https://launchpad.net/ubuntu/+archive/test-rebuild-20190906/+build/17551316 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-028 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:10:16 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_177 python-lpbuildd_177 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 14 Sep 01:56:34 ntpdate[1953]: adjust time server 10.211.37.1 offset -0.000064 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=eoan --arch=amd64 PACKAGEBUILD-17551316 --image-type chroot /home/buildd/filecache-default/6814d4bbdedc39163e5a7d0f0a1f6a039f04bcb5 Creating target for build PACKAGEBUILD-17551316 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=eoan --arch=amd64 PACKAGEBUILD-17551316 Starting target for build PACKAGEBUILD-17551316 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=eoan --arch=amd64 PACKAGEBUILD-17551316 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan main' 'deb http://ftpmaster.internal/ubuntu eoan main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-17551316 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=eoan --arch=amd64 PACKAGEBUILD-17551316 Adding trusted keys to build-PACKAGEBUILD-17551316 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=eoan --arch=amd64 PACKAGEBUILD-17551316 Updating target for build PACKAGEBUILD-17551316 Get:1 http://ftpmaster.internal/ubuntu eoan InRelease [255 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan InRelease [15.4 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main amd64 Packages [3792 B] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main Translation-en [4848 B] Get:5 http://ftpmaster.internal/ubuntu eoan/main amd64 Packages [972 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main Translation-en [505 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/restricted amd64 Packages [14.4 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/restricted Translation-en [4836 B] Get:9 http://ftpmaster.internal/ubuntu eoan/universe amd64 Packages [8865 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/universe Translation-en [5221 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/multiverse amd64 Packages [153 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/multiverse Translation-en [111 kB] Fetched 16.1 MB in 3s (4904 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: logsave The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu build-essential coreutils cpp cpp-9 dpkg dpkg-dev e2fsprogs g++ g++-9 gcc gcc-9 gcc-9-base libapparmor1 libasan5 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-9-dev libgcc1 libgnutls30 libgomp1 libisl21 libitm1 liblsan0 libquadmath0 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libtsan0 libubsan1 linux-libc-dev login passwd 45 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 MB of archives. After this operation, 862 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu eoan/main amd64 coreutils amd64 8.30-3ubuntu2 [1249 kB] Get:2 http://ftpmaster.internal/ubuntu eoan/main amd64 dpkg amd64 1.19.7ubuntu2 [1130 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main amd64 login amd64 1:4.5-1.1ubuntu4 [264 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main amd64 libc6-dev amd64 2.30-0ubuntu1 [2549 kB] Get:5 http://ftpmaster.internal/ubuntu eoan/main amd64 libc-dev-bin amd64 2.30-0ubuntu1 [71.7 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main amd64 linux-libc-dev amd64 5.3.0-10.11 [1062 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main amd64 libcc1-0 amd64 9.2.1-8ubuntu1 [49.1 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/main amd64 binutils-x86-64-linux-gnu amd64 2.32.51.20190905-0ubuntu1 [1639 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main amd64 libbinutils amd64 2.32.51.20190905-0ubuntu1 [474 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main amd64 binutils-common amd64 2.32.51.20190905-0ubuntu1 [203 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main amd64 binutils amd64 2.32.51.20190905-0ubuntu1 [3416 B] Get:12 http://ftpmaster.internal/ubuntu eoan/main amd64 gcc-9-base amd64 9.2.1-8ubuntu1 [19.2 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main amd64 libgcc1 amd64 1:9.2.1-8ubuntu1 [40.8 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/main amd64 libgomp1 amd64 9.2.1-8ubuntu1 [89.3 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main amd64 libitm1 amd64 9.2.1-8ubuntu1 [28.1 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main amd64 libatomic1 amd64 9.2.1-8ubuntu1 [9220 B] Get:17 http://ftpmaster.internal/ubuntu eoan/main amd64 libasan5 amd64 9.2.1-8ubuntu1 [395 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main amd64 liblsan0 amd64 9.2.1-8ubuntu1 [139 kB] Get:19 http://ftpmaster.internal/ubuntu eoan/main amd64 libtsan0 amd64 9.2.1-8ubuntu1 [301 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main amd64 libubsan1 amd64 9.2.1-8ubuntu1 [130 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main amd64 libquadmath0 amd64 9.2.1-8ubuntu1 [146 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main amd64 g++-9 amd64 9.2.1-8ubuntu1 [10.2 MB] Get:23 http://ftpmaster.internal/ubuntu eoan/main amd64 libstdc++-9-dev amd64 9.2.1-8ubuntu1 [1706 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main amd64 libgcc-9-dev amd64 9.2.1-8ubuntu1 [2360 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main amd64 gcc-9 amd64 9.2.1-8ubuntu1 [9762 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main amd64 cpp-9 amd64 9.2.1-8ubuntu1 [8957 kB] Get:27 http://ftpmaster.internal/ubuntu eoan/main amd64 libstdc++6 amd64 9.2.1-8ubuntu1 [512 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main amd64 libisl21 amd64 0.21-2 [576 kB] Get:29 http://ftpmaster.internal/ubuntu eoan/main amd64 libc6 amd64 2.30-0ubuntu1 [2727 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main amd64 libc-bin amd64 2.30-0ubuntu1 [636 kB] Get:31 http://ftpmaster.internal/ubuntu eoan/main amd64 libext2fs2 amd64 1.45.3-4ubuntu1 [181 kB] Get:32 http://ftpmaster.internal/ubuntu eoan/main amd64 e2fsprogs amd64 1.45.3-4ubuntu1 [526 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main amd64 logsave amd64 1.45.3-4ubuntu1 [9704 B] Get:34 http://ftpmaster.internal/ubuntu eoan/main amd64 passwd amd64 1:4.5-1.1ubuntu4 [815 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/main amd64 libgnutls30 amd64 3.6.9-4build1 [792 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main amd64 libcom-err2 amd64 1.45.3-4ubuntu1 [9012 B] Get:37 http://ftpmaster.internal/ubuntu eoan/main amd64 libss2 amd64 1.45.3-4ubuntu1 [11.3 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main amd64 libapparmor1 amd64 2.13.3-5ubuntu1 [35.5 kB] Get:39 http://ftpmaster.internal/ubuntu eoan/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-2ubuntu6 [127 kB] Get:40 http://ftpmaster.internal/ubuntu eoan/main amd64 libsqlite3-0 amd64 3.29.0-2 [536 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main amd64 g++ amd64 4:9.2.1-3.1ubuntu1 [1612 B] Get:42 http://ftpmaster.internal/ubuntu eoan/main amd64 gcc amd64 4:9.2.1-3.1ubuntu1 [5216 B] Get:43 http://ftpmaster.internal/ubuntu eoan/main amd64 cpp amd64 4:9.2.1-3.1ubuntu1 [27.6 kB] Get:44 http://ftpmaster.internal/ubuntu eoan/main amd64 dpkg-dev all 1.19.7ubuntu2 [679 kB] Get:45 http://ftpmaster.internal/ubuntu eoan/main amd64 libdpkg-perl all 1.19.7ubuntu2 [230 kB] Get:46 http://ftpmaster.internal/ubuntu eoan/main amd64 build-essential amd64 12.7ubuntu1 [4648 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.4 MB in 1s (55.2 MB/s) (Reading database ... 12730 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_amd64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu1) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 12730 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.7ubuntu2_amd64.deb ... Unpacking dpkg (1.19.7ubuntu2) over (1.19.7ubuntu1) ... Setting up dpkg (1.19.7ubuntu2) ... (Reading database ... 12730 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1ubuntu4_amd64.deb ... Unpacking login (1:4.5-1.1ubuntu4) over (1:4.5-1.1ubuntu3) ... Setting up login (1:4.5-1.1ubuntu4) ... (Reading database ... 12730 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.30-0ubuntu1_amd64.deb ... Unpacking libc6-dev:amd64 (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Preparing to unpack .../1-libc-dev-bin_2.30-0ubuntu1_amd64.deb ... Unpacking libc-dev-bin (2.30-0ubuntu1) over (2.29-0ubuntu3) ... 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Setting up linux-libc-dev:amd64 (5.3.0-10.11) ... Setting up libcom-err2:amd64 (1.45.3-4ubuntu1) ... Setting up libgomp1:amd64 (9.2.1-8ubuntu1) ... Setting up libasan5:amd64 (9.2.1-8ubuntu1) ... Setting up libquadmath0:amd64 (9.2.1-8ubuntu1) ... Setting up libatomic1:amd64 (9.2.1-8ubuntu1) ... Setting up libss2:amd64 (1.45.3-4ubuntu1) ... Setting up libdpkg-perl (1.19.7ubuntu2) ... Setting up logsave (1.45.3-4ubuntu1) ... Setting up libubsan1:amd64 (9.2.1-8ubuntu1) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.155-2ubuntu6) ... Setting up cpp-9 (9.2.1-8ubuntu1) ... Setting up libbinutils:amd64 (2.32.51.20190905-0ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu1) ... Setting up libcc1-0:amd64 (9.2.1-8ubuntu1) ... Setting up liblsan0:amd64 (9.2.1-8ubuntu1) ... Setting up libitm1:amd64 (9.2.1-8ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.32.51.20190905-0ubuntu1) ... Setting up libtsan0:amd64 (9.2.1-8ubuntu1) ... Setting up e2fsprogs (1.45.3-4ubuntu1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/e2scrub.conf ... Setting up binutils (2.32.51.20190905-0ubuntu1) ... Setting up dpkg-dev (1.19.7ubuntu2) ... Setting up libgcc-9-dev:amd64 (9.2.1-8ubuntu1) ... Setting up cpp (4:9.2.1-3.1ubuntu1) ... Setting up libc6-dev:amd64 (2.30-0ubuntu1) ... Setting up gcc-9 (9.2.1-8ubuntu1) ... Setting up libstdc++-9-dev:amd64 (9.2.1-8ubuntu1) ... Setting up gcc (4:9.2.1-3.1ubuntu1) ... Setting up g++-9 (9.2.1-8ubuntu1) ... Setting up g++ (4:9.2.1-3.1ubuntu1) ... Setting up build-essential (12.7ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17551316 amd64 eoan -c chroot:build-PACKAGEBUILD-17551316 --arch=amd64 --dist=eoan --nolog -A gmap_2019-05-12-1.dsc Initiating build PACKAGEBUILD-17551316 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:10:16 UTC 2019 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-028.buildd +==============================================================================+ | gmap 2019-05-12-1 (amd64) 14 Sep 2019 01:57 | +==============================================================================+ Package: gmap Version: 2019-05-12-1 Source Version: 2019-05-12-1 Distribution: eoan Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/gmap-m2ckug/gmap-2019-05-12' with '<>' I: NOTICE: Log filtering will replace 'build/gmap-m2ckug' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17551316/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gmap_2019-05-12-1.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 '/<>/resolver-M_TCId/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-M_TCId/apt_archive ./ InRelease Get:2 copy:/<>/resolver-M_TCId/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-M_TCId/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-M_TCId/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-M_TCId/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (0 B/s) Reading package lists... 