaded, largestMerylCount); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:1013:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1013 | fprintf(stderr, " Loaded "uint64FMT" mercounts; largest is "uint64FMT".\n", countsLoaded, largestMerylCount); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:1017:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1017 | fprintf(stderr, " Compress sizes from "uint32FMT" bits to "uint32FMT" bits.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:1017:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1017 | fprintf(stderr, " Compress sizes from "uint32FMT" bits to "uint32FMT" bits.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C: In member function ‘void positionDB::build(merStream*, existDB*, existDB*, merylStreamReader*, uint32, uint32, bool)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:324:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 324 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:433:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 433 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:641:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 641 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:672:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 672 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.C:683:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 683 | } catch (std::bad_alloc) { | ^~~~~~~~~ rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB-state.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-access.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-dump.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-file.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB-sort.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:72:2: warning: #warning not checking pmagic [-Wcpp] 72 | #warning not checking pmagic | ^~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:134:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 134 | fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "uint32FMT" but '%s' is mersize "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:134:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 134 | fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "uint32FMT" but '%s' is mersize "uint32FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:6:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 6 | static char *ImagicV = "merylStreamIv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:7:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 7 | static char *ImagicX = "merylStreamIvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:8:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 8 | static char *DmagicV = "merylStreamDv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:9:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 9 | static char *DmagicX = "merylStreamDvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:10:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 10 | static char *PmagicV = "merylStreamPv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:11:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 11 | static char *PmagicX = "merylStreamPvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C: In constructor ‘merylStreamReader::merylStreamReader(const char*, uint32)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:42:11: warning: variable ‘Pmagic’ set but not used [-Wunused-but-set-variable] 42 | char Pmagic[16] = {0}; | ^~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C: In member function ‘void merylStreamWriter::addMer(uint64, uint32, uint64, uint32, uint32, uint32*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.C:469:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 469 | (prefix <= _thisMerPre) && (mer < _thisMerMer)) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.o g++ -Wl,-z,relro -Wl,-z,now -o seatac/seatac seatac/seatac.o seatac/configuration.o seatac/encodedQuery.o seatac/hitMatrix.o seatac/thr-search.o seatac/thr-loader.o seatac/thr-deadlock.o seatac/hitMatrix-sort.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/heavychains-driver.o -c seatac/heavychains-driver.C In file included from seatac/heavychains.H:11, from seatac/heavychains-driver.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seatac/heavychains.H: In member function ‘double DPTree::matchScore(kd_node, Match&)’: seatac/heavychains.H:374:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/heavychains.o -c seatac/heavychains.C In file included from seatac/heavychains.H:11, from seatac/heavychains.C:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seatac/heavychains.C:96:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:96:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:96:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:164:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 164 | fprintf(stderr, "heavychains: out "uint32FMTW(8)" %8d %8d -- "uint32FMTW(8)" %8d %8d\n", | ^ seatac/heavychains.C:164:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 164 | fprintf(stderr, "heavychains: out "uint32FMTW(8)" %8d %8d -- "uint32FMTW(8)" %8d %8d\n", | ^ seatac/heavychains.C:169:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:169:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:169:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:186:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "HeavyChains: finished strands "uint32FMTW(8)" "uint32FMTW(8)" maxlen1=%f maxlen2=%f maxScoreFwd=%f maxScoreRef=%f\n", | ^ seatac/heavychains.C:186:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "HeavyChains: finished strands "uint32FMTW(8)" "uint32FMTW(8)" maxlen1=%f maxlen2=%f maxScoreFwd=%f maxScoreRef=%f\n", | ^ seatac/heavychains.H: In member function ‘double DPTree::matchScore(kd_node, Match&)’: seatac/heavychains.H:374:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seatac/heavychains seatac/heavychains-driver.o seatac/heavychains.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/filter-nop.o -c seatac/filter-nop.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seatac/filter-nop.C:9: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seatac/filter-nop.C:10: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seatac/filter-nop.C:67:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C: In function ‘void* construct(char*)’: seatac/filter-nop.C:116:16: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 116 | char *seq1 = "UNK"; | ^~~~~ seatac/filter-nop.C:117:16: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 117 | char *seq2 = "UNK"; | ^~~~~ rm -f seatac/filter-nop.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-nop.so seatac/filter-nop.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/filter-heavychains.o -c seatac/filter-heavychains.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seatac/filter-heavychains.C:24: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/filter-heavychains.C:25: seatac/heavychains.H: In member function ‘double DPTree::matchScore(kd_node, Match&)’: seatac/heavychains.H:374:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seatac/heavychains.H: In function ‘void addHit(void*, char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/heavychains.H:53:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ seatac/heavychains.H:53:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ seatac/heavychains.H:53:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ rm -f seatac/filter-heavychains.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-heavychains.so seatac/filter-heavychains.o seatac/heavychains.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/leaff.o -c leaff/leaff.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/leaff.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/leaff.C:311:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "WARNING: Didn't find sequence with iid '"uint32FMT"'\n", sid); | ^ leaff/leaff.C:400:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 400 | fprintf(stdout, "G\tseq\t%s:"uint32FMT"\t"uint32FMT"\t%s\n", | ^ leaff/leaff.C:400:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 400 | fprintf(stdout, "G\tseq\t%s:"uint32FMT"\t"uint32FMT"\t%s\n", | ^ leaff/leaff.C:469:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 469 | sprintf(def, "random"uint32FMTW(06), i); | ^ leaff/leaff.C:727:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 727 | fprintf(stderr, "Couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/blocks.o -c leaff/blocks.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/blocks.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/blocks.C:32:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:42:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C:42:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C:42:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C: In function ‘void dumpBlocks(char*)’: leaff/blocks.C:7:16: warning: unused variable ‘S’ [-Wunused-variable] 7 | seqInCore *S = 0L; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/dups.o -c leaff/dups.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/dups.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/dups.C:26:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stdout, uint32FMT" <-> "uint32FMT"\n", sa->getIID(), sb->getIID()); | ^ leaff/dups.C:28:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 28 | fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"uint32FMT" AND %s:"uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:28:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 28 | fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"uint32FMT" AND %s:"uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:52:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "Internal error: found two copies of the same sequence iid ("uint32FMT")!\n", result[idx].i); | ^ leaff/dups.C:60:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stdout, uint32FMT":%s\n"uint32FMT":%s\n\n", | ^ leaff/dups.C:64:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(stderr, "COLLISION DETECTED BETWEEN IID "uint32FMT" AND "uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:64:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(stderr, "COLLISION DETECTED BETWEEN IID "uint32FMT" AND "uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/gc.o -c leaff/gc.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/gc.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/gc.C:68:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/partition.o -c leaff/partition.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/partition.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/partition.C:55:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "ERROR: Failed to partition "uint32FMT"\n", i); | ^ leaff/partition.C:62:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | sprintf(filename, "%s-"uint32FMTW(03)".fasta", prefix, o); | ^ leaff/partition.C:77:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 77 | fprintf(stderr, "Huh? '%s' "uint32FMT" != "uint32FMT"\n", S->header(), S->sequenceLength(), p[i].length); | ^ leaff/partition.C:77:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 77 | fprintf(stderr, "Huh? '%s' "uint32FMT" != "uint32FMT"\n", S->header(), S->sequenceLength(), p[i].length); | ^ leaff/partition.C:96:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stdout, uint32FMT"]("uint32FMT")", o, sizeP); | ^ leaff/partition.C:99:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stdout, " "uint32FMT"("uint32FMT")", p[i].index, p[i].length); | ^ leaff/partition.C:99:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stdout, " "uint32FMT"("uint32FMT")", p[i].index, p[i].length); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/simseq.o -c leaff/simseq.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from leaff/simseq.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/stats.o -c leaff/stats.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/stats.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/stats.C:110:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "numSeqs "uint32FMT"\n", numSeq); | ^ leaff/stats.C:112:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 112 | fprintf(stdout, "SPAN (smallest "uint32FMT" largest "uint32FMT")\n", Ls[numSeq-1], Ls[0]); | ^ leaff/stats.C:112:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 112 | fprintf(stdout, "SPAN (smallest "uint32FMT" largest "uint32FMT")\n", Ls[numSeq-1], Ls[0]); | ^ leaff/stats.C:114:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:114:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:114:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:115:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(stdout, "totLen "uint64FMTW(10)"\n", Ss); | ^ leaff/stats.C:116:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stdout, "refLen "uint64FMTW(10)"\n", Rs); | ^ leaff/stats.C:118:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 118 | fprintf(stdout, "BASES (smallest "uint32FMT" largest "uint32FMT")\n", Lb[numSeq-1], Lb[0]); | ^ leaff/stats.C:118:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 118 | fprintf(stdout, "BASES (smallest "uint32FMT" largest "uint32FMT")\n", Lb[numSeq-1], Lb[0]); | ^ leaff/stats.C:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:120:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:121:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(stdout, "totLen "uint64FMTW(10)"\n", Sb); | ^ leaff/stats.C:122:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 122 | fprintf(stdout, "refLen "uint64FMTW(10)"\n", Rb); | ^ g++ -Wl,-z,relro -Wl,-z,now -o leaff/leaff leaff/leaff.o leaff/blocks.o leaff/dups.o leaff/gc.o leaff/partition.o leaff/simseq.o leaff/stats.