RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-31 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 Buildd toolchain package versions: launchpad-buildd_139 python-lpbuildd_139 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa8 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.5 git-build-recipe_0.3~git201603101733.90b6821~ubuntu14.04.2 git_1:1.9.1-1ubuntu0.3 dpkg-dev_1.17.5ubuntu5.6 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1 qemu-user-static_2.0.0+dfsg-2ubuntu1.22. Syncing the system clock with the buildd NTP service... 27 Apr 05:32:54 ntpdate[1663]: adjust time server 10.211.37.1 offset -0.031816 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9641405', '/home/buildd/filecache-default/9af1b65e710cc0b334e8c9a330a1d817d2c021bb'] Unpacking chroot for build PACKAGEBUILD-9641405 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9641405'] Mounting chroot for build PACKAGEBUILD-9641405 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9641405', 'deb http://ftpmaster.internal/ubuntu yakkety main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu yakkety-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-9641405 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9641405', 'i386'] Updating debian chroot for build PACKAGEBUILD-9641405 Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 Packages [1202 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/restricted i386 Packages [8676 B] Get:8 http://ftpmaster.internal/ubuntu yakkety/universe i386 Packages [7521 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4356 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/multiverse i386 Packages [140 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety-security/main i386 Packages [64 B] Get:12 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:13 http://ftpmaster.internal/ubuntu yakkety-security/restricted i386 Packages [64 B] Get:14 http://ftpmaster.internal/ubuntu yakkety-security/restricted Translation-en [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-security/universe i386 Packages [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-security/multiverse i386 Packages [64 B] Get:18 http://ftpmaster.internal/ubuntu yakkety-security/multiverse Translation-en [64 B] Get:19 http://ftpmaster.internal/ubuntu yakkety-updates/main i386 Packages [64 B] Get:20 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:21 http://ftpmaster.internal/ubuntu yakkety-updates/restricted i386 Packages [64 B] Get:22 http://ftpmaster.internal/ubuntu yakkety-updates/restricted Translation-en [64 B] Get:23 http://ftpmaster.internal/ubuntu yakkety-updates/universe i386 Packages [64 B] Get:24 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:25 http://ftpmaster.internal/ubuntu yakkety-updates/multiverse i386 Packages [64 B] Get:26 http://ftpmaster.internal/ubuntu yakkety-updates/multiverse Translation-en [64 B] Get:27 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 Packages [141 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [61.1 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety-proposed/restricted i386 Packages [64 B] Get:30 http://ftpmaster.internal/ubuntu yakkety-proposed/restricted Translation-en [64 B] Get:31 http://ftpmaster.internal/ubuntu yakkety-proposed/universe i386 Packages [508 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [382 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety-proposed/multiverse i386 Packages [3988 B] Get:34 http://ftpmaster.internal/ubuntu yakkety-proposed/multiverse Translation-en [7348 B] Fetched 15.4 MB in 3s (4561 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libpng16-16 The following packages will be upgraded: apt apt-transport-https bash binutils cpp-5 g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0 libasan2 libatomic1 libcc1-0 libcilkrts5 libgcc-5-dev libgcc1 libgcrypt20 libgomp1 libitm1 libmpx0 libperl5.22 libpng12-0 libquadmath0 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 linux-libc-dev make optipng perl perl-base perl-modules-5.22 policyrcd-script-zg2 sed systemd systemd-sysv sysv-rc sysvinit-utils tzdata 54 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 91.4 MB of archives. After this operation, 184 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu yakkety/main i386 bash i386 4.3-14ubuntu2 [591 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety/main i386 grep i386 2.25-1 [157 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main i386 hostname i386 3.17ubuntu1 [11.9 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libperl5.22 i386 5.22.1-10 [3014 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 perl i386 5.22.1-10 [237 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 perl-base i386 5.22.1-10 [1368 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 perl-modules-5.22 all 5.22.1-10 [2640 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 init-system-helpers all 1.31ubuntu1 [31.9 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 init i386 1.31ubuntu1 [4564 B] Get:10 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 sed i386 4.2.2-7.1 [139 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-6-base i386 6.0.1-2ubuntu13 [15.8 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcc1 i386 1:6.0.1-2ubuntu13 [46.9 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main i386 libstdc++6 i386 6.0.1-2ubuntu13 [434 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libapt-pkg5.0 i386 1.2.11 [736 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 apt i386 1.2.11 [1054 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main i386 sysvinit-utils i386 2.88dsf-59.3ubuntu4 [22.0 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety/main i386 sysv-rc all 2.88dsf-59.3ubuntu4 [18.2 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main i386 initscripts i386 2.88dsf-59.3ubuntu4 [24.4 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libselinux1 i386 2.5-1 [70.2 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsystemd0 i386 229-5ubuntu1 [228 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 systemd i386 229-5ubuntu1 [3682 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 systemd-sysv i386 229-5ubuntu1 [17.7 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libgcrypt20 i386 1.7.0-2 [372 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main i386 libsepol1 i386 2.5-1 [236 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsemanage-common all 2.4-3build2 [6558 B] Get:26 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsemanage1 i386 2.4-3build2 [86.9 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libudev1 i386 229-5ubuntu1 [63.5 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main i386 tzdata all 2016d-2 [168 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main i386 g++-5 i386 5.3.1-16ubuntu2 [30.4 MB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-5 i386 5.3.1-16ubuntu2 [8341 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main i386 cpp-5 i386 5.3.1-16ubuntu2 [28.3 MB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main i386 libcc1-0 i386 6.0.1-2ubuntu13 [33.0 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/main i386 binutils i386 2.26-8ubuntu3 [2482 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main i386 libgomp1 i386 6.0.1-2ubuntu13 [80.0 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main i386 libitm1 i386 6.0.1-2ubuntu13 [31.2 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety/main i386 libatomic1 i386 6.0.1-2ubuntu13 [9896 B] Get:37 http://ftpmaster.internal/ubuntu yakkety/main i386 libasan2 i386 5.3.1-16ubuntu2 [271 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety/main i386 libubsan0 i386 6.0.1-2ubuntu13 [120 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main i386 libcilkrts5 i386 6.0.1-2ubuntu13 [45.8 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main i386 libmpx0 i386 5.3.1-16ubuntu2 [11.1 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main i386 libquadmath0 i386 6.0.1-2ubuntu13 [204 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main i386 libstdc++-5-dev i386 5.3.1-16ubuntu2 [1438 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main i386 libgcc-5-dev i386 5.3.1-16ubuntu2 [2241 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety/main i386 gcc-5-base i386 5.3.1-16ubuntu2 [17.2 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/universe i386 libpng12-0 i386 1.2.54-6ubuntu1 [122 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libslang2 i386 2.3.0-2.3ubuntu1 [416 kB] Get:47 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libtasn1-6 i386 4.8-1 [44.8 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 apt-transport-https i386 1.2.11 [27.6 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsasl2-modules-db i386 2.1.26.dfsg1-15 [15.4 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libsasl2-2 i386 2.1.26.dfsg1-15 [51.8 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main i386 libpng16-16 i386 1.6.21-4 [181 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 linux-libc-dev i386 4.4.0-22.38 [840 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 make i386 4.1-9 [154 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main i386 optipng i386 0.7.6-1build1 [86.3 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main i386 policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 91.4 MB in 3s (27.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../bash_4.3-14ubuntu2_i386.deb ... Unpacking bash (4.3-14ubuntu2) over (4.3-14ubuntu1) ... Setting up bash (4.3-14ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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Setting up perl-base (5.22.1-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../perl-modules-5.22_5.22.1-10_all.deb ... Unpacking perl-modules-5.22 (5.22.1-10) over (5.22.1-9) ... Preparing to unpack .../init-system-helpers_1.31ubuntu1_all.deb ... Unpacking init-system-helpers (1.31ubuntu1) over (1.29ubuntu1) ... Setting up init-system-helpers (1.31ubuntu1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../libstdc++6_6.0.1-2ubuntu13_i386.deb ... Unpacking libstdc++6:i386 (6.0.1-2ubuntu13) over (5.3.1-14ubuntu2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libstdc++6:i386 (6.0.1-2ubuntu13) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.2.11_i386.deb ... Unpacking libapt-pkg5.0:i386 (1.2.11) over (1.2.10ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libapt-pkg5.0:i386 (1.2.11) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... 