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-M_TCId/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12744 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 12~), dh-exec, help2man, libbz2-dev, zlib1g-dev Filtered Build-Depends: debhelper (>= 12~), dh-exec, help2man, libbz2-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-gmap-dummy' in '/<>/resolver-BT28SC/apt_archive/sbuild-build-depends-gmap-dummy.deb'. Ign:1 copy:/<>/resolver-BT28SC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-BT28SC/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-BT28SC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-BT28SC/apt_archive ./ Sources [239 B] Get:5 copy:/<>/resolver-BT28SC/apt_archive ./ Packages [557 B] Fetched 2915 B in 0s (252 kB/s) Reading package lists... 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-exec dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-gmap-dummy zlib1g-dev 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 17.4 MB of archives. After this operation, 66.5 MB of additional disk space will be used. Get:1 copy:/<>/resolver-BT28SC/apt_archive ./ sbuild-build-depends-gmap-dummy 0.invalid.0 [884 B] Get:2 http://ftpmaster.internal/ubuntu eoan/main amd64 liblocale-gettext-perl amd64 1.07-3build3 [16.4 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:5 http://ftpmaster.internal/ubuntu eoan/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main amd64 groff-base amd64 1.22.4-3 [862 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main amd64 libpipeline1 amd64 1.5.1-2 [25.9 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/main amd64 man-db amd64 2.8.7-3 [1113 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main amd64 libmagic-mgc amd64 1:5.37-5 [209 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main amd64 libmagic1 amd64 1:5.37-5 [75.4 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main amd64 file amd64 1:5.37-5 [23.2 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/main amd64 libelf1 amd64 0.176-1.1 [44.1 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main amd64 libglib2.0-0 amd64 2.62.0-1 [1264 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/main amd64 libicu63 amd64 63.2-2 [8294 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main amd64 libxml2 amd64 2.9.4+dfsg1-7ubuntu3 [625 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main amd64 gettext-base amd64 0.19.8.1-9 [50.1 kB] Get:17 http://ftpmaster.internal/ubuntu eoan/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main amd64 m4 amd64 1.4.18-2 [199 kB] Get:19 http://ftpmaster.internal/ubuntu eoan/main amd64 autoconf all 2.69-11 [322 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main amd64 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main amd64 autopoint all 0.19.8.1-9 [412 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main amd64 libtool all 2.4.6-11 [194 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main amd64 dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main amd64 libarchive-zip-perl all 1.65-1 [83.6 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:27 http://ftpmaster.internal/ubuntu eoan/main amd64 libfile-stripnondeterminism-perl all 1.6.0-1 [16.2 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main amd64 dh-strip-nondeterminism all 1.6.0-1 [5208 B] Get:29 http://ftpmaster.internal/ubuntu eoan/main amd64 dwz amd64 0.13-1 [80.0 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:31 http://ftpmaster.internal/ubuntu eoan/main amd64 gettext amd64 0.19.8.1-9 [896 kB] Get:32 http://ftpmaster.internal/ubuntu eoan/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main amd64 po-debconf all 1.0.21 [233 kB] Get:34 http://ftpmaster.internal/ubuntu eoan/main amd64 debhelper all 12.4ubuntu1 [910 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/universe amd64 help2man amd64 1.47.11 [172 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main amd64 libbz2-dev amd64 1.0.6-9.2 [30.2 kB] Get:37 http://ftpmaster.internal/ubuntu eoan/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1ubuntu3 [172 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main amd64 dh-exec amd64 0.23.2 [25.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.4 MB in 1s (11.6 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12744 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3build3_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3build3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_11.1.2ubuntu2_amd64.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../03-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../04-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../05-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... 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Selecting previously unselected package sbuild-build-depends-gmap-dummy. Preparing to unpack .../37-sbuild-build-depends-gmap-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-gmap-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up libarchive-zip-perl (1.65-1) ... Setting up libglib2.0-0:amd64 (2.62.0-1) ... No schema files found: doing nothing. Setting up libmagic1:amd64 (1:5.37-5) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-5) ... Setting up libicu63:amd64 (63.2-2) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1ubuntu3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7ubuntu3) ... Setting up liblocale-gettext-perl (1.07-3build3) ... Setting up libbz2-dev:amd64 (1.0.6-9.2) ... Setting up libfile-stripnondeterminism-perl (1.6.0-1) ... Setting up libtool (2.4.6-11) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.11) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up debhelper (12.4ubuntu1) ... Setting up dh-exec (0.23.2) ... Setting up sbuild-build-depends-gmap-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-161-generic amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190905-0ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-8ubuntu1 gcc-9_9.2.1-8ubuntu1 libc6-dev_2.30-0ubuntu1 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 linux-libc-dev_5.3.0-10.11 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.3 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2ubuntu6 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.32.51.20190905-0ubuntu1 binutils-common_2.32.51.20190905-0ubuntu1 binutils-x86-64-linux-gnu_2.32.51.20190905-0ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.7ubuntu1 bzip2_1.0.6-9.2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-8ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.4ubuntu1 debianutils_4.8.6.3 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-1 e2fsprogs_1.45.3-4ubuntu1 fakeroot_1.23-1 fdisk_2.34-0.1ubuntu2 file_1:5.37-5 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-8ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-8ubuntu1 gcc-9-base_9.2.1-8ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.10-0ubuntu3 help2man_1.47.11 hostname_3.22 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapparmor1_2.13.3-5ubuntu1 libapt-pkg5.90_1.9.3 libarchive-zip-perl_1.65-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-8ubuntu1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-8ubuntu1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2ubuntu1 libaudit1_1:2.8.5-2ubuntu1 libbinutils_2.32.51.20190905-0ubuntu1 libblkid1_2.34-0.1ubuntu2 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.2 libbz2-dev_1.0.6-9.2 libc-bin_2.30-0ubuntu1 libc-dev-bin_2.30-0ubuntu1 libc6_2.30-0ubuntu1 libc6-dev_2.30-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_9.2.1-8ubuntu1 libcom-err2_1.45.3-4ubuntu1 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.0-3ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.249ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu6 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1 libext2fs2_1.45.3-4ubuntu1 libfakeroot_1.23-1 libfdisk1_2.34-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.0-1 libgcc-9-dev_9.2.1-8ubuntu1 libgcc1_1:9.2.1-8ubuntu1 libgcrypt20_1.8.4-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.0-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4build1 libgomp1_9.2.1-8ubuntu1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn11_1.33-2.2ubuntu2 libidn2-0_2.2.0-1 libip4tc2_1.8.3-2ubuntu2 libisl21_0.21-2 libitm1_9.2.1-8ubuntu1 libjson-c4_0.13.1+dfsg-4 libkmod2_26-1ubuntu1 liblocale-gettext-perl_1.07-3build3 liblockfile-bin_1.15-1 liblockfile1_1.15-1 liblsan0_9.2.1-8ubuntu1 liblz4-1_1.9.1-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1ubuntu1 libncursesw6_6.1+20190803-1ubuntu1 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.16.1-2 libpam-modules_1.3.1-5ubuntu1 libpam-modules-bin_1.3.1-5ubuntu1 libpam-runtime_1.3.1-5ubuntu1 libpam0g_1.3.1-5ubuntu1 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libquadmath0_9.2.1-8ubuntu1 libreadline8_8.0-3 libseccomp2_2.4.1-0ubuntu0.19.10.3 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu2 libsqlite3-0_3.29.0-2 libss2_1.45.3-4ubuntu1 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 libsub-override-perl_0.09-2 libsystemd0_241-7ubuntu1 libtasn1-6_4.14-2 libtinfo6_6.1+20190803-1ubuntu1 libtool_2.4.6-11 libtsan0_9.2.1-8ubuntu1 libubsan1_9.2.1-8ubuntu1 libuchardet0_0.0.6-3 libudev1_241-7ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu2 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.3.0-10.11 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu1 lsb-base_11.0.1ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17ubuntu3 mount_2.34-0.1ubuntu2 ncurses-base_6.1+20190803-1ubuntu1 ncurses-bin_6.1+20190803-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gmap-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_241-7ubuntu1 systemd-sysv_241-7ubuntu1 sysvinit-utils_2.95-5ubuntu2 tar_1.30+dfsg-6 tzdata_2019b-2 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Jun 6 09:56:59 2019 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gmap_2019-05-12-1.dsc dpkg-source: info: extracting gmap in gmap-2019-05-12 dpkg-source: info: unpacking gmap_2019-05-12.orig.tar.xz dpkg-source: info: unpacking gmap_2019-05-12-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying only-do-cpuid-on-amd64-i386.patch dpkg-source: info: applying install-data-local Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-17551316 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17551316 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17551316 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2019-05-12-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' configure.ac:111: installing 'config/compile' configure.ac:116: installing 'config/missing' src/Makefile.am: installing 'config/depcomp' src/Makefile.am:208: warning: variable 'dist_gmap_nosimd_SOURCES' is defined but no program or src/Makefile.am:208: library has 'gmap_nosimd' as canonical name (possible typo) src/Makefile.am:300: warning: variable 'dist_gmapl_nosimd_SOURCES' is defined but no program or src/Makefile.am:300: library has 'gmapl_nosimd' as canonical name (possible typo) src/Makefile.am:397: warning: variable 'dist_gsnap_nosimd_SOURCES' is defined