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/meryl.o -c meryl/meryl.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/args.o -c meryl/args.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/args.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/args.C:26:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "writeString()-- Failed to write string of length "uint32FMT": %s\n", len, strerror(errno)); | ^ meryl/args.C: In function ‘char* readString(FILE*)’: meryl/args.C:40:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 40 | fread(&len, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C:50:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 50 | fread(str, sizeof(char), len, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C: In constructor ‘merylArgs::merylArgs(const char*)’: meryl/args.C:513:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 513 | fread(magic, sizeof(char), 16, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C:521:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 521 | fread(this, sizeof(merylArgs), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/binaryOp.o -c meryl/binaryOp.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/binaryOp.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/binaryOp.C:43:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stderr, "ERROR - mersize of '%s' is "uint32FMT"\n", args->mergeFiles[0], A->merSize()); | ^ meryl/binaryOp.C:44:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "ERROR - mersize of '%s' is "uint32FMT"\n", args->mergeFiles[1], B->merSize()); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build.o -c meryl/build.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/build.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/build.C:153:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | sprintf(cmd, "qsub -t 1-"uint64FMT" -cwd -b n -j y -o %s-count-\\$TASK_ID.err %s -N mc%s %s-count.sh", | ^ meryl/build.C:156:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 156 | sprintf(cmd, "qsub -t 1-"uint64FMT" -cwd -b n -j y -o %s-count-\\$TASK_ID.err -N mc%s %s-count.sh", | ^ meryl/build.C:238:2: warning: #warning not submitting prepareBatch to grid [-Wcpp] 238 | #warning not submitting prepareBatch to grid | ^~~~~~~ meryl/build.C:293:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 293 | fprintf(stderr, " numMersActual = "uint64FMT"\n", args->numMersActual); | ^ meryl/build.C:294:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 294 | fprintf(stderr, " mersPerBatch = "uint64FMT"\n", args->mersPerBatch); | ^ meryl/build.C:295:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, " basesPerBatch = "uint64FMT"\n", args->basesPerBatch); | ^ meryl/build.C:296:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:296:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:297:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 297 | fprintf(stderr, " bucketPointerWidth = "uint32FMT"\n", args->bucketPointerWidth); | ^ meryl/build.C:298:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 298 | fprintf(stderr, " merDataWidth = "uint32FMT"\n", args->merDataWidth); | ^ meryl/build.C:305:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:314:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 314 | fprintf(stderr, " numMersActual = "uint64FMT"\n", args->numMersActual); | ^ meryl/build.C:315:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 315 | fprintf(stderr, " mersPerBatch = "uint64FMT"\n", args->mersPerBatch); | ^ meryl/build.C:316:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 316 | fprintf(stderr, " basesPerBatch = "uint64FMT"\n", args->basesPerBatch); | ^ meryl/build.C:317:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 317 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:317:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 317 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:318:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 318 | fprintf(stderr, " bucketPointerWidth = "uint32FMT"\n", args->bucketPointerWidth); | ^ meryl/build.C:319:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 319 | fprintf(stderr, " merDataWidth = "uint32FMT"\n", args->merDataWidth); | ^ meryl/build.C:342:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 342 | sprintf(filename, "%s.batch"uint64FMT".mcdat", args->outputFile, segment); | ^ meryl/build.C:346:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | fprintf(stderr, "Found result for batch "uint64FMT" in %s.\n", segment, filename); | ^ meryl/build.C:352:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 352 | fprintf(stderr, "Computing segment "uint64FMT" of "uint64FMT".\n", segment+1, args->segmentLimit); | ^ meryl/build.C:352:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 352 | fprintf(stderr, "Computing segment "uint64FMT" of "uint64FMT".\n", segment+1, args->segmentLimit); | ^ meryl/build.C:365:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, " Allocating "uint64FMT"MB for mer storage ("uint32FMT" bits wide).\n", | ^ meryl/build.C:365:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, " Allocating "uint64FMT"MB for mer storage ("uint32FMT" bits wide).\n", | ^ meryl/build.C:384:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 384 | fprintf(stderr, " Allocating "uint64FMT"MB for mer position storage.\n", | ^ meryl/build.C:390:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " Allocating "uint64FMT"MB for bucket pointer table ("uint32FMT" bits wide).\n", | ^ meryl/build.C:390:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " Allocating "uint64FMT"MB for bucket pointer table ("uint32FMT" bits wide).\n", | ^ meryl/build.C:396:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 396 | fprintf(stderr, " Allocating "uint64FMT"MB for counting the size of each bucket.\n", args->numBuckets >> 18); | ^ meryl/build.C:477:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 477 | fprintf(stderr, " Releasing "uint64FMT"MB from counting the size of each bucket.\n", args->numBuckets >> 18); | ^ meryl/build.C:532:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 532 | sprintf(batchOutputFile, "%s.batch"uint64FMT, args->outputFile, segment); | ^ meryl/build.C:552:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 552 | fprintf(stderr, "ERROR: In segment "uint64FMT"\n", segment); | ^ meryl/build.C:553:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") ends before it starts!\n", | ^ meryl/build.C:553:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") ends before it starts!\n", | ^ meryl/build.C:555:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 555 | fprintf(stderr, "ERROR: start="uint64FMT"\n", st); | ^ meryl/build.C:556:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 556 | fprintf(stderr, "ERROR: end ="uint64FMT"\n", ed); | ^ meryl/build.C:561:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 561 | fprintf(stderr, "ERROR: In segment "uint64FMT"\n", segment); | ^ meryl/build.C:562:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 562 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") is HUGE!\n", | ^ meryl/build.C:562:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 562 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") is HUGE!\n", | ^ meryl/build.C:564:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 564 | fprintf(stderr, "ERROR: start="uint64FMT"\n", st); | ^ meryl/build.C:565:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 565 | fprintf(stderr, "ERROR: end ="uint64FMT"\n", ed); | ^ meryl/build.C:667:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 667 | fprintf(stderr, "Segment "uint64FMT" finished.\n", segment); | ^ meryl/build.C:705:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 705 | fprintf(stdout, "%s -countbatch "uint64FMT" -o %s\n", args->execName, s, args->outputFile); | ^ meryl/build.C:783:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 783 | sprintf(argv[argc], "%s.batch"uint32FMT, args->outputFile, i); | ^ meryl/build.C:807:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 807 | sprintf(filename, "%s.batch"uint32FMT".mcidx", args->outputFile, i); | ^ meryl/build.C:809:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 809 | sprintf(filename, "%s.batch"uint32FMT".mcdat", args->outputFile, i); | ^ meryl/build.C:811:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 811 | sprintf(filename, "%s.batch"uint32FMT".mcpos", args->outputFile, i); | ^ meryl/build.C: In function ‘void prepareBatch(merylArgs*)’: meryl/build.C:310:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 311 | estimateMemory(args->merSize, args->mersPerBatch, args->positionsEnabled) * args->numThreads, 312 | estimateMemory(args->merSize, args->numMersActual, args->positionsEnabled)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long unsigned int} meryl/build.C:310:23: warning: format ‘%lu’ expects a matching ‘long unsigned int’ argument [-Wformat=] meryl/build.C:310:23: warning: format ‘%lu’ expects a matching ‘long unsigned int’ argument [-Wformat=] meryl/build.C: In function ‘void runSegment(merylArgs*, uint64)’: meryl/build.C:412:8: warning: unused variable ‘mstring’ [-Wunused-variable] 412 | char mstring[256]; | ^~~~~~~ meryl/build.C: In function ‘void build(merylArgs*)’: meryl/build.C:769:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 769 | arga[argc] = false; argv[argc++] = "meryl-build-merge"; | ^~~~~~~~~~~~~~~~~~~ meryl/build.C:770:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 770 | arga[argc] = false; argv[argc++] = "-M"; | ^~~~ meryl/build.C:771:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 771 | arga[argc] = false; argv[argc++] = "merge"; | ^~~~~~~ meryl/build.C:775:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 775 | argv[argc++] = "-v"; | ^~~~ meryl/build.C:780:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 780 | argv[argc++] = "-s"; | ^~~~ meryl/build.C:787:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 787 | arga[argc] = false; argv[argc++] = "-o"; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build-threads.o -c meryl/build-threads.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/build-threads.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/dump.o -c meryl/dump.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/dump.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/dump.C:17:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stdout, ">"uint64FMT"\n%s\n", | ^ meryl/dump.C:35:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stdout, ">"uint64FMT, M->theCount()); | ^ meryl/dump.C:37:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, " "uint32FMT, M->getPosition(i)); | ^ meryl/dump.C:50:2: warning: #warning make this a test [-Wcpp] 50 | #warning make this a test | ^~~~~~~ meryl/dump.C:72:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 72 | fprintf(stdout, "Found "uint64FMT" mers.\n", M->numberOfTotalMers()); | ^ meryl/dump.C:73:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 73 | fprintf(stdout, "Found "uint64FMT" distinct mers.\n", M->numberOfDistinctMers()); | ^ meryl/dump.C:74:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stdout, "Found "uint64FMT" unique mers.\n", M->numberOfUniqueMers()); | ^ meryl/dump.C:87:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Found "uint64FMT" mers.\n", M->numberOfTotalMers()); | ^ meryl/dump.C:88:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 88 | fprintf(stderr, "Found "uint64FMT" distinct mers.\n", M->numberOfDistinctMers()); | ^ meryl/dump.C:89:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "Found "uint64FMT" unique mers.\n", M->numberOfUniqueMers()); | ^ meryl/dump.C:91:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "Largest mercount is "uint64FMT"; "uint64FMT" mers are too big for histogram.\n", | ^ meryl/dump.C:91:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "Largest mercount is "uint64FMT"; "uint64FMT" mers are too big for histogram.\n", | ^ meryl/dump.C:101:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, uint32FMT"\t"uint64FMT"\t%.4f\t%.4f\n", | ^ meryl/dump.C:148:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, uint32FMT"\t"uint64FMT"\n", d, hist[d]); | ^ meryl/dump.C:151:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "huge\t"uint64FMT"\n", histHuge); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/estimate.o -c meryl/estimate.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/estimate.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/estimate.C:54:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "Can fit "uint64FMT" mers into table with prefix of "uint64FMT" bits, using %.3fMB (%.3fMB for positions)\n", | ^ meryl/estimate.C:54:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "Can fit "uint64FMT" mers into table with prefix of "uint64FMT" bits, using %.3fMB (%.3fMB for positions)\n", | ^ meryl/estimate.C:162:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 162 | fprintf(stderr, uint64FMT" "uint32FMT"-mers can be computed using "uint64FMT"MB memory.\n", | ^ meryl/estimate.C:162:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 162 | fprintf(stderr, uint64FMT" "uint32FMT"-mers can be computed using "uint64FMT"MB memory.\n", | ^ meryl/estimate.C: In function ‘uint64 estimateMemory(uint32, uint64, bool)’: meryl/estimate.C:77:13: warning: unused variable ‘N’ [-Wunused-variable] 77 | uint64 N = logBaseTwo64(numMers); // Width of the bucket pointer table | ^ meryl/estimate.C:73:11: warning: variable ‘tMin’ set but not used [-Wunused-but-set-variable] 73 | uint64 tMin = tMax; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/merge.o -c meryl/merge.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/merge.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/merge.C:14:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 14 | fprintf(stderr, "ERROR - must have at least two databases (you gave "uint32FMT")!