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Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libselinux1:i386 (2.5-1) ... Processing triggers for systemd (229-4ubuntu4) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../libsystemd0_229-5ubuntu1_i386.deb ... Unpacking libsystemd0:i386 (229-5ubuntu1) over (229-4ubuntu4) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libsystemd0:i386 (229-5ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12148 files and directories currently installed.) Preparing to unpack .../systemd_229-5ubuntu1_i386.deb ... Unpacking systemd (229-5ubuntu1) over (229-4ubuntu4) ... Setting up systemd (229-5ubuntu1) ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (Reading database ... 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Unpacking libubsan0:i386 (6.0.1-2ubuntu13) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libcilkrts5_6.0.1-2ubuntu13_i386.deb ... Unpacking libcilkrts5:i386 (6.0.1-2ubuntu13) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libmpx0_5.3.1-16ubuntu2_i386.deb ... Unpacking libmpx0:i386 (5.3.1-16ubuntu2) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libquadmath0_6.0.1-2ubuntu13_i386.deb ... Unpacking libquadmath0:i386 (6.0.1-2ubuntu13) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libstdc++-5-dev_5.3.1-16ubuntu2_i386.deb ... Unpacking libstdc++-5-dev:i386 (5.3.1-16ubuntu2) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libgcc-5-dev_5.3.1-16ubuntu2_i386.deb ... Unpacking libgcc-5-dev:i386 (5.3.1-16ubuntu2) over (5.3.1-14ubuntu2) ... Preparing to unpack .../gcc-5-base_5.3.1-16ubuntu2_i386.deb ... Unpacking gcc-5-base:i386 (5.3.1-16ubuntu2) over (5.3.1-14ubuntu2) ... Preparing to unpack .../libpng12-0_1.2.54-6ubuntu1_i386.deb ... Unpacking libpng12-0:i386 (1.2.54-6ubuntu1) over (1.2.54-1ubuntu1) ... Preparing to unpack .../libslang2_2.3.0-2.3ubuntu1_i386.deb ... Unpacking libslang2:i386 (2.3.0-2.3ubuntu1) over (2.3.0-2ubuntu1) ... Preparing to unpack .../libtasn1-6_4.8-1_i386.deb ... Unpacking libtasn1-6:i386 (4.8-1) over (4.7-3) ... Preparing to unpack .../apt-transport-https_1.2.11_i386.deb ... Unpacking apt-transport-https (1.2.11) over (1.2.10ubuntu1) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.26.dfsg1-15) over (2.1.26.dfsg1-14build1) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_i386.deb ... Unpacking libsasl2-2:i386 (2.1.26.dfsg1-15) over (2.1.26.dfsg1-14build1) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../libpng16-16_1.6.21-4_i386.deb ... Unpacking libpng16-16:i386 (1.6.21-4) ... Preparing to unpack .../linux-libc-dev_4.4.0-22.38_i386.deb ... Unpacking linux-libc-dev:i386 (4.4.0-22.38) over (4.4.0-21.37) ... Preparing to unpack .../archives/make_4.1-9_i386.deb ... Unpacking make (4.1-9) over (4.1-6) ... Preparing to unpack .../optipng_0.7.6-1build1_i386.deb ... Unpacking optipng (0.7.6-1build1) over (0.7.6-1) ... Preparing to unpack .../policyrcd-script-zg2_0.1-3_all.deb ... Unpacking policyrcd-script-zg2 (0.1-3) over (0.1-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up perl-modules-5.22 (5.22.1-10) ... Setting up libperl5.22:i386 (5.22.1-10) ... Setting up perl (5.22.1-10) ... Setting up sysv-rc (2.88dsf-59.3ubuntu4) ... Setting up initscripts (2.88dsf-59.3ubuntu4) ... Setting up tzdata (2016d-2) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Apr 27 05:33:25 UTC 2016. Universal Time is now: Wed Apr 27 05:33:25 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up gcc-5-base:i386 (5.3.1-16ubuntu2) ... Setting up cpp-5 (5.3.1-16ubuntu2) ... Setting up libcc1-0:i386 (6.0.1-2ubuntu13) ... Setting up binutils (2.26-8ubuntu3) ... Setting up libgomp1:i386 (6.0.1-2ubuntu13) ... Setting up libitm1:i386 (6.0.1-2ubuntu13) ... Setting up libatomic1:i386 (6.0.1-2ubuntu13) ... Setting up libasan2:i386 (5.3.1-16ubuntu2) ... Setting up libubsan0:i386 (6.0.1-2ubuntu13) ... Setting up libcilkrts5:i386 (6.0.1-2ubuntu13) ... Setting up libmpx0:i386 (5.3.1-16ubuntu2) ... Setting up libquadmath0:i386 (6.0.1-2ubuntu13) ... Setting up libgcc-5-dev:i386 (5.3.1-16ubuntu2) ... Setting up gcc-5 (5.3.1-16ubuntu2) ... Setting up libstdc++-5-dev:i386 (5.3.1-16ubuntu2) ... Setting up g++-5 (5.3.1-16ubuntu2) ... Setting up libpng12-0:i386 (1.2.54-6ubuntu1) ... Setting up libslang2:i386 (2.3.0-2.3ubuntu1) ... Setting up libtasn1-6:i386 (4.8-1) ... Setting up apt-transport-https (1.2.11) ... Setting up libsasl2-modules-db:i386 (2.1.26.dfsg1-15) ... Setting up libsasl2-2:i386 (2.1.26.dfsg1-15) ... Setting up libpng16-16:i386 (1.6.21-4) ... Setting up linux-libc-dev:i386 (4.4.0-22.38) ... Setting up make (4.1-9) ... Setting up optipng (0.7.6-1build1) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9641405', 'i386', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=i386', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'gmap_2015-12-31.v9-1.dsc'] Initiating build PACKAGEBUILD-9641405 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 i686 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lcy01-31.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ gmap 2015-12-31.v9-1 (i386) 27 Apr 2016 05:33 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: gmap Version: 2015-12-31.v9-1 Source Version: 2015-12-31.v9-1 Distribution: yakkety-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/gmap-tnSLmE/gmap-2015-12-31.v9' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/gmap-tnSLmE' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9641405/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── gmap_2015-12-31.v9-1.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-emzDbm/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ Sources [208 B] Get:5 copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ Packages [524 B] Fetched 2851 B in 0s (0 B/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 772 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-emzDbm/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12154 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), autotools-dev, debhelper (>= 9), help2man, libbz2-dev, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), autotools-dev, debhelper (>= 9), help2man, libbz2-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-gmap-dummy' in '/«BUILDDIR»/resolver-jD9DP6/apt_archive/sbuild-build-depends-gmap-dummy.deb'. Ign:1 copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ InRelease Get:2 copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ Release [2119 B] Ign:3 copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ Release.gpg Get:4 copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ Sources [442 B] Get:5 copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ Packages [707 B] Fetched 3268 B in 0s (311 kB/s) Reading package lists... W: The repository 'copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install gmap 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasprintf0v5 libbz2-dev libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc groff libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev bzip2-doc libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasprintf0v5 libbz2-dev libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-gmap-dummy zlib1g-dev 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 16.8 MB of archives. After this operation, 63.7 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-gmap-dummy Authentication warning overridden. Get:1 copy:/«BUILDDIR»/resolver-jD9DP6/apt_archive ./ sbuild-build-depends-gmap-dummy 0.invalid.0 [950 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main i386 liblocale-gettext-perl i386 1.07-1build1 [17.6 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main i386 groff-base i386 1.22.3-7 [1160 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main i386 bsdmainutils i386 9.0.6ubuntu3 [175 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main i386 libpipeline1 i386 1.4.1-2 [26.5 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main i386 man-db i386 2.7.5-1 [865 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main i386 libunistring0 i386 0.9.3-5.2ubuntu1 [277 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main i386 libmagic1 i386 1:5.25-2ubuntu1 [222 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main i386 file i386 1:5.25-2ubuntu1 [21.1 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main i386 libasprintf0v5 i386 0.19.7-2ubuntu3 [6462 B] Get:11 http://ftpmaster.internal/ubuntu yakkety/main i386 gettext-base i386 0.19.7-2ubuntu3 [48.8 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main i386 libglib2.0-0 i386 2.48.0-1ubuntu4 [1183 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main i386 libicu57 i386 57.1-1 [7806 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main i386 libxml2 i386 2.9.3+dfsg1-1build1 [729 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main i386 libsigsegv2 i386 2.10-5 [14.3 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety/main i386 m4 i386 1.4.17-5 [195 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 autoconf all 2.69-10 [321 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main i386 autotools-dev all 20150820.1 [39.8 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main i386 automake all 1:1.15-4ubuntu1 [510 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main i386 autopoint all 0.19.7-2ubuntu3 [406 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main i386 libcroco3 i386 0.6.11-1 [87.8 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main i386 gettext i386 0.19.7-2ubuntu3 [1085 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main i386 po-debconf all 1.0.19 [234 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety-proposed/main i386 libarchive-zip-perl all 1.57-1 [84.0 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main i386 libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main i386 dh-strip-nondeterminism all 0.016-1 [4858 B] Get:29 http://ftpmaster.internal/ubuntu yakkety/main i386 libtool all 2.4.6-0.1 [193 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main i386 dh-autoreconf all 12 [15.8 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main i386 debhelper all 9.20160403ubuntu1 [711 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/universe i386 help2man i386 1.47.3 [111 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/main i386 libbz2-dev i386 1.0.6-8 [28.7 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main i386 zlib1g-dev i386 1:1.2.8.dfsg-2ubuntu4 [167 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.8 MB in 1s (14.8 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12154 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-1build1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-7_i386.deb ... Unpacking groff-base (1.22.3-7) ... Selecting previously unselected package bsdmainutils. 