but no program or src/Makefile.am:397: library has 'gsnap_nosimd' as canonical name (possible typo) src/Makefile.am:497: warning: variable 'dist_gsnapl_nosimd_SOURCES' is defined but no program or src/Makefile.am:497: library has 'gsnapl_nosimd' as canonical name (possible typo) src/Makefile.am:883: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or src/Makefile.am:883: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:593: warning: variable 'dist_uniqscan_SOURCES' is defined but no program or src/Makefile.am:593: library has 'uniqscan' as canonical name (possible typo) src/Makefile.am:648: warning: variable 'dist_uniqscanl_SOURCES' is defined but no program or src/Makefile.am:648: library has 'uniqscanl' as canonical name (possible typo) src/Makefile.am:207: warning: variable 'gmap_nosimd_LDADD' is defined but no program or src/Makefile.am:207: library has 'gmap_nosimd' as canonical name (possible typo) src/Makefile.am:299: warning: variable 'gmapl_nosimd_LDADD' is defined but no program or src/Makefile.am:299: library has 'gmapl_nosimd' as canonical name (possible typo) src/Makefile.am:396: warning: variable 'gsnap_nosimd_LDADD' is defined but no program or src/Makefile.am:396: library has 'gsnap_nosimd' as canonical name (possible typo) src/Makefile.am:496: warning: variable 'gsnapl_nosimd_LDADD' is defined but no program or src/Makefile.am:496: library has 'gsnapl_nosimd' as canonical name (possible typo) src/Makefile.am:882: warning: variable 'iit_pileup_LDADD' is defined but no program or src/Makefile.am:882: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:591: warning: variable 'uniqscan_LDADD' is defined but no program or src/Makefile.am:591: library has 'uniqscan' as canonical name (possible typo) src/Makefile.am:646: warning: variable 'uniqscanl_LDADD' is defined but no program or src/Makefile.am:646: library has 'uniqscanl' as canonical name (possible typo) src/Makefile.am:206: warning: variable 'gmap_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:206: library has 'gmap_nosimd' as canonical name (possible typo) src/Makefile.am:298: warning: variable 'gmapl_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:298: library has 'gmapl_nosimd' as canonical name (possible typo) src/Makefile.am:395: warning: variable 'gsnap_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:395: library has 'gsnap_nosimd' as canonical name (possible typo) src/Makefile.am:495: warning: variable 'gsnapl_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:495: library has 'gsnapl_nosimd' as canonical name (possible typo) src/Makefile.am:881: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or src/Makefile.am:881: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:590: warning: variable 'uniqscan_LDFLAGS' is defined but no program or src/Makefile.am:590: library has 'uniqscan' as canonical name (possible typo) src/Makefile.am:645: warning: variable 'uniqscanl_LDFLAGS' is defined but no program or src/Makefile.am:645: library has 'uniqscanl' as canonical name (possible typo) debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap ./configure --build=x86_64-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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap checking package version... 2019-05-12 loading default site script ./config.site checking CFLAGS... -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 whether gcc understands -c and -o together... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no 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 whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no 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 understands -c and -o together... (cached) yes checking how to print strings... printf 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 how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop 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 dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no 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... yes 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 -m elf_x86_64) 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 C compiler vendor... gnu 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 for inline... inline 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... 8 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 disabled by default 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 whether C compiler accepts -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -mpopcnt... yes checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking compiler is defective and requires an immediate in sse2 shift commands... no checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... not specified so enabled by default checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2... yes checking for immintrin.h header file... yes checking gmapdb... /var/cache/gmap checking MAX_STACK_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 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/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_transcript_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 util/sam-exons.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 checking standard compiler and flags to be used... gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security checking standard linker flags to be used... checking pthread compiler flags to be used... -pthread checking popcnt flags to be used... -mpopcnt checking compile level... avx2 checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 make[1]: Leaving directory '/<>' dh_auto_build make -j4 make[1]: Entering directory '/<>' Making all in src make[2]: Entering directory '/<>/src' make all-am make[3]: Entering directory '/<>/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo './'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo './'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | 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 -fdebug-prefix-map=/<>=. -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 access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | 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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-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 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:2006:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2006 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-epu16-bitpack64-access.o `test -f 'epu16-bitpack64-access.c' || echo './'`epu16-bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-epu16-bitpack64-incr.o `test -f 'epu16-bitpack64-incr.c' || echo './'`epu16-bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-epu16-bitpack64-write.o `test -f 'epu16-bitpack64-write.c' || echo './'`epu16-bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo './'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-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 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo './'`parserange.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo './'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo './'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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 -fdebug-prefix-map=/<>=. -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 access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:2006:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2006 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-getline.o `test -f 'getline.c' || echo './'`getline.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | 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 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-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] 14 | 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] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_char’: 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-epu16-bitpack64-read.o `test -f 'epu16-bitpack64-read.c' || echo './'`epu16-bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-epu16-bitpack64-access.o `test -f 'epu16-bitpack64-access.c' || echo './'`epu16-bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-epu16-bitpack64-incr.o `test -f 'epu16-bitpack64-incr.c' || echo './'`epu16-bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-epu16-bitpack64-write.o `test -f 'epu16-bitpack64-write.c' || echo './'`epu16-bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:2006:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2006 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-localdb.o `test -f 'localdb.c' || echo './'`localdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-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 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-epu16-bitpack64-read.o `test -f 'epu16-bitpack64-read.c' || echo './'`epu16-bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-epu16-bitpack64-access.o `test -f 'epu16-bitpack64-access.c' || echo './'`epu16-bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-epu16-bitpack64-incr.o `test -f 'epu16-bitpack64-incr.c' || echo './'`epu16-bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-epu16-bitpack64-write.o `test -f 'epu16-bitpack64-write.c' || echo './'`epu16-bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:2006:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2006 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-localdb.o `test -f 'localdb.c' || echo './'`localdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-interval.o `test -f 'interval.c' || echo './'`interval.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-trindex.o `test -f 'trindex.c' || echo './'`trindex.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:207:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 207 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:212:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 212 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c samread.c: In function ‘Samread_print_as_duplicate_fromfile’: samread.c:1516:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1516 | fread(buffer,sizeof(char),CHUNK,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samread.c:1521:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1521 | 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c sam_sort.c: In function ‘Cell_print_fromfile’: sam_sort.c:403:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 403 | fread(buffer,sizeof(char),CHUNK,fp_input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c:408:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 408 | fread(buffer,sizeof(char),linelength,fp_input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo './'`md5.