\n", args->mergeFilesLen); | ^ meryl/merge.C: In function ‘void multipleOperations(merylArgs*)’: meryl/merge.C:237:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 237 | delete R; | ^ meryl/merge.C:37:71: note: returned from ‘void* operator new [](std::size_t)’ 37 | merylStreamReader **R = new merylStreamReader* [args->mergeFilesLen]; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/unaryOp.o -c meryl/unaryOp.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/unaryOp.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f meryl/libmerylguts.a && ar ruvs meryl/libmerylguts.a meryl/args.o meryl/binaryOp.o meryl/build.o meryl/build-threads.o meryl/dump.o meryl/estimate.o meryl/merge.o meryl/unaryOp.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating meryl/libmerylguts.a a - meryl/args.o a - meryl/binaryOp.o a - meryl/build.o a - meryl/build-threads.o a - meryl/dump.o a - meryl/estimate.o a - meryl/merge.o a - meryl/unaryOp.o g++ -Wl,-z,relro -Wl,-z,now -o meryl/meryl meryl/meryl.o meryl/libmerylguts.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/simple.o -c meryl/simple.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/simple.C:8: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/simple.C:98:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 98 | fprintf(stderr, "Guessing "uint64FMT" mers in input '%s'\n", numMers, inName); | ^ meryl/simple.C:99:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stderr, "Allocating "uint64FMT"MB for mer storage.\n", numMers * 8 >> 20); | ^ meryl/simple.C:129:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "Found "uint64FMT" mers in input '%s'\n", theMersLen, inName); | ^ g++ -Wl,-z,relro -Wl,-z,now -o meryl/simple meryl/simple.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers.o -c meryl/mapMers.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/mapMers.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/mapMers.C:135:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:135:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:137:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:165:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:165:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:165:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:171:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "%s\t"uint64FMT"\tuncovered\n", S->header(), MS->thePositionInSequence()); | ^ meryl/mapMers.C:176:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:176:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:176:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:178:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "numCovReg: "uint64FMT"\n", numCovReg); | ^ meryl/mapMers.C:179:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 179 | fprintf(stderr, "lenCovReg: "uint64FMT"\n", lenCovReg); | ^ meryl/mapMers.C:193:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C: In function ‘int main(int, char**)’: meryl/mapMers.C:21:13: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 21 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o meryl/mapMers meryl/mapMers.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers-depth.o -c meryl/mapMers-depth.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/mapMers-depth.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o meryl/mapMers-depth meryl/mapMers-depth.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/kmer-mask.o -c meryl/kmer-mask.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from meryl/kmer-mask.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/kmer-mask.C:754:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 754 | fprintf(stderr, "aClean "FW"\n", g->thresholdCounts[0][0]); | ^ meryl/kmer-mask.C:755:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 755 | fprintf(stderr, "aMurky "FW"\n", g->thresholdCounts[1][0]); | ^ meryl/kmer-mask.C:756:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 756 | fprintf(stderr, "aMatch "FW"\n", g->thresholdCounts[2][0]); | ^ meryl/kmer-mask.C:757:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 757 | fprintf(stderr, "aMixed "FW"\n", g->thresholdCounts[3][0]); | ^ meryl/kmer-mask.C:760:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:761:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:762:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:763:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C: In member function ‘bool fastqRecord::load(FILE*, FILE*)’: meryl/kmer-mask.C:69:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fgets(a1, 1024, FASTQ1); chomp(a1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:70:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | fgets(a2, maxLength, FASTQ1); chomp(a2); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:71:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | fgets(a3, 1024, FASTQ1); chomp(a3); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:72:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fgets(a4, maxLength, FASTQ1); chomp(a4); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:83:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | fgets(b1, 1024, FASTQ2); chomp(b1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:84:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fgets(b2, maxLength, FASTQ2); chomp(b2); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:85:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fgets(b3, 1024, FASTQ2); chomp(b3); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:86:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | fgets(b4, maxLength, FASTQ2); chomp(b4); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o meryl/kmer-mask meryl/kmer-mask.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitMatrix.o -c seagen/hitMatrix.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/hitMatrix.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.C:642:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/searchGENOME.o -c seagen/searchGENOME.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/searchGENOME.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/configuration.o -c seagen/configuration.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/configuration.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/configuration.C:84:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "\n"uint32FMTW(7)" sequences in %5.2f seconds, %8.3f per second.\n", nq, tm, nq/tm); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/encodedQuery.o -c seagen/encodedQuery.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seagen/encodedQuery.H:6, from seagen/encodedQuery.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/encodedQuery.C:142:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "encodedQuery::test()-- mersAvail incorrect: Recomputed:"uint32FMT" Real:"uint32FMT"\n", _mersAvail, _r_mersAvail); | ^ seagen/encodedQuery.C:142:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "encodedQuery::test()-- mersAvail incorrect: Recomputed:"uint32FMT" Real:"uint32FMT"\n", _mersAvail, _r_mersAvail); | ^ seagen/encodedQuery.C:152:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 152 | fprintf(stderr, "encodedQuery::test()-- skip["uint32FMTW(4)"] incorrect: Acc:%d Real:%d\n", i, getSkip(i, true), _r_skip[i]); | ^ seagen/encodedQuery.C:160:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:160:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:160:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:209:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stderr, "encodedQuery::addOutput()-- from "uint32FMT" to "uint32FMT" bytes.\n", | ^ seagen/encodedQuery.C:209:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stderr, "encodedQuery::addOutput()-- from "uint32FMT" to "uint32FMT" bytes.\n", | ^ seagen/encodedQuery.C: In member function ‘void encodedQuery::addOutput(void*, uint32)’: seagen/encodedQuery.C:207:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 207 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-deadlock.o -c seagen/thr-deadlock.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-deadlock.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-loader.o -c seagen/thr-loader.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-loader.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ seagen/thr-loader.C: In function ‘void* loaderThread(void*)’: seagen/thr-loader.C:14:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 14 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-search.o -c seagen/thr-search.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-search.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-output.o -c seagen/thr-output.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-output.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ seagen/thr-output.C: In function ‘void* writerThread(void*, void*)’: seagen/thr-output.C:48:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 48 | write(config._outputFile, query->theOutput(), query->theOutputLength()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seagen/thr-output.C:62:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | write(config._matchCountsFile, str, strlen(str)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitMatrix-sort.o -c seagen/hitMatrix-sort.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from seagen/hitMatrix.H:8, from seagen/hitMatrix-sort.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/hitMatrix.H:9: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/aHit.o -c seagen/aHit.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/aHit.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/aHit.C:20:14: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:98: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C: In function ‘void ahit_readBinary(aHit*, FILE*)’: seagen/aHit.C:12:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 12 | fread(a, sizeof(aHit), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/seagen seagen/hitMatrix.o seagen/searchGENOME.o seagen/configuration.o seagen/encodedQuery.o seagen/thr-deadlock.o seagen/thr-loader.o seagen/thr-search.o seagen/thr-output.o seagen/hitMatrix-sort.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitConverter.o -c seagen/hitConverter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/hitConverter.C:3: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/hitConverter.C: In function ‘void asc2bin(FILE*, FILE*)’: seagen/hitConverter.C:39:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | fgets(b, 1024, I); | ~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/hitConverter seagen/hitConverter.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterEST.o -c seagen/filterEST.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterEST.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterEST.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterEST.C:76:11: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 76 | " hits saved:"uint32FMTW(8)"/"uint32FMTW(8)" = %6.3f%%\r", | ^ seagen/filterEST.C:76:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 76 | " hits saved:"uint32FMTW(8)"/"uint32FMTW(8)" = %6.3f%%\r", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterEST-complicated.o -c seagen/filterEST-complicated.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterEST-complicated.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterEST-complicated.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterEST-complicated.C:67:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | fprintf(logFile, uint32FMT"] unique: aggressively filtered to "uint32FMT" hits out of "uint32FMT" hits.\n", | ^ seagen/filterEST-complicated.C:67:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | fprintf(logFile, uint32FMT"] unique: aggressively filtered to "uint32FMT" hits out of "uint32FMT" hits.\n", | ^ seagen/filterEST-complicated.C:115:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(logFile, uint32FMT"] knee: filtered "uint32FMT" hits down to "uint32FMT" hits using threshold %f\n", | ^ seagen/filterEST-complicated.C:115:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(logFile, uint32FMT"] knee: filtered "uint32FMT" hits down to "uint32FMT" hits using threshold %f\n", | ^ seagen/filterEST-complicated.C:139:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(logFile, uint32FMT"] uniform: uniform signal strength, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:139:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(logFile, uint32FMT"] uniform: uniform signal strength, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:174:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(logFile, uint32FMT"] diff: has no clear signal knee, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f, largestdiff=%f\n", | ^ seagen/filterEST-complicated.C:174:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(logFile, uint32FMT"] diff: has no clear signal knee, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f, largestdiff=%f\n", | ^ seagen/filterEST-complicated.C:228:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:228:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:228:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:277:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 277 | fprintf(logFile, uint32FMT"] is an unclassified signal, "uint32FMT" hits saved out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:277:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 277 | fprintf(logFile, uint32FMT"] is an unclassified signal, "uint32FMT" hits saved out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitReader.o -c seagen/hitReader.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/hitReader.H:7, from seagen/hitReader.