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Selecting previously unselected package sbuild-build-depends-gmap-dummy. Preparing to unpack .../sbuild-build-depends-gmap-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-gmap-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up liblocale-gettext-perl (1.07-1build1) ... Setting up groff-base (1.22.3-7) ... Setting up bsdmainutils (9.0.6ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpipeline1:i386 (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:i386 (0.9.3-5.2ubuntu1) ... Setting up libmagic1:i386 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:i386 (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libglib2.0-0:i386 (2.48.0-1ubuntu4) ... No schema files found: doing nothing. Setting up libicu57:i386 (57.1-1) ... Setting up libxml2:i386 (2.9.3+dfsg1-1build1) ... Setting up libsigsegv2:i386 (2.10-5) ... Setting up m4 (1.4.17-5) ... Setting up autoconf (2.69-10) ... Setting up autotools-dev (20150820.1) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.7-2ubuntu3) ... Setting up libcroco3:i386 (0.6.11-1) ... Setting up gettext (0.19.7-2ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.19) ... Setting up libarchive-zip-perl (1.57-1) ... Setting up libfile-stripnondeterminism-perl (0.016-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libtool (2.4.6-0.1) ... Setting up help2man (1.47.3) ... Setting up libbz2-dev:i386 (1.0.6-8) ... Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2ubuntu4) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160403ubuntu1) ... Setting up sbuild-build-depends-gmap-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.016-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.13.0-85-generic amd64 (i686) Toolchain package versions: binutils_2.26-8ubuntu3 dpkg-dev_1.18.4ubuntu1 g++-5_5.3.1-16ubuntu2 gcc-5_5.3.1-16ubuntu2 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-16ubuntu2 libstdc++6_6.0.1-2ubuntu13 linux-libc-dev_4.4.0-22.38 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.2.11 apt-transport-https_1.2.11 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20150820.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 binutils_2.26-8ubuntu3 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.27.1-6ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-16ubuntu2 dash_0.5.8-2.1ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.110-1ubuntu10 dpkg_1.18.4ubuntu1 dpkg-dev_1.18.4ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-16ubuntu2 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-16ubuntu2 gcc-5-base_5.3.1-16ubuntu2 gcc-6-base_6.0.1-2ubuntu13 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 help2man_1.47.3 hostname_3.17ubuntu1 init_1.31ubuntu1 init-system-helpers_1.31ubuntu1 initscripts_2.88dsf-59.3ubuntu4 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.2.11 libarchive-zip-perl_1.57-1 libasan2_5.3.1-16ubuntu2 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libasprintf0v5_0.19.7-2ubuntu3 libatomic1_6.0.1-2ubuntu13 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libblkid1_2.27.1-6ubuntu3 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.0.1-2ubuntu13 libcilkrts5_6.0.1-2ubuntu13 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.47.0-1ubuntu2 libdb5.3_5.3.28-11 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu10 libdpkg-perl_1.18.4ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-6ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgcc-5-dev_5.3.1-16ubuntu2 libgcc1_1:6.0.1-2ubuntu13 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.0-1ubuntu4 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.10-4ubuntu1 libgomp1_6.0.1-2ubuntu13 libgpg-error0_1.21-2ubuntu1 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhcrypto4-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimbase1-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimntlm0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhogweed4_3.2-1 libhx509-5-heimdal_1.7~git20150920+dfsg-4ubuntu1 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libisl15_0.16.1-1 libitm1_6.0.1-2ubuntu13 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkrb5-26-heimdal_1.7~git20150920+dfsg-4ubuntu1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 libldap-2.4-2_2.4.42+dfsg-2ubuntu3 liblocale-gettext-perl_1.07-1build1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-6ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libmpx0_5.3.1-16ubuntu2 libncurses5_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnettle6_3.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.38-3.1 libperl5.22_5.22.1-10 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-4 libprocps4_2:3.3.10-4ubuntu2 libquadmath0_6.0.1-2ubuntu13 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d-1build1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.5-1 libsemanage-common_2.4-3build2 libsemanage1_2.4-3build2 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsmartcols1_2.27.1-6ubuntu3 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-16ubuntu2 libstdc++6_6.0.1-2ubuntu13 libsystemd0_229-5ubuntu1 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libtool_2.4.6-0.1 libubsan0_6.0.1-2ubuntu13 libudev1_229-5ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6ubuntu3 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libxml2_2.9.3+dfsg1-1build1 linux-libc-dev_4.4.0-22.38 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-6ubuntu3 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.1-10 perl-base_5.22.1-10 perl-modules-5.22_5.22.1-10 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.10-4ubuntu2 readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gmap-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 systemd_229-5ubuntu1 systemd-sysv_229-5ubuntu1 sysv-rc_2.88dsf-59.3ubuntu4 sysvinit-utils_2.88dsf-59.3ubuntu4 tar_1.28-2.1 tzdata_2016d-2 ubuntu-keyring_2012.05.19 util-linux_2.27.1-6ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Fri Mar 18 09:28:24 2016 UTC using RSA key ID 1B5228B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./gmap_2015-12-31.v9-1.dsc dpkg-source: info: extracting gmap in gmap-2015-12-31.v9 dpkg-source: info: unpacking gmap_2015-12-31.v9.orig.tar.gz dpkg-source: info: unpacking gmap_2015-12-31.v9-1.debian.tar.xz dpkg-source: info: applying install-data-local Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package gmap dpkg-buildpackage: source version 2015-12-31.v9-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build gmap-2015-12-31.v9 dpkg-buildpackage: host architecture i386 fakeroot debian/rules clean dh clean --parallel --with autotools_dev dh_testdir -O--parallel dh_auto_clean -O--parallel dh_autotools-dev_restoreconfig -O--parallel dh_clean -O--parallel debian/rules build-arch dh build-arch --parallel --with autotools_dev dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_autotools-dev_updateconfig -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-sse4.1=no --disable-simd ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --enable-shared --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-sse4.1=no --disable-simd configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode checking package version... 2015-12-31 loading default site script ./config.site checking CFLAGS... -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security checking MPI_CFLAGS... checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc and cc understand -c and -o together... yes checking for mpicc... no checking for hcc... no checking for mpxlc_r... no checking for mpxlc... no checking for mpcc... no checking for cmpicc... no checking for cc... /usr/bin/cc checking for MPI_Init... no checking for MPI_Init in -lmpi... no checking for MPI_Init in -lmpich... no checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for rint in -lm... yes checking whether to use MPI_File for input... not specified so enabled by default checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 4 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether alloca is enabled... not specified so enabled by default checking for working alloca.h... yes checking for alloca... yes checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for builtin popcount/clz/ctz features... not specified so enabled by default checking whether -mpopcnt compiler flag works... 6B8B4567 clz=1 ctz=0 popcount=17 yes checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking whether sse2 is enabled... not specified so enabled by default checking compiler is defective and requires an immediate in sse2 shift commands... yes checking whether ssse3 is enabled... not specified so enabled by default checking whether sse4.1 is enabled... disabled by user checking whether sse4.2 is enabled... disabled because the user disabled sse4.1 checking whether avx is enabled... disabled because the user disabled sse4.2 checking whether avx2 is enabled... disabled because the user disabled avx checking whether simd is enabled... disabled checking gmapdb... /var/cache/gmap checking MAX_READLENGTH... 