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:2006:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2006 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-epu16-bitpack64-read.o `test -f 'epu16-bitpack64-read.c' || echo './'`epu16-bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-epu16-bitpack64-readtwo.o `test -f 'epu16-bitpack64-readtwo.c' || echo './'`epu16-bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:3146:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3146 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3142:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3142 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3123:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3123 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3119:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3119 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3112:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3112 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3107:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3107 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3038:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3038 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3035:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3035 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3032:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3032 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3209:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3209 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3206:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3206 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3203:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3203 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c pair.c: In function ‘Pair_compute_cigar’: pair.c:5196:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5196 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5200:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5200 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5321:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5321 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5369:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5369 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5365:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5365 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5351:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5351 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5347:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5347 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5339:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5339 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5334:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5334 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5235:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5235 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5232:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5232 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5229:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5229 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5399:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5399 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5396:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5396 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5393:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5393 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5422:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5422 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5426:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5426 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5416:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5416 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5477:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5477 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5481:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5481 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5605:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5605 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5661:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5661 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5657:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5657 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5690:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5690 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5678:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5678 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5643:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5643 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5639:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5639 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5635:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5635 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5627:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5627 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5622:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5622 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5618:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5618 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5519:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5519 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5516:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5516 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5513:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5513 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5510:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5510 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5724:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5721:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5721 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5718:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5718 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5715:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5715 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5747:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5747 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5751:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5751 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5741:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5741 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5735:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5735 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:207:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 207 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:212:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 212 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1950:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1950 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1954:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1954 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-epu16-bitpack64-read.o `test -f 'epu16-bitpack64-read.c' || echo './'`epu16-bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-epu16-bitpack64-readtwo.o `test -f 'epu16-bitpack64-readtwo.c' || echo './'`epu16-bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c pair.c: In function ‘print_gff3_exons_forward.constprop’: pair.c:3146:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3146 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3142:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3142 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3123:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3123 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3119:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3119 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3112:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3112 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3107:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3107 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3038:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3038 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3035:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3035 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3032:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3032 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3209:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3209 | sprintf(token,"D%d",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3206:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3206 | sprintf(token,"I%d",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:3203:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 3203 | sprintf(token,"M%d",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c pair.c: In function ‘Pair_compute_cigar’: pair.c:5196:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5196 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5200:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5200 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5321:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5321 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5369:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5369 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5365:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5365 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5351:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5351 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5347:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5347 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5339:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5339 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5334:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5334 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5235:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5235 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5232:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5232 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5229:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5229 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5399:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5399 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5396:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5396 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5393:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5393 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5422:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5422 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5426:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5426 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5416:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5416 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5477:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5477 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5481:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5481 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5605:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5605 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5661:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5661 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5657:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5657 