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5, from seagen/hitReader.H:8: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterEST seagen/filterEST.o seagen/filterEST-complicated.o seagen/hitReader.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterMRNA.o -c seagen/filterMRNA.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterMRNA.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterMRNA.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterMRNA.C:53:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 53 | fprintf(stderr, " scores at least %4.2f AND at least "uint32FMT" bases covered are always output\n", MC, ML); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterMRNA seagen/filterMRNA.o seagen/hitReader.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterNULL.o -c seagen/filterNULL.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterNULL.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterNULL.C:2: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterNULL seagen/filterNULL.o seagen/hitReader.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filtertest.o -c seagen/filtertest.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/filtertest.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seagen/filtertest.C:180:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "reading hits "uint32FMT"\r", hitsLen); | ^ seagen/filtertest.C:186:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "reading hits "uint32FMT"\n", hitsLen); | ^ seagen/filtertest.C:308:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C: In function ‘void ahit_readBinary(aHit*, FILE*)’: seagen/filtertest.C:39:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | fread(a, sizeof(aHit), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ seagen/filtertest.C: In function ‘int main(int, char**)’: seagen/filtertest.C:162:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fgets(hitLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filtertest seagen/filtertest.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/sortHits.o -c seagen/sortHits.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/sortHits.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/sortHits.C: In member function ‘bool aHitReader::readHit(aHit&)’: seagen/sortHits.C:52:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | fgets(buffer, 1024, theFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ seagen/sortHits.C: In member function ‘void aHitTemporary::nextHit()’: seagen/sortHits.C:119:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fread(&hit, sizeof(aHit), 1, theFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/sortHits seagen/sortHits.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterESTsimple.o -c seagen/filterESTsimple.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterESTsimple.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterESTsimple.C:12: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterESTsimple seagen/filterESTsimple.o seagen/hitReader.o seagen/aHit.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/cleanPolishes.o -c sim4dbutils/cleanPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/cleanPolishes.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/cleanPolishes.C:178:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "A big intron is one that is at least "uint32FMT"bp long.\n", intronLimit); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/cleanPolishes sim4dbutils/cleanPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/fixPolishesIID.o -c sim4dbutils/fixPolishesIID.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/fixPolishesIID.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/fixPolishesIID.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/fixPolishesIID sim4dbutils/fixPolishesIID.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/comparePolishes.o -c sim4dbutils/comparePolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/comparePolishes.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/comparePolishes.C:308:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:118: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:145: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:158: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:452:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 452 | fprintf(stderr, "ERROR! inA="uint32FMT" inB="uint32FMT"\n", inA, inB); | ^ sim4dbutils/comparePolishes.C:452:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 452 | fprintf(stderr, "ERROR! inA="uint32FMT" inB="uint32FMT"\n", inA, inB); | ^ sim4dbutils/comparePolishes.C:484:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:156: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:520:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C: In function ‘int main(int, char**)’: sim4dbutils/comparePolishes.C:74:20: warning: variable ‘doGFF3’ set but not used [-Wunused-but-set-variable] 74 | bool doGFF3; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/s4p_overlap.o -c sim4dbutils/s4p_overlap.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from sim4dbutils/s4p_overlap.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/comparePolishes sim4dbutils/comparePolishes.o sim4dbutils/s4p_overlap.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertToAtac.o -c sim4dbutils/convertToAtac.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertToAtac.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/convertToAtac.C:279:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:134: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:134: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:330:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 330 | fprintf(stderr, "Fixed "uint32FMT" indel/mismatches.\n", totalFixed); | ^ sim4dbutils/convertToAtac.C: In function ‘int main(int, char**)’: sim4dbutils/convertToAtac.C:241:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 241 | if (e->_estAlignment[aPos] != '-') | ^ sim4dbutils/convertToAtac.C:310:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 310 | if (e->_estAlignment[aPos] != '-') | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertToAtac sim4dbutils/convertToAtac.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertToExtent.o -c sim4dbutils/convertToExtent.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertToExtent.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/convertToExtent.C:43:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:118: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C: In function ‘int main(int, char**)’: sim4dbutils/convertToExtent.C:59:8: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 59 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertToExtent sim4dbutils/convertToExtent.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertPolishes.o -c sim4dbutils/convertPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/convertPolishes.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertPolishes.C:8: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertPolishes sim4dbutils/convertPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/detectChimera.o -c sim4dbutils/detectChimera.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/detectChimera.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/detectChimera.C:129:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:129:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:129:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:153:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stdout, "first "uint32FMT" alignments.\n", maxPts); | ^ sim4dbutils/detectChimera.C: In function ‘int main(int, char**)’: sim4dbutils/detectChimera.C:19:10: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 19 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/detectChimera sim4dbutils/detectChimera.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/depthOfPolishes.o -c sim4dbutils/depthOfPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/depthOfPolishes.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/depthOfPolishes.C:103:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/depthOfPolishes sim4dbutils/depthOfPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/filterPolishes.o -c sim4dbutils/filterPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/filterPolishes.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/filterPolishes.C:8: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/filterPolishes.C:178:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:178:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:178:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:181:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT" and genomic idx "uint32FMT"\n", cdna, geno); | ^ sim4dbutils/filterPolishes.C:181:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT" and genomic idx "uint32FMT"\n", cdna, geno); | ^ sim4dbutils/filterPolishes.C:183:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT".\n", cdna); | ^ sim4dbutils/filterPolishes.C:185:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 185 | fprintf(stderr, "Filtering for genomic idx "uint32FMT".\n", geno); | ^ sim4dbutils/filterPolishes.C:259:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\r", | ^ sim4dbutils/filterPolishes.C:259:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\r", | ^ sim4dbutils/filterPolishes.C:264:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 264 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed)\r", | ^ sim4dbutils/filterPolishes.C:274:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 274 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\n", | ^ sim4dbutils/filterPolishes.C:274:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 274 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\n", | ^ sim4dbutils/filterPolishes.C:279:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed)\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/filterPolishes sim4dbutils/filterPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/headPolishes.o -c sim4dbutils/headPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/headPolishes.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/headPolishes sim4dbutils/headPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/mappedCoverage.o -c sim4dbutils/mappedCoverage.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/mappedCoverage.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/mappedCoverage.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/mappedCoverage.C:94:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 94 | fprintf(stderr, "Found "uint32FMT" sequences in the input file.\n", covMax); | ^ sim4dbutils/mappedCoverage.C:130:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:130:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:153:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:153:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:219:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:219:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:219:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:242:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C:242:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C:242:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C: In function ‘int main(int, char**)’: sim4dbutils/mappedCoverage.C:106:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fgets(inLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/mappedCoverage sim4dbutils/mappedCoverage.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/mergePolishes.o -c sim4dbutils/mergePolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/mergePolishes.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/mergePolishes.C: In function ‘int main(int, char**)’: sim4dbutils/mergePolishes.C:139:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 139 | delete inMatch; | ^~~~~~~ sim4dbutils/mergePolishes.C:28:62: note: returned from ‘void* operator new [](std::size_t)’ 28 | sim4polishReader **inMatch = new sim4polishReader * [argc]; | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/mergePolishes sim4dbutils/mergePolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/parseSNP.o -c sim4dbutils/parseSNP.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/parseSNP.C:9: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/parseSNP.C:10: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/parseSNP.C:229:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:269:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:98: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:113: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:143: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:538:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 538 | fprintf(stderr, "ERROR: Polishes not sorted by SNP idx! this="uint32FMT", looking for "uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:538:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 538 | fprintf(stderr, "ERROR: Polishes not sorted by SNP idx! this="uint32FMT", looking for "uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/parseSNP sim4dbutils/parseSNP.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickBestPolish.o -c sim4dbutils/pickBestPolish.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickBestPolish.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickBestPolish.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/pickBestPolish.C:35:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:35:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:35:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:39:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:69:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(stderr, "Picking Best for estID="uint32FMT" with %5d choices.