300 checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating mpi/Makefile config.status: creating util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode configure: WARNING: WARNING: Your C compiler does not know how to handle a particular form of the SSE2 shift commands, and must be somewhat old (probably gcc 4.1 or gcc 4.2). The configure script has therefore substituted alternate C code that your compiler can handle. However, for optimal performance, you may want to obtain a more recent C compiler and build the code with that. checking Standard compiler and flags to be used... gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security checking Standard linker flags to be used... checking MPI compiler and flags to be used... /usr/bin/cc checking MPI linker flags to be used... checking pthread compiler flags to be used... -pthread checking popcnt compiler flags to be used... -mpopcnt checking SIMD features available on computer... checking SIMD compiler flags to be used... make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_build -a -O--parallel make -j4 make[1]: Entering directory '/«PKGBUILDDIR»' Making all in src make[2]: Entering directory '/«PKGBUILDDIR»/src' make all-am make[3]: Entering directory '/«PKGBUILDDIR»/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘positions_move_absolute’: indexdb_hr.c:593:20: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %zd*%d=%zd\n", ^ indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:624:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,input); ^ samheader.c:206:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),headerlen,input); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1253:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1253:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1398:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1398:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1695:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_high_fd,buffer,1); ^ indexdb.c:1699:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_low_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘heap_even_dump’: indexdb_hr.c:1446:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_genomic_sequence’: pair.c:689:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function ‘print_genomicalt_sequence’: pair.c:716:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function ‘compute_margin’: pair.c:743:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ^ pair.c:750:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function ‘Splicetrie_dump’: splicetrie_build.c:132:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("%d %u",(int) leaf,position); ^ splicetrie_build.c:146:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("%d %u",(int) leaf,position); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,input); ^ samheader.c:206:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),headerlen,input); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c parserange.c: In function ‘translate_chromosomepos_universal’: parserange.c:187:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", ^ parserange.c:187:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] parserange.c:187:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c: In function ‘Bitpack64_write_fixed10_huge’: bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘positions_move_absolute_1’: indexdb-write.c:1189:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset); ^ indexdb-write.c: In function ‘positions_move_absolute_4’: indexdb-write.c:1201:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset); ^ indexdb-write.c: In function ‘Indexdb_write_positions’: indexdb-write.c:2064:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2068:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2102:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2117:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2124:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2139:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2167:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2196:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2211:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c: In function ‘Indexdb_write_positions_huge’: indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:268:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:271:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ uint8list.c:277:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:280:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c sarray-write.c: In function ‘Sarray_write_index_separate’: sarray-write.c:530:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ^ sarray-write.c:530:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] sarray-write.c: In function ‘Sarray_write_index_interleaved’: sarray-write.c:634:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ^ sarray-write.c:634:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] In file included from sarray-write.c:34:0: sarray-write.c: In function ‘Sarray_write_csa’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:793:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&sa_i,sa_fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:800:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:813:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&sa_i,sa_fp); ^ sarray-write.c: In function ‘Sarray_compute_lcp’: littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1005:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1016:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1047:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1063:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&rank_i,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1094:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1095:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1116:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&rank_i,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1117:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ ^ sarray-write.c: In function ‘Sarray_discriminating_chars’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1774:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1777:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1899:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c iit_store.c: In function ‘parse_fieldlist’: iit_store.c:494:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(&(Buffer[1]),LINELENGTH-1,fp); ^ iit_store.c: In function ‘parse_fasta’: iit_store.c:530:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(Buffer,LINELENGTH,fp); ^ iit_store.c:533:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(&(Buffer[1]),LINELENGTH-1,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ parserange.c: In function ‘translate_chromosomepos_universal’: parserange.c:187:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n", ^ parserange.c:187:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] parserange.c:187:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c indexdb_hr.c: In function ‘positions_move_absolute’: indexdb_hr.c:593:20: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %zd*%d=%zd\n", ^ indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:624:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-junction.o `test -f 'junction.c' || echo './'`junction.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,input); ^ samheader.c:206:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),headerlen,input); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:268:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:271:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ uint8list.c:277:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:280:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1253:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1253:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1398:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1398:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1695:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_high_fd,buffer,1); ^ indexdb.c:1699:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_low_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function ‘heap_even_dump’: indexdb_hr.c:1446:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-junction.o `test -f 'junction.c' || echo './'`junction.c junction.c: In function ‘Junction_print’: junction.c:31:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("Deletion of %d at %u\n",this->nindels,this->deletionpos); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_genomic_sequence’: pair.c:689:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function ‘print_genomicalt_sequence’: pair.c:716:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function ‘compute_margin’: pair.c:743:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ^ pair.c:750:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c splicetrie_build.c: In function ‘Splicetrie_dump’: splicetrie_build.c:132:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("%d %u",(int) leaf,position); ^ splicetrie_build.c:146:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("%d %u",(int) leaf,position); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,input); ^ samheader.c:206:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),headerlen,input); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c indexdb_hr.c: In function ‘positions_move_absolute’: indexdb_hr.c:593:20: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %zd*%d=%zd\n", ^ indexdb_hr.c: In function ‘positions_read_multiple’: indexdb_hr.c:624:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-junction.o `test -f 'junction.c' || echo './'`junction.