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5690:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5690 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5678:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5678 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5643:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5643 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5639:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5639 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5635:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5635 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5627:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5627 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5622:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5622 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5618:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5618 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5519:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5519 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5516:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5516 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5513:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5513 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5510:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5510 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5724:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5724 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5721:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5721 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5718:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5718 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5715:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5715 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5747:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5747 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5751:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5751 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5741:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5741 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pair.c:5735:20: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 5735 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from pair.h:9, from pair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:207:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 207 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:212:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 212 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function ‘Transcriptome_new’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:7: note: in expansion of macro ‘FREAD_INT’ 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:179:7: note: in expansion of macro ‘FREAD_INT’ 179 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-epu16-bitpack64-read.o `test -f 'epu16-bitpack64-read.c' || echo './'`epu16-bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-epu16-bitpack64-readtwo.o `test -f 'epu16-bitpack64-readtwo.c' || echo './'`epu16-bitpack64-readtwo.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:2006:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2006 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-localdb.o `test -f 'localdb.c' || echo './'`localdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo './'`junction.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-method.o `test -f 'method.c' || echo './'`method.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c simplepair.c: In function ‘Simplepair_overlap_print_sam’: simplepair.c:559:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 559 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:563:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 563 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:684:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 684 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:732:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 732 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:728:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 728 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:714:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 714 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:710:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 710 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:702:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 702 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:697:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 697 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:598:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 598 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:595:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 595 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:592:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 592 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:762:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 762 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:759:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 759 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:756:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 756 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:785:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 785 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:789:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 789 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:840:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 840 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:844:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 844 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:968:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 968 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1024:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1024 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1020:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1020 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1053:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1053 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1041:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1041 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1006:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1006 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1002:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1002 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:998:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 998 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:990:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 990 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:985:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 985 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:981:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 981 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:882:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 882 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:879:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 879 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:876:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 876 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:873:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 873 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1087:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1087 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1084:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1084 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1081:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1081 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1078:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1078 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1110:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1110 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1114:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1114 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:207:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 207 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:212:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 212 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-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] 14 | 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] 27 | 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] 44 | 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] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 63 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-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] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:215:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:532:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:537:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:543:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:548:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:554:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:559:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c:565:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c access.c:570:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:596:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:598:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:604:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:606:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:612:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:614:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:620:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:622:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1538:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1538 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1542:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1542 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1546:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1546 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1550:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1550 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1554:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1554 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c In file included from iit-read.c:12: iit-read.c: In function ‘IIT_read_divint’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’ 2619 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c iit-read.c: In function ‘IIT_read’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3134:5: note: in expansion of macro ‘FREAD_INT’ 3134 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c iit-read.c: In function ‘read_tree’: iit-read.c:1742:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1742 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1743 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1744:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1744 