\r", p[0]->_estID, pNum); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickBestPolish sim4dbutils/pickBestPolish.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickBestPair.o -c sim4dbutils/pickBestPair.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickBestPair.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickBestPair.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/pickBestPair.C:546:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:584:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 584 | fprintf(STA, "alignments: "uint32FMT" "uint32FMT"\n", mr1END, mr2END); | ^ sim4dbutils/pickBestPair.C:584:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 584 | fprintf(STA, "alignments: "uint32FMT" "uint32FMT"\n", mr1END, mr2END); | ^ sim4dbutils/pickBestPair.C: In function ‘int main(int, char**)’: sim4dbutils/pickBestPair.C:266:19: warning: variable ‘minIdent’ set but not used [-Wunused-but-set-variable] 266 | double minIdent = 0; | ^~~~~~~~ sim4dbutils/pickBestPair.C:267:19: warning: variable ‘minLength’ set but not used [-Wunused-but-set-variable] 267 | double minLength = 0; | ^~~~~~~~~ sim4dbutils/pickBestPair.C:268:19: warning: variable ‘minCoverage’ set but not used [-Wunused-but-set-variable] 268 | double minCoverage = 0; | ^~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘bool readMR(FILE*, mapResult&)’: sim4dbutils/pickBestPair.C:54:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:57:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘bool readMRcoords(FILE*, mapResult&)’: sim4dbutils/pickBestPair.C:123:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 123 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:124:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 124 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:125:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:126:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 126 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:129:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘bool readMRcoords(FILE*, mapResult&, bool&)’: sim4dbutils/pickBestPair.C:189:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:190:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:191:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 191 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:192:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 192 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:195:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 195 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘int main(int, char**)’: sim4dbutils/pickBestPair.C:354:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 354 | fgets(LL, 10240, IN); | ~~~~~^~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:365:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 365 | fgets(LL, 10240, IN); | ~~~~~^~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickBestPair sim4dbutils/pickBestPair.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickUniquePolish.o -c sim4dbutils/pickUniquePolish.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickUniquePolish.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickUniquePolish.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickUniquePolish sim4dbutils/pickUniquePolish.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/plotCoverageVsIdentity.o -c sim4dbutils/plotCoverageVsIdentity.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/plotCoverageVsIdentity.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/plotCoverageVsIdentity.C:32:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(S, uint32FMT" "uint32FMT"\n", p->_percentIdentity, p->_querySeqIdentity); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/plotCoverageVsIdentity sim4dbutils/plotCoverageVsIdentity.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/removeDuplicate.o -c sim4dbutils/removeDuplicate.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/removeDuplicate.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/removeDuplicate sim4dbutils/removeDuplicate.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/sortPolishes.o -c sim4dbutils/sortPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/sortPolishes.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/sortPolishes.C:87:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:125: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C: In function ‘sim4polish* savePolish(sim4polish*, uint64*)’: sim4dbutils/sortPolishes.C:39:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polish’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 39 | memcpy(r, q, sizeof(sim4polish)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:99:7: note: ‘class sim4polish’ declared here 99 | class sim4polish { | ^~~~~~~~~~ sim4dbutils/sortPolishes.C:59:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 59 | memcpy(r->_exons, q->_exons, sizeof(sim4polishExon) * q->_numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/sortPolishes sim4dbutils/sortPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/summarizePolishes.o -c sim4dbutils/summarizePolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/summarizePolishes.C:4: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/summarizePolishes.C:167:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 167 | fprintf(stderr, "numSeqs: "uint32FMT"\n", numSeqs); | ^ sim4dbutils/summarizePolishes.C:169:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stderr, "ids: "uint32FMT" -- ", idLen); | ^ sim4dbutils/summarizePolishes.C:171:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stderr, " "uint32FMT"", id[i]); | ^ sim4dbutils/summarizePolishes.C:173:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stderr, "cvs: "uint32FMT" -- ", cvLen); | ^ sim4dbutils/summarizePolishes.C:175:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 175 | fprintf(stderr, " "uint32FMT"", cv[i]); | ^ sim4dbutils/summarizePolishes.C:244:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:125: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/summarizePolishes sim4dbutils/summarizePolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/uniqPolishes.o -c sim4dbutils/uniqPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/uniqPolishes.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/uniqPolishes sim4dbutils/uniqPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/vennPolishes.o -c sim4dbutils/vennPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/vennPolishes.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/vennPolishes.C:115:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(stderr, "WARNING: You gave me "uint32FMT" files! That's pretty big. I don't know\n", numFiles); | ^ sim4dbutils/vennPolishes.C:175:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 175 | fprintf(stdout, " "uint32FMTW(8)" ", counts[index]); | ^ sim4dbutils/vennPolishes.C:183:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stdout, "%c = ("uint32FMTW(8)" total) %s\n", 'A' + (char)i, sizes[i], argv[i+numArgs]); | ^ sim4dbutils/vennPolishes.C:189:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 189 | fprintf(stdout, "] "uint32FMT"\n", counts[index]); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/vennPolishes sim4dbutils/vennPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/realignPolishes.o -c sim4dbutils/realignPolishes.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/realignPolishes.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/realignPolishes.C:160:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:161:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:243:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | fprintf(stdout, "WARNING: CHANGED! "uint32FMT" -> "uint32FMT"\n", nm, p->_numMatches); | ^ sim4dbutils/realignPolishes.C:243:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | fprintf(stdout, "WARNING: CHANGED! "uint32FMT" -> "uint32FMT"\n", nm, p->_numMatches); | ^ sim4dbutils/realignPolishes.C:248:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(mergeLog, "MERGED\tEST\t"uint32FMT"\tfrom\t%8.3f\t%8.3f\tto\t%8.3f\t%8.3f\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/realignPolishes sim4dbutils/realignPolishes.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/removeRedundant.o -c sim4dbutils/removeRedundant.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/removeRedundant.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/removeRedundant.C:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:107:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:107:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:212:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "\nNOT A PERFECT CLIQUE! Found "uint32FMT" overlaps, wanted "uint32FMT" in the clique.\n", | ^ sim4dbutils/removeRedundant.C:212:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "\nNOT A PERFECT CLIQUE! Found "uint32FMT" overlaps, wanted "uint32FMT" in the clique.\n", | ^ sim4dbutils/removeRedundant.C:260:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(stderr, "\nmatches withOvl:"uint32FMT" withoutOvl:"uint32FMT"\n", | ^ sim4dbutils/removeRedundant.C:260:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(stderr, "\nmatches withOvl:"uint32FMT" withoutOvl:"uint32FMT"\n", | ^ sim4dbutils/removeRedundant.C:262:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 262 | fprintf(stderr, "not perfect clique:"uint32FMT"\n", notPerfectClique); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/removeRedundant sim4dbutils/removeRedundant.o sim4dbutils/s4p_overlap.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/reportAlignmentDifferences.o -c sim4dbutils/reportAlignmentDifferences.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/reportAlignmentDifferences.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/reportAlignmentDifferences.C: In function ‘int main(int, char**)’: sim4dbutils/reportAlignmentDifferences.C:155:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 155 | if (e->_estAlignment[aPos] != '-') | ^ sim4dbutils/reportAlignmentDifferences.C:201:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | system(gnuCmd); | ~~~~~~^~~~~~~~ sim4dbutils/reportAlignmentDifferences.C:200:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4086 [-Wformat-overflow=] 200 | sprintf(gnuCmd, "gnuplot < %s", gnuName); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:970, from sim4dbutils/reportAlignmentDifferences.C:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int main(int, char**)’ at sim4dbutils/reportAlignmentDifferences.C:200:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 11 and 4106 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/reportAlignmentDifferences sim4dbutils/reportAlignmentDifferences.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4db/sim4th.o -c sim4db/sim4th.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4db/sim4th.C:34: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4db/sim4th.C:327:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 327 | sprintf(str, "%s -Y "uint32FMT" "uint32FMT"\n", | ^ sim4db/sim4th.C:327:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 327 | sprintf(str, "%s -Y "uint32FMT" "uint32FMT"\n", | ^ sim4db/sim4th.C: In function ‘void writer(void*, void*)’: sim4db/sim4th.C:316:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 316 | write(fOutput, o, strlen(o) * sizeof(char)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sim4db/sim4th.C:332:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 332 | write(fYesNo, str, strlen(str) * sizeof(char)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4db/sim4db sim4db/sim4th.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/snapper2.o -c snapper/snapper2.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/snapper2.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.C:59:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:248:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "WARNING: Found "uint32FMT" queries shorter than minimum reportable size (-discardexonlength = "uint32FMT")\n", | ^ snapper/snapper2.C:248:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "WARNING: Found "uint32FMT" queries shorter than minimum reportable size (-discardexonlength = "uint32FMT")\n", | ^ snapper/snapper2.C:254:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^ snapper/snapper2.C:254:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^ snapper/snapper2.C:295:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, "Created "uint32FMT" filters (out of "uint32FMT" available) to test/validate.\n", | ^ snapper/snapper2.C:295:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, "Created "uint32FMT" filters (out of "uint32FMT" available) to test/validate.\n", | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ snapper/snapper2.C: In function ‘void writerThread(void*, void*)’: snapper/snapper2.C:155:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | write(resultFILE, qry->theOutput, sizeof(char) * qry->theOutputLen); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H: In member function ‘void logMsg::write(int, const char*)’: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:85:12: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | ::write(file, _log, sizeof(char) * _logLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/configuration.o -c snapper/configuration.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/configuration.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/configuration.C:205:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 205 | fprintf(stderr, "ERROR: Invalid afLength "uint32FMT", should be < 64.