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:268:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:271:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ uint8list.c:277:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:280:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1253:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1253:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1398:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1398:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Positionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1695:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_high_fd,buffer,1); ^ indexdb.c:1699:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_low_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c indexdb_hr.c: In function ‘heap_even_dump’: indexdb_hr.c:1446:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("#%d--%d:%u ",i,batch->nentries,batch->position); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-junction.o `test -f 'junction.c' || echo './'`junction.c junction.c: In function ‘Junction_print’: junction.c:31:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("Deletion of %d at %u\n",this->nindels,this->deletionpos); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c pair.c: In function ‘print_genomic_sequence’: pair.c:689:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function ‘print_genomicalt_sequence’: pair.c:716:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP); ^ pair.c: In function ‘compute_margin’: pair.c:743:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP); ^ pair.c:750:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c splicetrie_build.c: In function ‘Splicetrie_dump’: splicetrie_build.c:132:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("%d %u",(int) leaf,position); ^ splicetrie_build.c:146:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=] printf("%d %u",(int) leaf,position); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c: In function ‘Bitpack64_write_fixed10_huge’: bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘positions_move_absolute_1’: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c indexdb-write.c:1189:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset); ^ indexdb-write.c: In function ‘positions_move_absolute_4’: indexdb-write.c:1201:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset); ^ indexdb-write.c: In function ‘Indexdb_write_positions’: indexdb-write.c:2064:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2068:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2102:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2117:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2124:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2139:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2167:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2196:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2211:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c: In function ‘Indexdb_write_positions_huge’: indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c: In function ‘Bitpack64_write_fixed10_huge’: bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c indexdb-write.c: In function ‘positions_move_absolute_1’: indexdb-write.c:1189:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset); ^ indexdb-write.c: In function ‘positions_move_absolute_4’: indexdb-write.c:1201:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset); ^ indexdb-write.c: In function ‘Indexdb_write_positions’: indexdb-write.c:2064:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2068:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2102:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2117:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2124:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2139:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2167:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2196:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2211:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c: In function ‘Indexdb_write_positions_huge’: indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:268:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:271:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ uint8list.c:277:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:280:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c sarray-write.c: In function ‘Sarray_write_index_separate’: sarray-write.c:530:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ^ sarray-write.c:530:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] sarray-write.c: In function ‘Sarray_write_index_interleaved’: sarray-write.c:634:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ^ sarray-write.c:634:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] In file included from sarray-write.c:34:0: sarray-write.c: In function ‘Sarray_write_csa’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:793:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&sa_i,sa_fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:800:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:813:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&sa_i,sa_fp); ^ sarray-write.c: In function ‘Sarray_compute_lcp’: littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1005:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1016:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1047:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1063:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&rank_i,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1094:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1095:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1116:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&rank_i,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1117:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ ^ sarray-write.c: In function ‘Sarray_discriminating_chars’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1774:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1777:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1899:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5022:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5050:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5084:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c: In function ‘Bitpack64_write_fixed10_huge’: bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5192:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5224:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu", ^ bitpack64-write.c:5263:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] indexdb.c: In function ‘Indexdb_get_filenames_bitpack’: indexdb.c:783:19: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=] fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", ^ indexdb.c: In function ‘Indexdb_new_genome’: indexdb.c:1259:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c:1404:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n", ^ indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb-write.c: In function ‘positions_move_absolute_1’: indexdb-write.c:1189:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset); ^ indexdb-write.c: In function ‘positions_move_absolute_4’: indexdb-write.c:1201:20: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘Positionsptr_T {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset); ^ indexdb-write.c: In function ‘Indexdb_write_positions’: indexdb-write.c:2064:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2068:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2102:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2117:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2124:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2139:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2167:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2196:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2211:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c: In function ‘Indexdb_write_positions_huge’: indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2327:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2342:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2349:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2364:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n", ^ indexdb-write.c:2407:17: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘Hugepositionsptr_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu@gene.com of this error.\n", ^ indexdb-write.c:2422:19: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t {aka long long int}’ [-Wformat=] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c genome.c: In function ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c uint8list.c: In function ‘Uint8list_to_string’: uint8list.c:268:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:271:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ uint8list.c:277:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u,",Uint8list_head(p)); ^ uint8list.c:280:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=] sprintf(Buffer,"%u",Uint8list_head(p)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bytecoding.o `test -f 'bytecoding.c' || echo './'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c sarray-write.c: In function ‘Sarray_write_index_separate’: sarray-write.c:530:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ^ sarray-write.c:530:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] sarray-write.c: In function ‘Sarray_write_index_interleaved’: sarray-write.c:634:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace); ^ sarray-write.c:634:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=] In file included from sarray-write.c:34:0: sarray-write.c: In function ‘Sarray_write_csa’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:793:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&sa_i,sa_fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:800:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:813:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&sa_i,sa_fp); ^ sarray-write.c: In function ‘Sarray_compute_lcp’: littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1005:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1016:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1047:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1063:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&rank_i,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1094:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_1,RW_BATCH,fp); ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1095:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1116:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&rank_i,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1117:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ ^ sarray-write.c: In function ‘Sarray_discriminating_chars’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1774:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ ^ littleendian.h:23:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) ^ sarray-write.c:1777:5: note: in expansion of macro ‘FREAD_UINTS’ FREAD_UINTS(read_buffer,RW_BATCH,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ sarray-write.c:1899:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&SA_i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-intlist.o `test -f 'intlist.c' || echo './'`intlist.c bigendian.c: In function ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration] if (stat64(filename,&sb) == 0) { ^ access.c: In function ‘Access_allocate’: access.c:685:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n", ^ access.c: In function ‘Access_mmap_offset’: access.c:861:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 5 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_rw’: access.c:932:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (3): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_offset_rw’: access.c:999:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 4 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (4): Got mmap failure on offset %jd, length %jd. Error %d: %s\n", ^ access.c: In function ‘Access_mmap_and_preload’: access.c:1086:22: warning: format ‘%jd’ expects argument of type ‘intmax_t’, but argument 3 has type ‘size_t {aka unsigned int}’ [-Wformat=] fprintf(stderr,"Error in access.c (5): Got mmap failure on len %jd from length %jd. Error %d: %s\n", ^ access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); ^ access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),filesize/eltsize - i,fp); ^ access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),filesize/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&version,fp); ^ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c In file included from iit-read.c:12:0: iit-read.c: In function ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’ FREAD_INT(&new->version,fp); ^ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’ FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’ FREAD_UINT(&length,fp); ^ samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,input); ^ samheader.c:206:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),headerlen,input); ^ samread.c: In function ‘Samread_print_as_duplicate_fromfile’: samread.c:1498:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,fp); ^ samread.c:1503:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),linelength,fp); ^ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm sam_sort.c: In function ‘Cell_print_fromfile’: sam_sort.c:394:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,fp_input); ^ sam_sort.c:399:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),linelength,fp_input); ^ /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-filestring.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-popcount.o gmapl-genome128_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-bitpack64-readtwo.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-dynprog_simd.o gmapl-dynprog_single.o gmapl-dynprog_genome.o gmapl-dynprog_cdna.o gmapl-dynprog_end.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-output.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm libtool: link: gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-filestring.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-popcount.o gmapl-genome128_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-bitpack64-readtwo.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-dynprog_simd.o gmapl-dynprog_single.o gmapl-dynprog_genome.o gmapl-dynprog_cdna.o gmapl-dynprog_end.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-output.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-genome128_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-uint8list.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -mpopcnt -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-genome128_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-uint8list.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-filestring.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-popcount.o gsnap-genome128_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-bitpack64-readtwo.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-junction.o gsnap-stage3hr.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-dynprog_simd.o gsnap-dynprog_single.o gsnap-dynprog_genome.o gsnap-dynprog_cdna.o gsnap-dynprog_end.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-bytecoding.o gsnap-univdiag.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-output.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm -pthread libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-filestring.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-popcount.o gsnapl-genome128_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-bitpack64-readtwo.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-junction.o gsnapl-stage3hr.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-dynprog_simd.o gsnapl-dynprog_single.o gsnapl-dynprog_genome.o gsnapl-dynprog_cdna.o gsnapl-dynprog_end.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-output.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-filestring.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-popcount.o uniqscan-genome128_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-bitpack64-readtwo.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-junction.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-dynprog_simd.o uniqscan-dynprog_single.o uniqscan-dynprog_genome.o uniqscan-dynprog_cdna.o uniqscan-dynprog_end.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-bytecoding.o uniqscan-univdiag.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-filestring.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-popcount.o gsnap-genome128_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-bitpack64-readtwo.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-junction.o gsnap-stage3hr.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-dynprog_simd.o gsnap-dynprog_single.o gsnap-dynprog_genome.o gsnap-dynprog_cdna.o gsnap-dynprog_end.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-bytecoding.o gsnap-univdiag.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-output.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-filestring.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-popcount.o uniqscan-genome128_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-bitpack64-readtwo.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-junction.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-dynprog_simd.o uniqscan-dynprog_single.o uniqscan-dynprog_genome.o uniqscan-dynprog_cdna.o uniqscan-dynprog_end.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-bytecoding.o uniqscan-univdiag.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-filestring.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-popcount.o gsnapl-genome128_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-bitpack64-readtwo.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-junction.o gsnapl-stage3hr.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-dynprog_simd.o gsnapl-dynprog_single.o gsnapl-dynprog_genome.o gsnapl-dynprog_cdna.o gsnapl-dynprog_end.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-output.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-filestring.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-popcount.o uniqscanl-genome128_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-bitpack64-readtwo.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-junction.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-dynprog_simd.o uniqscanl-dynprog_single.o uniqscanl-dynprog_genome.o uniqscanl-dynprog_cdna.o uniqscanl-dynprog_end.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-genome128_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-genome128_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-saca-k.o cmetindex-uint8list.o cmetindex-bytecoding.o cmetindex-sarray-write.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -mpopcnt -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-filestring.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-popcount.o uniqscanl-genome128_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-bitpack64-readtwo.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-junction.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-dynprog_simd.o uniqscanl-dynprog_single.o uniqscanl-dynprog_genome.o uniqscanl-dynprog_cdna.o uniqscanl-dynprog_end.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-genome128_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-genome128_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-saca-k.o cmetindex-uint8list.o cmetindex-bytecoding.o cmetindex-sarray-write.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-genome128_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-saca-k.o atoiindex-uint8list.o atoiindex-bytecoding.o atoiindex-sarray-write.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -mpopcnt -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-genome128_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-saca-k.o atoiindex-uint8list.o atoiindex-bytecoding.o atoiindex-sarray-write.