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1745:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1745 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1746:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1746 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1871:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1871 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1872:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1872 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1874:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1874 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1878:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘read_words’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2126:5: note: in expansion of macro ‘FREAD_UINT8’ 2126 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2132:5: note: in expansion of macro ‘FREAD_UINT’ 2132 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2513:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2513 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2517:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2517 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2522:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2522 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2528:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2528 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2533:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2533 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2544:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2544 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2550:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2550 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2555:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2555 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2566:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 2566 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function ‘IIT_debug’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3547:5: note: in expansion of macro ‘FREAD_INT’ 3547 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:27:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 27 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2270:5: note: in expansion of macro ‘FREAD_UINT8’ 2270 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:22:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 22 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2275:5: note: in expansion of macro ‘FREAD_UINT’ 2275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c genome.c: In function ‘fill_buffer’: genome.c:10592:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10592 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:462:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 462 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from transcriptome.c:28: transcriptome.c: In function ‘Transcriptome_new’: littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:7: note: in expansion of macro ‘FREAD_INT’ 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ littleendian.h:21:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 21 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:179:7: note: in expansion of macro ‘FREAD_INT’ 179 | FREAD_INT(&divint,fp); | ^~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10723:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10723 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10843:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10843 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11012:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11012 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11330:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11330 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-epu16-bitpack64-read.o `test -f 'epu16-bitpack64-read.c' || echo './'`epu16-bitpack64-read.c indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1950:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1950 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1954:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1954 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-epu16-bitpack64-readtwo.o `test -f 'epu16-bitpack64-readtwo.c' || echo './'`epu16-bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-localdb.o `test -f 'localdb.c' || echo './'`localdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-substring.o `test -f 'substring.c' || echo './'`substring.c substring.c: In function ‘Substring_print_alts_coords’: substring.c:3594:15: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long long unsigned int’} [-Wformat=] 3594 | printf(" %u",this->alts_coords[i] - this->chroffset); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo './'`junction.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo './'`method.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c simplepair.c: In function ‘Simplepair_overlap_print_sam’: simplepair.c:559:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 559 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:563:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 563 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:684:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 684 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:732:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 732 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:728:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 728 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:714:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 714 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:710:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 710 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:702:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 702 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:697:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 697 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:598:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 598 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:595:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 595 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:592:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 592 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:762:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 762 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:759:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 759 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:756:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 756 | sprintf(token,"%dM",Mlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:785:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 785 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:789:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 789 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:840:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 840 | sprintf(token,"%dH",*hardclip_start); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:844:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 844 | sprintf(token,"%dS",ptr->querypos - (*hardclip_start)); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:968:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 968 | sprintf(token,"%uI",query_gap); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1024:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1024 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1020:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1020 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1053:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1053 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1041:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1041 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1006:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1006 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1002:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1002 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:998:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 998 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:990:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 990 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:985:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 985 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:981:24: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 981 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:882:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 882 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:879:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 879 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:876:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 876 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:873:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 873 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1087:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1087 | sprintf(token,"%dD",Dlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1084:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1084 | sprintf(token,"%dI",Ilength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1081:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1081 | sprintf(token,"%dX",Xlength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1078:23: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1078 | sprintf(token,"%d=",Elength); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1110:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1110 | sprintf(token,"%dS",querylength_given - 1 - (*hardclip_end) - last_querypos); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simplepair.c:1114:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1114 | sprintf(token,"%dH",*hardclip_end); | ^ In file included from /usr/include/stdio.h:867, from iit-read-univ.h:11, from chrnum.h:8, from simplepair.h:10, from simplepair.c:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:207:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 207 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:212:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 212 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c /bin/bash ../libtool --tag=CC --mode=link gcc -DMAIN=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm libtool: link: gcc -DMAIN=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o cpuid cpuid-cpuid.o -lm libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-fopen.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-getline.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-fopen.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-genome128_consec.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-epu16-bitpack64-access.o gmapindex-epu16-bitpack64-incr.o gmapindex-epu16-bitpack64-write.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-fopen.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-getline.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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-getline.