\n", _afLength), err++; | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-search.o -c snapper/thr-search.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-search.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-filter.o -c snapper/thr-filter.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-filter.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-polish.o -c snapper/thr-polish.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-polish.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/thr-polish.C:311:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/thr-polish.C:311:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-polish-dp.o -c snapper/thr-polish-dp.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-polish-dp.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/thr-polish-dp.C:89:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "dpMatrix-- reallocate to "uint32FMT" x "uint32FMT"\n", aMax, bMax); | ^ snapper/thr-polish-dp.C:89:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "dpMatrix-- reallocate to "uint32FMT" x "uint32FMT"\n", aMax, bMax); | ^ snapper/thr-polish-dp.C:441:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 441 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/thr-polish-dp.C:441:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 441 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/hitMatrix.o -c snapper/hitMatrix.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/hitMatrix.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/hitMatrix.C:385:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 385 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT".\n", theHitsPos, theHitsMax); | ^ snapper/hitMatrix.C:385:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 385 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT".\n", theHitsPos, theHitsMax); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ snapper/hitMatrix.C: In member function ‘void hitMatrix::filter(char, double, uint32, aHit*&, uint32&, uint32&)’: snapper/hitMatrix.C:383:23: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 383 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/hitMatrix-sort.o -c snapper/hitMatrix-sort.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/hitMatrix-sort.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o snapper/snapper2 snapper/snapper2.o snapper/configuration.o snapper/thr-search.o snapper/thr-filter.o snapper/thr-polish.o snapper/thr-polish-dp.o snapper/hitMatrix.o snapper/hitMatrix-sort.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tagger.o -c tapper/tagger.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tagger.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tagger.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tagger.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tagger.C:151:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stdout, "%s\tlength\t"uint32FMT"\n", tagfile, TF->metaData()->tagSize()); | ^ tapper/tagger.C:152:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 152 | fprintf(stdout, "%s\tnumMates\t"uint64FMT"\n", tagfile, TF->numberOfMatePairs()); | ^ tapper/tagger.C:153:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stdout, "%s\tmean\t"uint32FMT"\n", tagfile, TF->metaData()->mean()); | ^ tapper/tagger.C:154:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 154 | fprintf(stdout, "%s\tstddev\t"uint32FMT"\n", tagfile, TF->metaData()->stddev()); | ^ tapper/tagger.C:157:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | fprintf(stdout, "%s\tlength\t"uint32FMT"\n", tagfile, TF->metaData()->tagSize()); | ^ tapper/tagger.C:158:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 158 | fprintf(stdout, "%s\tnumTags\t"uint64FMT"\n", tagfile, TF->numberOfFragmentTags()); | ^ tapper/tagger.C:182:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:362:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tagger.C: In function ‘bool readTag(uint32, FILE*, FILE*, tapperTag*)’: tapper/tagger.C:52:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | fgets(seqhdr, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:54:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fgets(seqhdr, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:55:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fgets(seqseq, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:57:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fgets(qlthdr, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:59:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | fgets(qlthdr, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:60:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fgets(qltseq, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tagger tapper/tagger.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tapper.o -c tapper/tapper.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tapper.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tapper.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tapper.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tapper.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapper.C:633:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 633 | fprintf(stderr, "Reallocate t->numHappiesMax to "uint32FMT"\n", t->numHappiesMax); | ^ tapper/tapper.C:1048:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1048 | fprintf(stderr, "sizeof(tapperResultIndex) -- "sizetFMT"\n", sizeof(tapperResultIndex)); | ^ tapper/tapper.C:1049:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1049 | fprintf(stderr, "sizeof(tapperResultQV) -- "sizetFMT"\n", sizeof(tapperResultQV)); | ^ tapper/tapper.C:1050:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1050 | fprintf(stderr, "sizeof(tapperResultFragment) -- "sizetFMT"\n", sizeof(tapperResultFragment)); | ^ tapper/tapper.C:1051:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1051 | fprintf(stderr, "sizeof(tapperResultMated) -- "sizetFMT"\n", sizeof(tapperResultMated)); | ^ tapper/tapper.C:1052:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1052 | fprintf(stderr, "sizeof(tapperResultTangled) -- "sizetFMT"\n", sizeof(tapperResultTangled)); | ^ tapper/tapper.C:1053:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1053 | fprintf(stderr, "sizeof(tapperHit) -- "sizetFMT"\n", sizeof(tapperHit)); | ^ tapper/tapper.C:1054:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1054 | fprintf(stderr, "sizeof(tapperTag) -- "sizetFMT"\n", sizeof(tapperTag)); | ^ tapper/tapper.C:1124:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1124 | fprintf(stderr, " all alignments. The default is "uint32FMT".\n", g->repeatThreshold); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tapper.C: In member function ‘bool tapperHit::alignToReference(tapperGlobalData*, uint32, uint32, char*, uint32)’: tapper/tapper.C:399:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32’ {aka ‘unsigned int’} [-Wsign-compare] 399 | if (_colorMismatch + _colorInconsistent > g->maxColorError) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ tapper/tapper.C:415:23: warning: comparison of integer expressions of different signedness: ‘uint32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 415 | for (uint32 ti=0; ti<_len-1; ti++) { | ~~^~~~~~~ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/recordFile.H:6, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:39: tapper/tapper.C:468:13: warning: comparison of integer expressions of different signedness: ‘uint32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 468 | assert(nn == _colorMismatch + _colorInconsistent); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tapper/tapper.C:7: tapper/tapperComputation.H: In constructor ‘tapperComputation::tapperComputation(tapperTag*, tapperTag*)’: tapper/tapperComputation.H:51:28: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 51 | tag1rseq[tag1size-1] = complementSymbol[tag1rseq[tag1size-1]]; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tapper/tapperComputation.H:186:38: note: at offset 4294967295 into destination object ‘tapperComputation::tag1rseq’ of size 32 186 | char tag1fseq[TAG_LEN_MAX], tag1rseq[TAG_LEN_MAX]; | ^~~~~~~~ tapper/tapperComputation.H:75:28: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 75 | tag2rseq[tag2size-1] = complementSymbol[tag2rseq[tag2size-1]]; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tapper/tapperComputation.H:187:38: note: at offset 4294967295 into destination object ‘tapperComputation::tag2rseq’ of size 32 187 | char tag2fseq[TAG_LEN_MAX], tag2rseq[TAG_LEN_MAX]; | ^~~~~~~~ In constructor ‘tapperComputation::tapperComputation(tapperTag*, tapperTag*)’, inlined from ‘void* tapperReader(void*)’ at tapper/tapper.C:28:39: tapper/tapperComputation.H:51:28: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 51 | tag1rseq[tag1size-1] = complementSymbol[tag1rseq[tag1size-1]]; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tapper/tapperComputation.H: In function ‘void* tapperReader(void*)’: tapper/tapperComputation.H:186:38: note: at offset 4294967295 into destination object ‘tapperComputation::tag1rseq’ of size 32 186 | char tag1fseq[TAG_LEN_MAX], tag1rseq[TAG_LEN_MAX]; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tapper tapper/tapper.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tapperconvert.o -c tapper/tapperconvert.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tapperconvert.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tapperconvert.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tapperconvert.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tapperconvert.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tapperconvert tapper/tapperconvert.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappermerge.o -c tapper/tappermerge.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tappermerge.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappermerge.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappermerge.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappermerge.C:5: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappermerge tapper/tappermerge.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappersort.o -c tapper/tappersort.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from tapper/tappersort.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from tapper/tappersort.C:3: tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappersort.C:4: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappersort.C:6: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappersort.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tappersort.C:148:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, outputIndex); | ^ tapper/tappersort.C:150:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 150 | fprintf(stderr, "Writing "uint32FMT" sorted alignments to '%s'\n", aliLen, filename); | ^ tapper/tappersort.C:202:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:202:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:202:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:257:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 257 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, x); | ^ tapper/tappersort.C:299:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, x); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappersort tapper/tappersort.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappererrorcorrect.o -c tapper/tappererrorcorrect.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:4, from tapper/tappererrorcorrect.C:1: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from tapper/tappererrorcorrect.C:3: tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappererrorcorrect.C:4: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappererrorcorrect.C:6: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappererrorcorrect.C:7: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tappererrorcorrect.C:25:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", i, alignsLen[i]); | ^ tapper/tappererrorcorrect.C:25:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", i, alignsLen[i]); | ^ tapper/tappererrorcorrect.C:49:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 49 | fprintf(stderr, "block[0] - seq "uint32FMT" pos "uint32FMT"\n", | ^ tapper/tappererrorcorrect.C:49:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 49 | fprintf(stderr, "block[0] - seq "uint32FMT" pos "uint32FMT"\n", | ^ tapper/tappererrorcorrect.C:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", alignsMax-1, alignsLen[alignsMax-1]); | ^ tapper/tappererrorcorrect.C:62:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", alignsMax-1, alignsLen[alignsMax-1]); | ^ tapper/tappererrorcorrect.C:160:2: warning: #warning need the real read size here [-Wcpp] 160 | #warning need the real read size here | ^~~~~~~ tapper/tappererrorcorrect.C:213:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 213 | fprintf(stdout, "\nALIGN "uint32FMT"-"uint32FMT"\n", winLo, winHi); | ^ tapper/tappererrorcorrect.C:213:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 213 | fprintf(stdout, "\nALIGN "uint32FMT"-"uint32FMT"\n", winLo, winHi); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tappererrorcorrect.C: In function ‘int main(int, char**)’: tapper/tappererrorcorrect.C:102:13: warning: variable ‘memoryLimit’ set but not used [-Wunused-but-set-variable] 102 | uint64 memoryLimit = 1024 * 1024 * 1024; | ^~~~~~~~~~~ tapper/tappererrorcorrect.C:141:21: warning: unused variable ‘id’ [-Wunused-variable] 141 | uint16 id[4]; | ^~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappererrorcorrect tapper/tappererrorcorrect.