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -o sam_sort sam_sort-except.o sam_sort-assert.o sam_sort-mem.o sam_sort-littleendian.o sam_sort-bigendian.o sam_sort-intlist.o sam_sort-list.o sam_sort-stopwatch.o sam_sort-access.o sam_sort-univinterval.o sam_sort-interval.o sam_sort-uintlist.o sam_sort-filestring.o sam_sort-iit-read-univ.o sam_sort-iit-read.o sam_sort-samheader.o sam_sort-samread.o sam_sort-datadir.o sam_sort-getopt.o sam_sort-getopt1.o sam_sort-sam_sort.o -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -o sam_sort sam_sort-except.o sam_sort-assert.o sam_sort-mem.o sam_sort-littleendian.o sam_sort-bigendian.o sam_sort-intlist.o sam_sort-list.o sam_sort-stopwatch.o sam_sort-access.o sam_sort-univinterval.o sam_sort-interval.o sam_sort-uintlist.o sam_sort-filestring.o sam_sort-iit-read-univ.o sam_sort-iit-read.o sam_sort-samheader.o sam_sort-samread.o sam_sort-datadir.o sam_sort-getopt.o sam_sort-getopt1.o sam_sort-sam_sort.o -lm -pthread make[3]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Leaving directory '/«PKGBUILDDIR»/src' Making all in mpi make[2]: Entering directory '/«PKGBUILDDIR»/mpi' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/«PKGBUILDDIR»/mpi' Making all in util make[2]: Entering directory '/«PKGBUILDDIR»/util' cp gmap_compress.pl gmap_compress cp gmap_uncompress.pl gmap_uncompress cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_compress chmod +x gmap_process chmod +x gmap_uncompress chmod +x gmap_build cp gmap_reassemble.pl gmap_reassemble cp md_coords.pl md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x gmap_reassemble chmod +x md_coords chmod +x psl_splicesites chmod +x fa_coords cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x psl_introns chmod +x ensembl_genes chmod +x psl_genes chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gtf_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes chmod +x gtf_genes chmod +x gff3_introns cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[2]: Leaving directory '/«PKGBUILDDIR»/util' Making all in tests make[2]: Entering directory '/«PKGBUILDDIR»/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/«PKGBUILDDIR»/tests' make[2]: Entering directory '/«PKGBUILDDIR»' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_test -a -O--parallel make -j4 check VERBOSE=1 make[1]: Entering directory '/«PKGBUILDDIR»' Making check in src make[2]: Entering directory '/«PKGBUILDDIR»/src' make[2]: Leaving directory '/«PKGBUILDDIR»/src' Making check in mpi make[2]: Entering directory '/«PKGBUILDDIR»/mpi' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/«PKGBUILDDIR»/mpi' Making check in util make[2]: Entering directory '/«PKGBUILDDIR»/util' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/«PKGBUILDDIR»/util' Making check in tests make[2]: Entering directory '/«PKGBUILDDIR»/tests' make check-TESTS make[3]: Entering directory '/«PKGBUILDDIR»/tests' GMAP version 2015-12-31 called with args: /«PKGBUILDDIR»/src/gmap -A -g /«PKGBUILDDIR»/tests/ss.chr17test /«PKGBUILDDIR»/tests/ss.her2 Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 __builtin_popcount=17 Finished checking compiler assumptions Starting alignment Processed 1 queries in 0.03 seconds (33.33 queries/sec) PASS: align.test Opening file /«PKGBUILDDIR»/tests/ss.chr17test Processed short contigs (<1000000 nt): . ============================================================ Contig mapping information has been written to file coords.chr17test. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make -f Makefile.chr17test gmapdb ============================================================ PASS: coords1.test Sorting chromosomes in chrom order. To turn off or sort other ways, use the -s flag. Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 __builtin_popcount=17 Finished checking compiler assumptions Creating files in directory ./chr17test Running "/«PKGBUILDDIR»/src/fa_coords" -o "./chr17test.coords" -f "./chr17test.sources" Opening file /«PKGBUILDDIR»/tests/ss.chr17test Processed short contigs (<1000000 nt): . ============================================================ Contig mapping information has been written to file ./chr17test.coords. You should look at this file, and edit it if necessary If everything is okay, you should proceed by running make gmapdb ============================================================ Running "/«PKGBUILDDIR»/src/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/«PKGBUILDDIR»/src/gmapindex" -d chr17test -D "./chr17test" -A Reading coordinates from file ./chr17test.coords Logging contig chr17test at chr17test:1..200000 in genome chr17test Total genomic length = 200000 bp Have a total of 1 chromosomes Chromosome chr17test has universal coordinates 1..200000 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (1 intervals) Writing IIT file footer information...done Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (1 intervals) Writing IIT file footer information...done Running "/«PKGBUILDDIR»/src/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/«PKGBUILDDIR»/src/gmapindex" -d chr17test -F "./chr17test" -D "./chr17test" -G Genome length is 200000 nt Trying to allocate 18750*4 bytes of memory...succeeded. Building genome in memory. Reading coordinates from file ./chr17test.coords Writing contig chr17test to universal coordinates 1..200000 A total of 0 non-ACGTNX characters were seen in the genome. Running cat "./chr17test/chr17test.genomecomp" | "/«PKGBUILDDIR»/src/gmapindex" -d chr17test -U > "./chr17test/chr17test.genomebits128" Running cat "./chr17test/chr17test.genomecomp" | "/«PKGBUILDDIR»/src/gmapindex" -k 12 -q 3 -d chr17test -F "./chr17test" -D "./chr17test" -N Counting positions in genome chr17test (12 bp every 3 bp), position 0 Number of offsets: 66663 => pages file not required Running "/«PKGBUILDDIR»/src/gmapindex" -k 12 -q 3 -d chr17test -F "./chr17test" -D "./chr17test" -O "./chr17test/chr17test.genomecomp" Offset compression types: bitpack64 Allocating 16777217*4 bytes for offsets Indexing offsets of oligomers in genome chr17test (12 bp every 3 bp), position 0 Writing 16777217 offsets compressed via bitpack64 to file with total of 66663 k-mers...Checking bitpack...done Entered Bitpack64_write_differential with n 16777216 Running "/«PKGBUILDDIR»/src/gmapindex" -k 12 -q 3 -d chr17test -F "./chr17test" -D "./chr17test" -P "./chr17test/chr17test.genomecomp" Looking for index files in directory ./chr17test Pointers file is chr17test.ref123offsets64meta Offsets file is chr17test.ref123offsets64strm Positions file is chr17test.ref123positions Allocating memory (16777217 4-byte words) for offsets, kmer 12...done Expanding offsetsstrm into offsets...done Trying to allocate 66663*4 bytes of memory for positions...succeeded. Building positions in memory. Indexing positions of oligomers in genome chr17test (12 bp every 3 bp), position 0 Writing 66663 genomic positions to file ./chr17test/chr17test.ref123positions ... Running "/«PKGBUILDDIR»/src/gmapindex" -d chr17test -F "./chr17test" -D "./chr17test" -S Genome length is 200000 Building suffix array SACA_K called with n = 200001, K = 5, level 0 SACA_K called with n = 53965, K = 0, level 1 SACA_K called with n = 16773, K = 0, level 2 SACA_K called with n = 5395, K = 0, level 3 For indexsize 12, occupied 179914/0 Optimal indexsize = 12 Entered Bitpack64_write_differential with n 33554431 Running "/«PKGBUILDDIR»/src/gmapindex" -d chr17test -F "./chr17test" -D "./chr17test" -L Building LCP array Writing temporary file for rank...done Writing temporary file for permuted sarray...done Byte-coding: 200001 values < 255, 0 exceptions >= 255 (0.0%) Building DC array Building child array Writing file ./chr17test/chr17test.salcpchilddcdone Byte-coding: 199317 values < 255, 684 exceptions >= 255 (0.3%) GMAP version 2015-12-31 called with args: /«PKGBUILDDIR»/src/gmap -D . -d chr17test /«PKGBUILDDIR»/tests/ss.her2 Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 __builtin_popcount=17 Finished checking compiler assumptions Looking for index files in directory ./chr17test Pointers file is chr17test.ref123offsets64meta Offsets file is chr17test.ref123offsets64strm Positions file is chr17test.ref123positions Offsets compression type: bitpack64 Allocating memory for ref offset pointers, kmer 12, interval 3...Attached new memory for ./chr17test/chr17test.ref123offsets64meta...done (2,097,168 bytes, 0.01 sec) Starting alignment Processed 1 queries in 0.02 seconds (50.00 queries/sec) Removed existing memory for shmid 0 PASS: setup1.test Finished reading FASTA file -- total entries: 3 Maximum coordinate: 40000 Total label length: 3 + 3 separators Total annotation length: 80 + 3 separators Saw 0 distinct divisions/chromosomes Saw 3 distinct tags/types No divs/chromosomes provided, so storing as IIT version 1 Writing IIT file header information...coordinates require 4 bytes each...done Processing null division/chromosome...sorting...writing...done (3 intervals) Writing IIT file footer information...done PASS: iit.test ================== All 4 tests passed ================== make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[2]: Leaving directory '/«PKGBUILDDIR»/tests' make[2]: Entering directory '/«PKGBUILDDIR»' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch --parallel --with autotools_dev dh_testroot -a -O--parallel dh_prep -a -O--parallel debian/rules override_dh_auto_install make[1]: Entering directory '/«PKGBUILDDIR»' mkdir -p /«PKGBUILDDIR»/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string="2015-12-31.v9-1" --name='Genomic Mapping and Alignment Program' \ /«PKGBUILDDIR»/src/gmap |debian/filter.pl >/«PKGBUILDDIR»/debian/gmap/usr/share/man/man1/gmap.1; /usr/bin/help2man --no-info --version-string="2015-12-31.v9-1" --name='Genomic Short-read Nucleotide Alignment Program' \ /«PKGBUILDDIR»/src/gsnap |debian/filter.pl >/«PKGBUILDDIR»/debian/gmap/usr/share/man/man1/gsnap.1; /usr/bin/help2man --no-info --version-string="2015-12-31.v9-1" --name='Tool for genome database creation for GMAP or GSNAP' \ /«PKGBUILDDIR»/util/gmap_build |debian/filter.pl >/«PKGBUILDDIR»/debian/gmap/usr/share/man/man1/gmap_build.1; dh_auto_install make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/«PKGBUILDDIR»' Making install in src make[3]: Entering directory '/«PKGBUILDDIR»/src' make[4]: Entering directory '/«PKGBUILDDIR»/src' test -z "/usr/lib/gmap" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/gmap/usr/lib/gmap" make[4]: Nothing to be done for 'install-data-am'. /bin/bash ../libtool --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex sam_sort '/«PKGBUILDDIR»/debian/gmap/usr/lib/gmap' libtool: install: /usr/bin/install -c gmap /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/gmap libtool: install: /usr/bin/install -c gmapl /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/gmapl libtool: install: /usr/bin/install -c get-genome /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/get-genome libtool: install: /usr/bin/install -c gmapindex /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/gmapindex libtool: install: /usr/bin/install -c iit_store /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/iit_store libtool: install: /usr/bin/install -c iit_get /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/iit_get libtool: install: /usr/bin/install -c iit_dump /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/iit_dump libtool: install: /usr/bin/install -c gsnap /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/gsnap libtool: install: /usr/bin/install -c gsnapl /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/gsnapl libtool: install: /usr/bin/install -c uniqscan /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/uniqscan libtool: install: /usr/bin/install -c uniqscanl /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/uniqscanl libtool: install: /usr/bin/install -c snpindex /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/snpindex libtool: install: /usr/bin/install -c cmetindex /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/cmetindex libtool: install: /usr/bin/install -c atoiindex /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/atoiindex libtool: install: /usr/bin/install -c sam_sort /«PKGBUILDDIR»/debian/gmap/usr/lib/gmap/sam_sort make[4]: Leaving directory '/«PKGBUILDDIR»/src' make[3]: Leaving directory '/«PKGBUILDDIR»/src' Making install in mpi make[3]: Entering directory '/«PKGBUILDDIR»/mpi' make[4]: Entering directory '/«PKGBUILDDIR»/mpi' test -z "/usr/lib/gmap" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/gmap/usr/lib/gmap" make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/«PKGBUILDDIR»/mpi' make[3]: Leaving directory '/«PKGBUILDDIR»/mpi' Making install in util make[3]: Entering directory '/«PKGBUILDDIR»/util' make[4]: Entering directory '/«PKGBUILDDIR»/util' test -z "/usr/lib/gmap" || /bin/mkdir -p "/«PKGBUILDDIR»/debian/gmap/usr/lib/gmap" make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/«PKGBUILDDIR»/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/«PKGBUILDDIR»/util' make[3]: Leaving directory '/«PKGBUILDDIR»/util' Making install in tests make[3]: Entering directory '/«PKGBUILDDIR»/tests' make[4]: Entering directory '/«PKGBUILDDIR»/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Leaving directory '/«PKGBUILDDIR»/tests' make[3]: Entering directory '/«PKGBUILDDIR»' make[4]: Entering directory '/«PKGBUILDDIR»' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /«PKGBUILDDIR»/config/install-sh -d /«PKGBUILDDIR»/debian/gmap/var/cache/gmap make[4]: Leaving directory '/«PKGBUILDDIR»' make[3]: Leaving directory '/«PKGBUILDDIR»' make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_install make[1]: Entering directory '/«PKGBUILDDIR»' dh_install mkdir -p debian/gmap/usr/bin ln -s /usr/lib/gmap/gmap debian/gmap/usr/bin/gmap ln -s /usr/lib/gmap/gsnap debian/gmap/usr/bin/gsnap ln -s /usr/lib/gmap/gmap_build debian/gmap/usr/bin/gmap_build make[1]: Leaving directory '/«PKGBUILDDIR»' dh_installdocs -a -O--parallel dh_installchangelogs -a -O--parallel dh_installman -a -O--parallel dh_perl -a -O--parallel dh_link -a -O--parallel dh_strip_nondeterminism -a -O--parallel dh_compress -a -O--parallel dh_fixperms -a -O--parallel dh_strip -a -O--parallel dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: gmap dh_strip debug symbol extraction: packages to act on: gmap dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package gmap: unused substitution variable ${perl:Depends} /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform i386: gmap dh_gencontrol debug symbol wrapper: packages to act on: gmap dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package gmap (pkgdir debian/gmap, ddeb package dir debian/gmap-dbgsym) dh_gencontrol debug symbol wrapper: building gmap-dbgsym_2015-12-31.v9-1_i386.ddeb dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2015-12-31.v9-1_i386.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile gmap-dbgsym_2015-12-31.v9-1_i386.ddeb non-free/science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 129 pkgstriptranslations: processing gmap (in debian/gmap); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gmap/DEBIAN/control, package gmap, directory debian/gmap pkgstripfiles: Truncating usr/share/doc/gmap/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gmap ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gmap' in '../gmap_2015-12-31.v9-1_i386.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../gmap_2015-12-31.v9-1_i386.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build gmap-2015-12-31.v9 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160427-0537 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ gmap_2015-12-31.v9-1_i386.changes: ────────────────────────────────── Format: 1.8 Date: Fri, 18 Mar 2016 10:12:35 +0100 Source: gmap Binary: gmap Architecture: i386 Version: 2015-12-31.v9-1 Distribution: yakkety-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Alexandre Mestiashvili Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2015-12-31.v9-1) unstable; urgency=medium . * Imported Upstream version 2015-12-31.v9 * Export all hardening flags, remove DH_VERBOSE and DH_OPTIONS Checksums-Sha1: c5c9d0e61679a7797d2a328e696699f81ca36539 3337604 gmap-dbgsym_2015-12-31.v9-1_i386.ddeb ec894d3abb50fceae26d7f49a913e437cd6a7886 7791390 gmap_2015-12-31.v9-1_i386.deb Checksums-Sha256: 86f4246edce1b14506292edfad89566ffa85bc893a9231f7e4718bc9e8aa9d2e 3337604 gmap-dbgsym_2015-12-31.v9-1_i386.ddeb 0a170f871635d9cc328b1a5f1ed76b4d894c5549a9365853b2a4486143bb5a1f 7791390 gmap_2015-12-31.v9-1_i386.deb Files: 8015eb27e3e640a56c4b4bfd8300e1b7 3337604 non-free/science extra gmap-dbgsym_2015-12-31.v9-1_i386.ddeb 6f5ae4a972b9c46251447bbfeb7e0f8b 7791390 non-free/science optional gmap_2015-12-31.v9-1_i386.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ gmap_2015-12-31.v9-1_i386.deb ───────────────────────────── new debian package, version 2.0. size 7791390 bytes: control archive=1998 bytes. 1000 bytes, 21 lines control 2607 bytes, 44 lines md5sums Package: gmap Version: 2015-12-31.v9-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 71869 Depends: perl, libbz2-1.0, libc6 (>= 2.11), zlib1g (>= 1:1.2.6) Section: non-free/science Priority: optional Homepage: http://research-pub.gene.com/gmap Description: spliced and SNP-tolerant alignment for mRNA and short reads This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA. drwxr-xr-x root/root 0 2016-04-27 05:36 ./ drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/bin/ lrwxrwxrwx root/root 0 2016-04-27 05:36 ./usr/bin/gmap -> ../lib/gmap/gmap lrwxrwxrwx root/root 0 2016-04-27 05:36 ./usr/bin/gmap_build -> ../lib/gmap/gmap_build lrwxrwxrwx root/root 0 2016-04-27 05:36 ./usr/bin/gsnap -> ../lib/gmap/gsnap drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/lib/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/lib/gmap/ -rwxr-xr-x root/root 3851988 2016-04-27 05:36 ./usr/lib/gmap/atoiindex -rwxr-xr-x root/root 3851988 2016-04-27 05:36 ./usr/lib/gmap/cmetindex -rwxr-xr-x root/root 7863 2016-04-27 05:36 ./usr/lib/gmap/dbsnp_iit -rwxr-xr-x root/root 1256 2016-04-27 05:36 ./usr/lib/gmap/ensembl_genes -rwxr-xr-x root/root 15893 2016-04-27 05:36 ./usr/lib/gmap/fa_coords -rwxr-xr-x root/root 1607684 2016-04-27 05:36 ./usr/lib/gmap/get-genome -rwxr-xr-x root/root 6268 2016-04-27 05:36 ./usr/lib/gmap/gff3_genes -rwxr-xr-x root/root 14312 2016-04-27 05:36 ./usr/lib/gmap/gff3_introns -rwxr-xr-x root/root 15883 2016-04-27 05:36 ./usr/lib/gmap/gff3_splicesites -rwxr-xr-x root/root 9166180 2016-04-27 05:36 ./usr/lib/gmap/gmap -rwxr-xr-x root/root 15119 2016-04-27 05:36 ./usr/lib/gmap/gmap_build -rwxr-xr-x root/root 10487 2016-04-27 05:36 ./usr/lib/gmap/gmap_compress -rwxr-xr-x root/root 4574 2016-04-27 05:36 ./usr/lib/gmap/gmap_process -rwxr-xr-x root/root 533 2016-04-27 05:36 ./usr/lib/gmap/gmap_reassemble -rwxr-xr-x root/root 16519 2016-04-27 05:36 ./usr/lib/gmap/gmap_uncompress -rwxr-xr-x root/root 3372596 2016-04-27 05:36 ./usr/lib/gmap/gmapindex -rwxr-xr-x root/root 9211268 2016-04-27 05:36 ./usr/lib/gmap/gmapl -rwxr-xr-x root/root 9637636 2016-04-27 05:36 ./usr/lib/gmap/gsnap -rwxr-xr-x root/root 9670404 2016-04-27 05:36 ./usr/lib/gmap/gsnapl -rwxr-xr-x root/root 5017 2016-04-27 05:36 ./usr/lib/gmap/gtf_genes -rwxr-xr-x root/root 11399 2016-04-27 05:36 ./usr/lib/gmap/gtf_introns -rwxr-xr-x root/root 12626 2016-04-27 05:36 ./usr/lib/gmap/gtf_splicesites -rwxr-xr-x root/root 1367 2016-04-27 05:36 ./usr/lib/gmap/gvf_iit -rwxr-xr-x root/root 144964 2016-04-27 05:36 ./usr/lib/gmap/iit_dump -rwxr-xr-x root/root 165604 2016-04-27 05:36 ./usr/lib/gmap/iit_get -rwxr-xr-x root/root 104024 2016-04-27 05:36 ./usr/lib/gmap/iit_store -rwxr-xr-x root/root 29421 2016-04-27 05:36 ./usr/lib/gmap/md_coords -rwxr-xr-x root/root 1177 2016-04-27 05:36 ./usr/lib/gmap/psl_genes -rwxr-xr-x root/root 5915 2016-04-27 05:36 ./usr/lib/gmap/psl_introns -rwxr-xr-x root/root 6985 2016-04-27 05:36 ./usr/lib/gmap/psl_splicesites -rwxr-xr-x root/root 181908 2016-04-27 05:36 ./usr/lib/gmap/sam_sort -rwxr-xr-x root/root 3299028 2016-04-27 05:36 ./usr/lib/gmap/snpindex -rwxr-xr-x root/root 9513556 2016-04-27 05:36 ./usr/lib/gmap/uniqscan -rwxr-xr-x root/root 9546356 2016-04-27 05:36 ./usr/lib/gmap/uniqscanl -rwxr-xr-x root/root 1567 2016-04-27 05:36 ./usr/lib/gmap/vcf_iit drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/share/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/share/doc/gmap/ -rw-r--r-- root/root 181 2015-08-27 16:00 ./usr/share/doc/gmap/AUTHORS -rw-r--r-- root/root 1815 2015-08-27 16:00 ./usr/share/doc/gmap/NOTICE.gz -rw-r--r-- root/root 171 2016-03-18 09:13 ./usr/share/doc/gmap/README.Debian -rw-r--r-- root/root 20403 2016-03-17 17:45 ./usr/share/doc/gmap/README.gz -rw-r--r-- root/root 744 2016-04-27 05:36 ./usr/share/doc/gmap/changelog.Debian.gz -rw-r--r-- root/root 7919 2016-03-18 09:13 ./usr/share/doc/gmap/copyright drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/share/man/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./usr/share/man/man1/ -rw-r--r-- root/root 4908 2016-04-27 05:36 ./usr/share/man/man1/gmap.1.gz -rw-r--r-- root/root 1687 2016-04-27 05:36 ./usr/share/man/man1/gmap_build.1.gz -rw-r--r-- root/root 6941 2016-04-27 05:36 ./usr/share/man/man1/gsnap.1.gz drwxr-xr-x root/root 0 2016-04-27 05:36 ./var/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./var/cache/ drwxr-xr-x root/root 0 2016-04-27 05:36 ./var/cache/gmap/ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: i386 Build-Space: 302748 Build-Time: 217 Distribution: yakkety-proposed Host Architecture: i386 Install-Time: 9 Job: gmap_2015-12-31.v9-1.dsc Machine Architecture: amd64 Package: gmap Package-Time: 227 Source-Version: 2015-12-31.v9-1 Space: 302748 Status: successful Version: 2015-12-31.v9-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160427-0537 Build needed 00:03:47, 302748k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9641405'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9641405/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9641405'] Unmounting chroot for build PACKAGEBUILD-9641405... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9641405'] Removing build PACKAGEBUILD-9641405