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-fopen.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-genome128_consec.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-epu16-bitpack64-access.o gmapindex-epu16-bitpack64-incr.o gmapindex-epu16-bitpack64-write.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-getline.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-getline.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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-getline.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm libtool: link: gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-genome128_consec.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-genome128_consec.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-epu16-bitpack64-read.o cmetindex-epu16-bitpack64-access.o cmetindex-epu16-bitpack64-incr.o cmetindex-epu16-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-localdb.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lz -lbz2 -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-genome128_consec.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-epu16-bitpack64-read.o atoiindex-epu16-bitpack64-access.o atoiindex-epu16-bitpack64-incr.o atoiindex-epu16-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-localdb.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-genome128_consec.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-genome128_consec.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-epu16-bitpack64-read.o cmetindex-epu16-bitpack64-access.o cmetindex-epu16-bitpack64-incr.o cmetindex-epu16-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-localdb.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.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-genome128_consec.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-epu16-bitpack64-read.o atoiindex-epu16-bitpack64-access.o atoiindex-epu16-bitpack64-incr.o atoiindex-epu16-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-localdb.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-datadir.o trindex-getline.o trindex-getopt.o trindex-getopt1.o trindex-trindex.o -lz -lbz2 -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.o sam_sort-access.o sam_sort-univinterval.o sam_sort-interval.o sam_sort-uintlist.o sam_sort-filestring.o sam_sort-parserange.o sam_sort-iit-read-univ.o sam_sort-iit-read.o sam_sort-samheader.o sam_sort-samread.o sam_sort-getline.o sam_sort-datadir.o sam_sort-getopt.o sam_sort-getopt1.o sam_sort-sam_sort.o -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-genome128_hr.o gmap_avx2-genome_sites.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-epu16-bitpack64-read.o gmap_avx2-epu16-bitpack64-readtwo.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-transcript.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-getopt.o gmap_avx2-getopt1.o gmap_avx2-gmap.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-datadir.o trindex-getline.o trindex-getopt.o trindex-getopt1.o trindex-trindex.o -lz -lbz2 -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-genome128_hr.o gmapl_avx2-genome_sites.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-epu16-bitpack64-read.o gmapl_avx2-epu16-bitpack64-readtwo.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-transcript.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-getopt.o gmapl_avx2-getopt1.o gmapl_avx2-gmap.o -lz -lbz2 -lm libtool: link: gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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-semaphore.o sam_sort-access.o sam_sort-univinterval.o sam_sort-interval.o sam_sort-uintlist.o sam_sort-filestring.o sam_sort-parserange.o sam_sort-iit-read-univ.o sam_sort-iit-read.o sam_sort-samheader.o sam_sort-samread.o sam_sort-getline.o sam_sort-datadir.o sam_sort-getopt.o sam_sort-getopt1.o sam_sort-sam_sort.o -lm -pthread /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genome128_hr.o gsnap_avx2-genome128_consec.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-epu16-bitpack64-read.o gsnap_avx2-epu16-bitpack64-readtwo.o gsnap_avx2-localdb.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-cigar.o gsnap_avx2-samprint.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-substring.o gsnap_avx2-junction.o gsnap_avx2-transcript.o gsnap_avx2-method.o gsnap_avx2-stage3hr.o gsnap_avx2-ladder.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-maxent.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-knownsplicing.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-bitpack64-access.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-intersect.o gsnap_avx2-kmer-search.o gsnap_avx2-path-solve.o gsnap_avx2-extension-search.o gsnap_avx2-segment-search.o gsnap_avx2-terminal.o gsnap_avx2-distant-rna.o gsnap_avx2-distant-dna.o gsnap_avx2-uint8table_rh.o gsnap_avx2-uinttable_rh.o gsnap_avx2-stage1hr.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-outbuffer.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-getopt.o gsnap_avx2-getopt1.o gsnap_avx2-gsnap.o -lz -lbz2 -lm /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genome128_hr.o gsnapl_avx2-genome128_consec.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-merge-diagonals-heap.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-epu16-bitpack64-read.o gsnapl_avx2-epu16-bitpack64-readtwo.o gsnapl_avx2-localdb.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-cigar.o gsnapl_avx2-samprint.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-substring.o gsnapl_avx2-junction.o gsnapl_avx2-transcript.o gsnapl_avx2-method.o gsnapl_avx2-stage3hr.o gsnapl_avx2-ladder.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-maxent.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-intersect.o gsnapl_avx2-intersect-large.o gsnapl_avx2-kmer-search.o gsnapl_avx2-path-solve.o gsnapl_avx2-extension-search.o gsnapl_avx2-segment-search.o gsnapl_avx2-terminal.o gsnapl_avx2-distant-rna.o gsnapl_avx2-distant-dna.o gsnapl_avx2-uint8table_rh.o gsnapl_avx2-stage1hr.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-outbuffer.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-getopt.o gsnapl_avx2-getopt1.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm libtool: link: gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-genome128_hr.o gmap_avx2-genome_sites.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-epu16-bitpack64-read.o gmap_avx2-epu16-bitpack64-readtwo.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-transcript.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-getopt.o gmap_avx2-getopt1.o gmap_avx2-gmap.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-genome128_hr.o gmapl_avx2-genome_sites.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-epu16-bitpack64-read.o gmapl_avx2-epu16-bitpack64-readtwo.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-transcript.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-getopt.o gmapl_avx2-getopt1.o gmapl_avx2-gmap.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genome128_hr.o gsnap_avx2-genome128_consec.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-epu16-bitpack64-read.o gsnap_avx2-epu16-bitpack64-readtwo.o gsnap_avx2-localdb.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-cigar.o gsnap_avx2-samprint.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-substring.o gsnap_avx2-junction.o gsnap_avx2-transcript.o gsnap_avx2-method.o gsnap_avx2-stage3hr.o gsnap_avx2-ladder.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-maxent.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-knownsplicing.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-bitpack64-access.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-intersect.o gsnap_avx2-kmer-search.o gsnap_avx2-path-solve.o gsnap_avx2-extension-search.o gsnap_avx2-segment-search.o gsnap_avx2-terminal.o gsnap_avx2-distant-rna.o gsnap_avx2-distant-dna.o gsnap_avx2-uint8table_rh.o gsnap_avx2-uinttable_rh.o gsnap_avx2-stage1hr.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-outbuffer.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-getopt.o gsnap_avx2-getopt1.o gsnap_avx2-gsnap.o -lz -lbz2 -lm -pthread libtool: link: gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genome128_hr.o gsnapl_avx2-genome128_consec.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-merge-diagonals-heap.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-epu16-bitpack64-read.o gsnapl_avx2-epu16-bitpack64-readtwo.o gsnapl_avx2-localdb.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-cigar.o gsnapl_avx2-samprint.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-substring.o gsnapl_avx2-junction.o gsnapl_avx2-transcript.o gsnapl_avx2-method.o gsnapl_avx2-stage3hr.o gsnapl_avx2-ladder.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-maxent.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-intersect.o gsnapl_avx2-intersect-large.o gsnapl_avx2-kmer-search.o gsnapl_avx2-path-solve.o gsnapl_avx2-extension-search.o gsnapl_avx2-segment-search.o gsnapl_avx2-terminal.o gsnapl_avx2-distant-rna.o gsnapl_avx2-distant-dna.o gsnapl_avx2-uint8table_rh.o gsnapl_avx2-stage1hr.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-outbuffer.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-getopt.o gsnapl_avx2-getopt1.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm -pthread make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' Making all in util make[2]: Entering directory '/<>/util' cp gmap_compress.pl gmap_compress cp gmap_uncompress.pl gmap_uncompress cp gmap_process.pl gmap_process chmod +x gmap_compress chmod +x gmap_uncompress chmod +x gmap_process cp gmap_build.pl gmap_build cp gmap_reassemble.pl gmap_reassemble cp md_coords.pl md_coords chmod +x gmap_build chmod +x gmap_reassemble chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites cp psl_introns.pl psl_introns chmod +x fa_coords chmod +x psl_splicesites cp psl_genes.pl psl_genes chmod +x psl_introns cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x psl_genes chmod +x ensembl_genes chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_introns chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes chmod +x gff3_introns cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit make[2]: Leaving directory '/<>/util' Making all in tests make[2]: Entering directory '/<>/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/tests' make[2]: Entering directory '/<>' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test --no-parallel make -j1 check VERBOSE=1 make[2]: Entering directory '/<>' Making check in src make[3]: Entering directory '/<>/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/src' Making check in util make[3]: Entering directory '/<>/util' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/util' Making check in tests make[3]: Entering directory '/<>/tests' make check-TESTS make[4]: Entering directory '/<>/tests' make[5]: Entering directory '/<>/tests' PASS: align.test PASS: coords1.test PASS: setup1.test PASS: iit.test ============================================================================ Testsuite summary for gmap 2019-05-12 ============================================================================ # TOTAL: 4 # PASS: 4 