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:53:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 53 | fprintf(stderr, "mer "uint64HEX" not found : e=%d f=%d g=%d\n", m, ee, ef, eg); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:56:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | fprintf(stderr, "mer "uint64HEX" count differs : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:65:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "mer "uint64HEX" : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:96:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:96:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:128:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "Found "uint64FMT" mers in the meryl database.\n", expected); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:148:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.C:148:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/existDB /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-existDB.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/ -I/build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:6: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:8: /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:68:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | fprintf(stdout, "Found no matches for mer=%s at pos="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:255:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stderr, "ERROR: merbegin="uint64FMT" and merend="uint64FMT" are incompatible.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:255:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stderr, "ERROR: merbegin="uint64FMT" and merend="uint64FMT" are incompatible.\n", | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:275:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | fprintf(stderr, "Building table with merSize "uint32FMT", merSkip "uint32FMT"\n", mersize, merskip); | ^ /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.C:275:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | fprintf(stderr, "Building table with merSize "uint32FMT", merSkip "uint32FMT"\n", mersize, merskip); | ^ g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/positionDB /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/driver-posDB.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqCache.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-seqStream.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/test-merStream.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-GRpvsw/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.o -c /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.c rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/mt19937ar/test.o rm -f /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a && ar ruvs /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.o /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/dict.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/except.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/hash.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/list.o a - /build/kmer-GRpvsw/kmer-0~20150903+r2013/libutil/kazlib/sfx.o make[2]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' mv installdir/bin/atac.pl installdir/bin/atac mv -v installdir/lib/halignmodule.so installdir/lib/halign.so renamed 'installdir/lib/halignmodule.so' -> 'installdir/lib/halign.so' mv -v installdir/lib/localAlignerInterfacemodule.so installdir/lib/localAlignerInterface.so renamed 'installdir/lib/localAlignerInterfacemodule.so' -> 'installdir/lib/localAlignerInterface.so' make[1]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j2 install DESTDIR=/build/kmer-GRpvsw/kmer-0\~20150903\+r2013/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' make[1]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' dh_installdocs dh_installchangelogs dh_installman debian/rules override_dh_python3 make[1]: Entering directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' dh_python3 --no-ext-rename I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/AtacDriver.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/AtacFile.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/MyFile.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/PerfectRuns.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/UniqueFilter.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/dedashMatches.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/lib/mkstats.py I: dh_python3 tools:114: replacing shebang in debian/atac/usr/lib/atac/bin/AtacDriver.py make[1]: Leaving directory '/build/kmer-GRpvsw/kmer-0~20150903+r2013' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libkmer-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libmeryl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'kmer' in '../kmer_0~20150903+r2013-9_all.deb'. dpkg-deb: building package 'leaff-dbgsym' in '../leaff-dbgsym_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'libkmer-dev' in '../libkmer-dev_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'sim4db' in '../sim4db_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'meryl' in '../meryl_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'meryl-dbgsym' in '../meryl-dbgsym_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'sim4db-dbgsym' in '../sim4db-dbgsym_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'libmeryl-dev' in '../libmeryl-dev_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'leaff' in '../leaff_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'atac' in '../atac_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'atac-dbgsym' in '../atac-dbgsym_0~20150903+r2013-9_amd64.deb'. dpkg-deb: building package 'kmer-examples' in '../kmer-examples_0~20150903+r2013-9_all.deb'. dpkg-genbuildinfo -O../kmer_0~20150903+r2013-9_amd64.buildinfo dpkg-genchanges -O../kmer_0~20150903+r2013-9_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-06-30T18:44:20Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 30 Jun 2025 18:44:20 +0000 | +------------------------------------------------------------------------------+ kmer_0~20150903+r2013-9_amd64.changes: -------------------------------------- Format: 1.8 Date: Tue, 10 Sep 2024 10:35:03 +0200 Source: kmer Binary: atac atac-dbgsym kmer kmer-examples leaff leaff-dbgsym libkmer-dev libmeryl-dev meryl meryl-dbgsym sim4db sim4db-dbgsym Architecture: source amd64 all Version: 0~20150903+r2013-9 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: atac - genome assembly-to-assembly comparison kmer - suite of tools for DNA sequence analysis kmer-examples - sample data for kmer suite of tools for DNA sequence analysis leaff - biological sequence library utilities and applications libkmer-dev - suite of tools for DNA sequence analysis (development lib) libmeryl-dev - in- and out-of-core kmer counting and utilities (development lib) meryl - in- and out-of-core kmer counting and utilities sim4db - batch spliced alignment of cDNA sequences to a target genome Closes: 1080608 Changes: kmer (0~20150903+r2013-9) unstable; urgency=medium . * Team upload. * Added patch to replace distutils with stdlib usage. Closes: #1080608 * Standards-Version: 4.6.2 (routine-update) * debhelper-compat 13 (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * No tab in license text (routine-update) * Add missing build dependency on dh-python | dh-sequence-python3 for command dh_python3. * d/rules: set -std=c++03 to reduce warnings Checksums-Sha1: 634bca5314754ce9a661d1affba07071d7bb4288 1488 kmer_0~20150903+r2013-9.dsc bff8b0b6f815807795d55bf9adb33c18dee8cf94 2380056 kmer_0~20150903+r2013-9.debian.tar.xz 9a37eb4ef93d9c5cc8c5bc820bcc672ec8dcacba 2699024 atac-dbgsym_0~20150903+r2013-9_amd64.deb 5cea635a46d06ece3a2a0010cea99e4a4b6cd192 388856 atac_0~20150903+r2013-9_amd64.deb d6599cd20af73ece16f926b3d408f8305e856f2f 2352256 kmer-examples_0~20150903+r2013-9_all.deb e3bd8210e4572e5c9870136d178f46d0e181edaf 4956 kmer_0~20150903+r2013-9_all.deb d2377427a88f3fdfe6d018b5fe974b7a85473138 9035 kmer_0~20150903+r2013-9_amd64.buildinfo bf7956e5091d3de8de26bdf06e7e60522bcaf7f3 177696 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/build/kmer-GRpvsw/kmer-0~20150903+r2013 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 (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-exec (= 0.30), dh-python (= 6.20250414), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libexpat1 (= 2.7.1-1), libexpat1-dev (= 2.7.1-1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libhwasan0 (= 14.2.0-19), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 8.1.3-5), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), liblastlog2-2 (= 2.41-5), liblsan0 (= 14.2.0-19), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libncursesw6 (= 6.5+20250216-2), 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 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libpython3-dev (= 3.13.5-1), libpython3-stdlib (= 3.13.5-1), libpython3.13 (= 3.13.5-2), libpython3.13-dev (= 3.13.5-2), libpython3.13-minimal (= 3.13.5-2), libpython3.13-stdlib (= 3.13.5-2), libquadmath0 (= 14.2.0-19), libreadline8t64 (= 8.2-6), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 13.0.0), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), po-debconf (= 1.0.21+nmu1), python3 (= 3.13.5-1), python3-dev (= 3.13.5-1), python3-minimal (= 3.13.5-1), python3.13 (= 3.13.5-2), python3.13-dev (= 3.13.5-2), python3.13-minimal (= 3.13.5-2), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), tzdata (= 2025b-4), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 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="1725957303" +------------------------------------------------------------------------------+ | Package contents Mon, 30 Jun 2025 18:44:20 +0000 | +------------------------------------------------------------------------------+ atac-dbgsym_0~20150903+r2013-9_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 2699024 bytes: control archive=1608 bytes. 1242 bytes, 12 lines control 2413 bytes, 23 lines md5sums Package: atac-dbgsym Source: kmer Version: 0~20150903+r2013-9 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3494 Depends: atac (= 0~20150903+r2013-9) Section: debug Priority: optional Description: debug symbols for atac Build-Ids: 0252731f5337e0208bb4f4b448d0d4eb52510ec5 1a67ca47af4bab1b3cf876396e15a9dadcedd27e 1d075de65fcced104f090d51052cb390b0b9438a 42a2bb547d9d11c7d8b0163c7c3e7c65bbcdb8da 4dd822c9edd4f9b2dede0e778bd991fd551ac02f 61c0088767839ed1eee910e41aef5828844fb735 6de758a02d32a5926532a6f2f26e1e31e2c4ff13 7da7d3b0d15b952a1014a6b924ea9bab69556f96 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Packaging Team Installed-Size: 2792 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), python3 (<< 3.14), python3 (>= 3.13~), python3.13, python3:any, perl:any, libfile-which-perl, leaff, meryl, gnuplot Recommends: kmer-examples Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: genome assembly-to-assembly comparison atac computes a one-to-one pairwise alignment of large DNA sequences. It first finds the unique k-mers in each sequence, chains them to larger blocks, and fills in spaces between blocks. It was written primarily to transfer annotations between different assemblies of the human genome. . The output is a set of ungapped 'matches', and a set of gapped 'runs' formed from the matches. Each match or run associates one sequence with the other sequence. The association is 'unique', in that there is no other (sizeable) associations for either sequence. Thus, large repeats and duplications are not present in the output - they appear as unmapped regions. . Though the output is always pairwise, atac can cache intermediate results to speed a comparisons of multiple sequences. . 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It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers. . This package contains a test data set as well as sample scripts running some test suite provided by Debian also as autopkgtest. drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/kmer-examples/ -rw-r--r-- root/root 275 2024-09-10 08:19 ./usr/share/doc/kmer-examples/README.Debian -rw-r--r-- root/root 997 2024-09-10 08:35 ./usr/share/doc/kmer-examples/changelog.Debian.gz -rw-r--r-- root/root 7520 2024-09-10 08:35 ./usr/share/doc/kmer-examples/copyright -rw-r--r-- root/root 2345682 2024-09-10 08:35 ./usr/share/doc/kmer-examples/test_data.tar.gz kmer_0~20150903+r2013-9_all.deb ------------------------------- new Debian package, version 2.0. size 4956 bytes: control archive=716 bytes. 626 bytes, 16 lines control 136 bytes, 2 lines md5sums Package: kmer Version: 0~20150903+r2013-9 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 15 Depends: meryl, leaff, sim4db, atac Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: suite of tools for DNA sequence analysis The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers. . This is a metapackage depending on the executable components of the kmer suite. drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/kmer/ -rw-r--r-- root/root 996 2024-09-10 08:35 ./usr/share/doc/kmer/changelog.Debian.gz -rw-r--r-- root/root 7520 2024-09-10 08:35 ./usr/share/doc/kmer/copyright leaff-dbgsym_0~20150903+r2013-9_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 177696 bytes: control archive=544 bytes. 383 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: leaff-dbgsym Source: kmer Version: 0~20150903+r2013-9 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 231 Depends: leaff (= 0~20150903+r2013-9) Section: debug Priority: optional Description: debug symbols for leaff Build-Ids: a0138785345b1a7a3db114bc5bebce13a916b120 drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/a0/ -rw-r--r-- root/root 225512 2024-09-10 08:35 ./usr/lib/debug/.build-id/a0/138785345b1a7a3db114bc5bebce13a916b120.