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/<>/tests' make[4]: Leaving directory '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p /<>/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string=2019-05-12-1 --name='Genomic Mapping and Alignment Program' \ /<>/src/gmap |debian/filter.pl >/<>/debian/gmap/usr/share/man/man1/gmap.1 /usr/bin/help2man --no-info --version-string=2019-05-12-1 --name='Genomic Short-read Nucleotide Alignment Program' \ /<>/src/gsnap |debian/filter.pl >/<>/debian/gmap/usr/share/man/man1/gsnap.1 /usr/bin/help2man --no-info --version-string=2019-05-12-1 --name='Tool for genome database creation for GMAP or GSNAP' \ /<>/util/gmap_build |debian/filter.pl >/<>/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install make -j1 install DESTDIR=/<>/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in src make[3]: Entering directory '/<>/src' make[4]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/gmap/usr/lib/gmap' /bin/bash ../libtool --mode=install /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex sam_sort gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/<>/debian/gmap/usr/lib/gmap' libtool: install: /usr/bin/install -c cpuid /<>/debian/gmap/usr/lib/gmap/cpuid libtool: install: /usr/bin/install -c gmap /<>/debian/gmap/usr/lib/gmap/gmap libtool: install: /usr/bin/install -c gmapl /<>/debian/gmap/usr/lib/gmap/gmapl libtool: install: /usr/bin/install -c get-genome /<>/debian/gmap/usr/lib/gmap/get-genome libtool: install: /usr/bin/install -c gmapindex /<>/debian/gmap/usr/lib/gmap/gmapindex libtool: install: /usr/bin/install -c iit_store /<>/debian/gmap/usr/lib/gmap/iit_store libtool: install: /usr/bin/install -c iit_get /<>/debian/gmap/usr/lib/gmap/iit_get libtool: install: /usr/bin/install -c iit_dump /<>/debian/gmap/usr/lib/gmap/iit_dump libtool: install: /usr/bin/install -c gsnap /<>/debian/gmap/usr/lib/gmap/gsnap libtool: install: /usr/bin/install -c gsnapl /<>/debian/gmap/usr/lib/gmap/gsnapl libtool: install: /usr/bin/install -c snpindex /<>/debian/gmap/usr/lib/gmap/snpindex libtool: install: /usr/bin/install -c cmetindex /<>/debian/gmap/usr/lib/gmap/cmetindex libtool: install: /usr/bin/install -c atoiindex /<>/debian/gmap/usr/lib/gmap/atoiindex libtool: install: /usr/bin/install -c trindex /<>/debian/gmap/usr/lib/gmap/trindex libtool: install: /usr/bin/install -c sam_sort /<>/debian/gmap/usr/lib/gmap/sam_sort libtool: install: /usr/bin/install -c gmap.avx2 /<>/debian/gmap/usr/lib/gmap/gmap.avx2 libtool: install: /usr/bin/install -c gmapl.avx2 /<>/debian/gmap/usr/lib/gmap/gmapl.avx2 libtool: install: /usr/bin/install -c gsnap.avx2 /<>/debian/gmap/usr/lib/gmap/gsnap.avx2 libtool: install: /usr/bin/install -c gsnapl.avx2 /<>/debian/gmap/usr/lib/gmap/gsnapl.avx2 make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' Making install in util make[3]: Entering directory '/<>/util' make[4]: Entering directory '/<>/util' /bin/mkdir -p '/<>/debian/gmap/usr/lib/gmap' /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 gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/<>/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/util' make[3]: Leaving directory '/<>/util' Making install in tests make[3]: Entering directory '/<>/tests' make[4]: Entering directory '/<>/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 '/<>/tests' make[3]: Leaving directory '/<>/tests' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' mkdir -p debian/gmap/usr/bin dh_install for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \ cd /<>/debian/gmap/usr/lib/gmap/; \ ls -1 gmap*.* gsnap*.* `; do \ ln -s /usr/lib/gmap/$bin debian/gmap/usr/bin/$bin; \ done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/<>' mkdir /<>/debian/gmap/usr/share/doc/gmap/examples tar --sort=name \ --mtime="@1559814814" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ -cJf /<>/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests make[1]: Leaving directory '/<>' dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 144 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_2019-05-12-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../gmap_2019-05-12-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190914-0159 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gmap_2019-05-12-1_amd64.changes: -------------------------------- Format: 1.8 Date: Thu, 06 Jun 2019 11:53:34 +0200 Source: gmap Binary: gmap Architecture: amd64 Version: 2019-05-12-1 Distribution: eoan Urgency: low Maintainer: Launchpad Build Daemon Changed-By: Steffen Moeller Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2019-05-12-1) unstable; urgency=low . * Team upload. . * New upstream version. Checksums-Sha1: 85603796c2692409c66c95454ec0dde610e470aa 4859 gmap_2019-05-12-1_amd64.buildinfo 19928c0c9db9f3960e6df0cb596d55dac73cf4a3 5745064 gmap_2019-05-12-1_amd64.deb Checksums-Sha256: bb248c2a00a708b8d7d7eb937a7a045baf52143c99aba42035196fcedd35910a 4859 gmap_2019-05-12-1_amd64.buildinfo 747f898e98132f0fc3a580dc5c24b25df21ebeefb36549fecb48d831b9ff51af 5745064 gmap_2019-05-12-1_amd64.deb Files: c1d51f2076f3afa68acd6d7e6e7abf31 4859 non-free/science optional gmap_2019-05-12-1_amd64.buildinfo 80e453c224de2530c8bd227c5f3e7ec9 5745064 non-free/science optional gmap_2019-05-12-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gmap_2019-05-12-1_amd64.deb --------------------------- new debian package, version 2.0. size 5745064 bytes: control archive=2188 bytes. 1002 bytes, 21 lines control 3050 bytes, 51 lines md5sums Package: gmap Version: 2019-05-12-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 51965 Depends: perl:any, libbz2-1.0, libc6 (>= 2.29), 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 2019-06-06 09:53 ./ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/bin/ lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gmap -> ../lib/gmap/gmap lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gmap.avx2 -> ../lib/gmap/gmap.avx2 lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gmap_build -> ../lib/gmap/gmap_build lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gmapl -> ../lib/gmap/gmapl lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gmapl.avx2 -> ../lib/gmap/gmapl.avx2 lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gsnap -> ../lib/gmap/gsnap lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gsnap.avx2 -> ../lib/gmap/gsnap.avx2 lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gsnapl -> ../lib/gmap/gsnapl lrwxrwxrwx root/root 0 2019-06-06 09:53 ./usr/bin/gsnapl.avx2 -> ../lib/gmap/gsnapl.avx2 drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/lib/ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/lib/gmap/ -rwxr-xr-x root/root 4205352 2019-06-06 09:53 ./usr/lib/gmap/atoiindex -rwxr-xr-x root/root 4205352 2019-06-06 09:53 ./usr/lib/gmap/cmetindex -rwxr-xr-x root/root 14640 2019-06-06 09:53 ./usr/lib/gmap/cpuid -rwxr-xr-x root/root 7863 2019-06-06 09:53 ./usr/lib/gmap/dbsnp_iit -rwxr-xr-x root/root 1256 2019-06-06 09:53 ./usr/lib/gmap/ensembl_genes -rwxr-xr-x root/root 20056 2019-06-06 09:53 ./usr/lib/gmap/fa_coords -rwxr-xr-x root/root 2924040 2019-06-06 09:53 ./usr/lib/gmap/get-genome -rwxr-xr-x root/root 6268 2019-06-06 09:53 ./usr/lib/gmap/gff3_genes -rwxr-xr-x root/root 14312 2019-06-06 09:53 ./usr/lib/gmap/gff3_introns -rwxr-xr-x root/root 15883 2019-06-06 09:53 ./usr/lib/gmap/gff3_splicesites -rwxr-xr-x root/root 14640 2019-06-06 09:53 ./usr/lib/gmap/gmap -rwxr-xr-x root/root 8829736 2019-06-06 09:53 ./usr/lib/gmap/gmap.avx2 -rwxr-xr-x root/root 16444 2019-06-06 09:53 ./usr/lib/gmap/gmap_build -rwxr-xr-x root/root 10487 2019-06-06 09:53 ./usr/lib/gmap/gmap_compress -rwxr-xr-x root/root 6421 2019-06-06 09:53 ./usr/lib/gmap/gmap_process -rwxr-xr-x root/root 533 2019-06-06 09:53 ./usr/lib/gmap/gmap_reassemble -rwxr-xr-x root/root 16519 2019-06-06 09:53 ./usr/lib/gmap/gmap_uncompress -rwxr-xr-x root/root 3693072 2019-06-06 09:53 ./usr/lib/gmap/gmapindex -rwxr-xr-x root/root 14640 2019-06-06 09:53 ./usr/lib/gmap/gmapl -rwxr-xr-x root/root 8842024 2019-06-06 09:53 ./usr/lib/gmap/gmapl.avx2 -rwxr-xr-x root/root 14640 2019-06-06 09:53 ./usr/lib/gmap/gsnap -rwxr-xr-x root/root 7674504 2019-06-06 09:53 ./usr/lib/gmap/gsnap.avx2 -rwxr-xr-x root/root 14640 2019-06-06 09:53 ./usr/lib/gmap/gsnapl -rwxr-xr-x root/root 7690888 2019-06-06 09:53 ./usr/lib/gmap/gsnapl.avx2 -rwxr-xr-x root/root 5492 2019-06-06 09:53 ./usr/lib/gmap/gtf_genes -rwxr-xr-x root/root 11407 2019-06-06 09:53 ./usr/lib/gmap/gtf_introns -rwxr-xr-x root/root 12630 2019-06-06 09:53 ./usr/lib/gmap/gtf_splicesites -rwxr-xr-x root/root 13846 2019-06-06 09:53 ./usr/lib/gmap/gtf_transcript_splicesites -rwxr-xr-x root/root 1367 2019-06-06 09:53 ./usr/lib/gmap/gvf_iit -rwxr-xr-x root/root 162472 2019-06-06 09:53 ./usr/lib/gmap/iit_dump -rwxr-xr-x root/root 179176 2019-06-06 09:53 ./usr/lib/gmap/iit_get -rwxr-xr-x root/root 109264 2019-06-06 09:53 ./usr/lib/gmap/iit_store -rwxr-xr-x root/root 29421 2019-06-06 09:53 ./usr/lib/gmap/md_coords -rwxr-xr-x root/root 1177 2019-06-06 09:53 ./usr/lib/gmap/psl_genes -rwxr-xr-x root/root 5915 2019-06-06 09:53 ./usr/lib/gmap/psl_introns -rwxr-xr-x root/root 6985 2019-06-06 09:53 ./usr/lib/gmap/psl_splicesites -rwxr-xr-x root/root 199528 2019-06-06 09:53 ./usr/lib/gmap/sam_sort -rwxr-xr-x root/root 3644232 2019-06-06 09:53 ./usr/lib/gmap/snpindex -rwxr-xr-x root/root 191016 2019-06-06 09:53 ./usr/lib/gmap/trindex -rwxr-xr-x root/root 1567 2019-06-06 09:53 ./usr/lib/gmap/vcf_iit drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/doc/gmap/ -rw-r--r-- root/root 181 2013-06-27 19:42 ./usr/share/doc/gmap/AUTHORS -rw-r--r-- root/root 1815 2013-07-25 22:08 ./usr/share/doc/gmap/NOTICE.gz -rw-r--r-- root/root 171 2019-06-06 09:51 ./usr/share/doc/gmap/README.Debian -rw-r--r-- root/root 20396 2016-08-16 18:42 ./usr/share/doc/gmap/README.gz -rw-r--r-- root/root 1270 2019-06-06 09:53 ./usr/share/doc/gmap/changelog.Debian.gz -rw-r--r-- root/root 6852 2019-06-06 09:51 ./usr/share/doc/gmap/copyright drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/doc/gmap/examples/ -rw-r--r-- root/root 285784 2019-06-06 09:53 ./usr/share/doc/gmap/examples/tests.tar.xz drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/lintian/ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 89 2019-06-06 09:51 ./usr/share/lintian/overrides/gmap drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/man/ drwxr-xr-x root/root 0 2019-06-06 09:53 ./usr/share/man/man1/ -rw-r--r-- root/root 5393 2019-06-06 09:53 ./usr/share/man/man1/gmap.1.gz -rw-r--r-- root/root 1552 2019-06-06 09:53 ./usr/share/man/man1/gmap_build.1.gz -rw-r--r-- root/root 6777 2019-06-06 09:53 ./usr/share/man/man1/gsnap.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 327448 Build-Time: 138 Distribution: eoan Host Architecture: amd64 Install-Time: 10 Job: gmap_2019-05-12-1.dsc Machine Architecture: amd64 Package: gmap Package-Time: 148 Source-Version: 2019-05-12-1 Space: 327448 Status: successful Version: 2019-05-12-1 -------------------------------------------------------------------------------- Finished at 20190914-0159 Build needed 00:02:28, 327448k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=eoan --arch=amd64 PACKAGEBUILD-17551316 Scanning for processes to kill in build PACKAGEBUILD-17551316