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-09-10 08:35 ./usr/share/doc/leaff-dbgsym -> leaff leaff_0~20150903+r2013-9_amd64.deb ---------------------------------- new Debian package, version 2.0. size 70472 bytes: control archive=868 bytes. 635 bytes, 16 lines control 320 bytes, 5 lines md5sums Package: leaff Source: kmer Version: 0~20150903+r2013-9 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 202 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: biological sequence library utilities and applications LEAFF (Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/bin/ -rwxr-xr-x root/root 180512 2024-09-10 08:35 ./usr/bin/leaff drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/leaff/ -rw-r--r-- root/root 3373 2011-01-20 03:32 ./usr/share/doc/leaff/README.leaff.gz -rw-r--r-- root/root 998 2024-09-10 08:35 ./usr/share/doc/leaff/changelog.Debian.gz -rw-r--r-- root/root 7520 2024-09-10 08:35 ./usr/share/doc/leaff/copyright drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/man/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/man/man1/ -rw-r--r-- root/root 2732 2024-09-10 08:35 ./usr/share/man/man1/leaff.1.gz libkmer-dev_0~20150903+r2013-9_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 202684 bytes: control archive=2168 bytes. 635 bytes, 17 lines control 3725 bytes, 54 lines md5sums Package: libkmer-dev Source: kmer Version: 0~20150903+r2013-9 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 867 Depends: libmeryl-dev Section: libdevel Priority: optional Homepage: http://kmer.sourceforge.net Description: suite of tools for DNA sequence analysis (development lib) The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers. . 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08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/libkmer-dev/ -rw-r--r-- root/root 1002 2024-09-10 08:35 ./usr/share/doc/libkmer-dev/changelog.Debian.gz -rw-r--r-- root/root 7520 2024-09-10 08:35 ./usr/share/doc/libkmer-dev/copyright libmeryl-dev_0~20150903+r2013-9_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 53212 bytes: control archive=996 bytes. 910 bytes, 21 lines control 413 bytes, 6 lines md5sums Package: libmeryl-dev Source: kmer Version: 0~20150903+r2013-9 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 202 Section: libdevel Priority: optional Homepage: http://kmer.sourceforge.net Description: in- and out-of-core kmer counting and utilities (development lib) meryl computes the kmer content of genomic sequences. Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences. The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location). Meryl can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. . This package contains the static libraries and header files. drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/include/ -rw-r--r-- root/root 5822 2014-04-11 20:17 ./usr/include/libmeryl.H -rw-r--r-- root/root 3420 2015-05-29 12:35 ./usr/include/meryl.H drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 46420 2024-09-10 08:35 ./usr/lib/x86_64-linux-gnu/libmeryl.a drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/x86_64-linux-gnu/meryl/ -rw-r--r-- root/root 129988 2024-09-10 08:35 ./usr/lib/x86_64-linux-gnu/meryl/libmerylguts.a drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/libmeryl-dev/ -rw-r--r-- root/root 1004 2024-09-10 08:35 ./usr/share/doc/libmeryl-dev/changelog.Debian.gz -rw-r--r-- root/root 7520 2024-09-10 08:35 ./usr/share/doc/libmeryl-dev/copyright meryl-dbgsym_0~20150903+r2013-9_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 1492652 bytes: control archive=916 bytes. 630 bytes, 12 lines control 824 bytes, 8 lines md5sums Package: meryl-dbgsym Source: kmer Version: 0~20150903+r2013-9 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1856 Depends: meryl (= 0~20150903+r2013-9) Section: debug Priority: optional Description: debug symbols for meryl Build-Ids: 1583786ae6996c1cf6ea9f0e13009516e7c7a74e 35f73faa1c4de6ab378d611cfcd9a7a03b1057f5 60dd32576063475276db24c81d6afe183fbc7970 618827c09c084bc0cea83c8731709885d1988681 6b6cbec49f4dbade001d973433f7d21442bd4fe4 a85f6c0987b3e6862bde10446c1fbcdc868ea456 f252200fc94de278c35818e0256b7b9b3042655f drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 245008 2024-09-10 08:35 ./usr/lib/debug/.build-id/15/83786ae6996c1cf6ea9f0e13009516e7c7a74e.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/35/ -rw-r--r-- root/root 245448 2024-09-10 08:35 ./usr/lib/debug/.build-id/35/f73faa1c4de6ab378d611cfcd9a7a03b1057f5.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/60/ -rw-r--r-- root/root 242976 2024-09-10 08:35 ./usr/lib/debug/.build-id/60/dd32576063475276db24c81d6afe183fbc7970.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/61/ -rw-r--r-- root/root 293160 2024-09-10 08:35 ./usr/lib/debug/.build-id/61/8827c09c084bc0cea83c8731709885d1988681.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/6b/ -rw-r--r-- root/root 337800 2024-09-10 08:35 ./usr/lib/debug/.build-id/6b/6cbec49f4dbade001d973433f7d21442bd4fe4.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/a8/ -rw-r--r-- root/root 208864 2024-09-10 08:35 ./usr/lib/debug/.build-id/a8/5f6c0987b3e6862bde10446c1fbcdc868ea456.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.build-id/f2/ -rw-r--r-- root/root 271648 2024-09-10 08:35 ./usr/lib/debug/.build-id/f2/52200fc94de278c35818e0256b7b9b3042655f.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 33680 2024-09-10 08:35 ./usr/lib/debug/.dwz/x86_64-linux-gnu/meryl.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-09-10 08:35 ./usr/share/doc/meryl-dbgsym -> meryl meryl_0~20150903+r2013-9_amd64.deb ---------------------------------- new Debian package, version 2.0. size 204948 bytes: control archive=1312 bytes. 960 bytes, 23 lines control 1036 bytes, 17 lines md5sums Package: meryl Source: kmer Version: 0~20150903+r2013-9 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1473 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Suggests: gridengine-client Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: in- and out-of-core kmer counting and utilities meryl computes the kmer content of genomic sequences. Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences. The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location). Meryl can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/bin/ -rwxr-xr-x root/root 201816 2024-09-10 08:35 ./usr/bin/existDB -rwxr-xr-x root/root 218200 2024-09-10 08:35 ./usr/bin/kmer-mask -rwxr-xr-x root/root 193624 2024-09-10 08:35 ./usr/bin/mapMers -rwxr-xr-x root/root 201816 2024-09-10 08:35 ./usr/bin/mapMers-depth -rwxr-xr-x root/root 222296 2024-09-10 08:35 ./usr/bin/meryl -rwxr-xr-x root/root 263320 2024-09-10 08:35 ./usr/bin/positionDB -rwxr-xr-x root/root 169048 2024-09-10 08:35 ./usr/bin/simple drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/meryl/ -rw-r--r-- root/root 2684 2015-05-20 07:56 ./usr/share/doc/meryl/README.meryl.gz -rw-r--r-- root/root 998 2024-09-10 08:35 ./usr/share/doc/meryl/changelog.Debian.gz -rw-r--r-- root/root 7520 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Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2873 Depends: sim4db (= 0~20150903+r2013-9) Section: debug Priority: optional Description: debug symbols for sim4db Build-Ids: 06992ac3a292e43b353521c8d5d235c757921e7a 0a1019078362b19ce7a9de35ab431dae17c624e2 29fcba73872ec69cf5b661f1912e7d42711f0c5d 2ac49c249dcff37848b0557f3dee7c7844088af6 2b0587aa986544c1575b5546d7467b63aa5891ac 326e6eda098ff4d8af25583d548d4bcacb307379 3477292a74e0bc952e711abecdaa83a41598d2b3 4049ef66c9208c6dfb12af6b522fa55b5150c5b3 5a4a73c03ef1908c2b030a4caa8280aa4492a5a4 5c989e5c22e0e04d7027b533eb3239fc9135cee4 6beeff53df98264aa5f4ea6269de6878d91eadbf 6fe9e461efaf34166bcbfdb562564d8d1c546bf5 7126cb01d2000d7237fa2bb07c0fbde3ec25aa87 7155c5d5fdf3aee4028e8a5119f8dbd390930ac2 74fbd594e0b7cdeef06ad712bb07104e70fb10b4 90d8137358496953496f0b71236e1636e1627636 90ea24e240e1247956606eb1d0be06e07179c9a8 a7a1cf95f671579e431eaa1a1b30c15709b46349 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./usr/lib/debug/.build-id/f3/f44b108966cd6f81471dfd37441b8ed3c35202.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 34232 2024-09-10 08:35 ./usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-09-10 08:35 ./usr/share/doc/sim4db-dbgsym -> sim4db sim4db_0~20150903+r2013-9_amd64.deb ----------------------------------- new Debian package, version 2.0. size 446260 bytes: control archive=2128 bytes. 1551 bytes, 30 lines control 3551 bytes, 54 lines md5sums Package: sim4db Source: kmer Version: 0~20150903+r2013-9 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3367 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2) Recommends: leaff, kmer-examples Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: batch spliced alignment of cDNA sequences to a target genome Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package 'leaff', to speedily process large volumes of sequences. . While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2024-09-10 08:35 ./ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/bin/ -rwxr-xr-x root/root 102600 2024-09-10 08:35 ./usr/bin/cleanPolishes -rwxr-xr-x root/root 123080 2024-09-10 08:35 ./usr/bin/comparePolishes -rwxr-xr-x root/root 90312 2024-09-10 08:35 ./usr/bin/convertPolishes -rwxr-xr-x root/root 94408 2024-09-10 08:35 ./usr/bin/convertToAtac -rwxr-xr-x root/root 94408 2024-09-10 08:35 ./usr/bin/convertToExtent -rwxr-xr-x root/root 98504 2024-09-10 08:35 ./usr/bin/depthOfPolishes -rwxr-xr-x root/root 98504 2024-09-10 08:35 ./usr/bin/detectChimera -rwxr-xr-x root/root 98504 2024-09-10 08:35 ./usr/bin/filterPolishes -rwxr-xr-x root/root 152024 2024-09-10 08:35 ./usr/bin/fixPolishesIID -rwxr-xr-x root/root 90312 2024-09-10 08:35 ./usr/bin/headPolishes -rwxr-xr-x root/root 156120 2024-09-10 08:35 ./usr/bin/mappedCoverage -rwxr-xr-x root/root 156120 2024-09-10 08:35 ./usr/bin/mergePolishes -rwxr-xr-x root/root 102632 2024-09-10 08:35 ./usr/bin/parseSNP -rwxr-xr-x root/root 110824 2024-09-10 08:35 ./usr/bin/pickBestPolish -rwxr-xr-x root/root 98536 2024-09-10 08:35 ./usr/bin/pickUniquePolish -rwxr-xr-x root/root 90312 2024-09-10 08:35 ./usr/bin/plotCoverageVsIdentity -rwxr-xr-x root/root 168440 2024-09-10 08:35 ./usr/bin/realignPolishes -rwxr-xr-x root/root 90312 2024-09-10 08:35 ./usr/bin/removeDuplicate -rwxr-xr-x root/root 94408 2024-09-10 08:35 ./usr/bin/reportAlignmentDifferences -rwxr-xr-x root/root 855768 2024-09-10 08:35 ./usr/bin/sim4db -rwxr-xr-x root/root 102632 2024-09-10 08:35 ./usr/bin/sortPolishes -rwxr-xr-x root/root 98504 2024-09-10 08:35 ./usr/bin/summarizePolishes -rwxr-xr-x root/root 90312 2024-09-10 08:35 ./usr/bin/uniqPolishes -rwxr-xr-x root/root 94440 2024-09-10 08:35 ./usr/bin/vennPolishes drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/doc/sim4db/ -rw-r--r-- root/root 4962 2011-01-20 03:32 ./usr/share/doc/sim4db/README.sim4db.gz -rw-r--r-- root/root 244 2024-09-10 08:19 ./usr/share/doc/sim4db/README.test -rw-r--r-- root/root 999 2024-09-10 08:35 ./usr/share/doc/sim4db/changelog.Debian.gz -rw-r--r-- root/root 7520 2024-09-10 08:35 ./usr/share/doc/sim4db/copyright -rw-r--r-- root/root 1008 2024-09-10 08:19 ./usr/share/doc/sim4db/sim4db-unit-test drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/man/ drwxr-xr-x root/root 0 2024-09-10 08:35 ./usr/share/man/man1/ -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/cleanPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/comparePolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/convertPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/convertToAtac.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/convertToExtent.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/depthOfPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/detectChimera.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/filterPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/fixPolishesIID.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/headPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/mappedCoverage.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/mergePolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/parseSNP.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/pickBestPolish.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/pickUniquePolish.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/plotCoverageVsIdentity.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/realignPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/removeDuplicate.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/reportAlignmentDifferences.1.gz -rw-r--r-- root/root 2206 2024-09-10 08:35 ./usr/share/man/man1/sim4db.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/sim4dbutils.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/sortPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/summarizePolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/uniqPolishes.1.gz -rw-r--r-- root/root 1058 2024-09-10 08:35 ./usr/share/man/man1/vennPolishes.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 30 Jun 2025 18:44:22 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 30 Jun 2025 18:44:22 +0000 | +------------------------------------------------------------------------------+ Purging /build/kmer-GRpvsw Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 30 Jun 2025 18:44:23 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 173480 Build-Time: 113 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 7 Job: /srv/debomatic/incoming/kmer_0~20150903+r2013-9.dsc Machine Architecture: amd64 Package: kmer Package-Time: 129 Source-Version: 0~20150903+r2013-9 Space: 173480 Status: successful Version: 0~20150903+r2013-9 -------------------------------------------------------------------------------- Finished at 2025-06-30T18:44:20Z Build needed 00:02:09, 173480k disk space