I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 30 19:27:40 +14 2021 I: pbuilder-time-stamp: 1627622860 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gmap_2021-02-22+ds-1.dsc] I: copying [./gmap_2021-02-22+ds.orig.tar.xz] I: copying [./gmap_2021-02-22+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.GhwVvd6c/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 26 22:32:25 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gmap_2021-02-22+ds-1.dsc dpkg-source: info: extracting gmap in gmap-2021-02-22+ds dpkg-source: info: unpacking gmap_2021-02-22+ds.orig.tar.xz dpkg-source: info: unpacking gmap_2021-02-22+ds-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 dpkg-source: info: applying remove_getopt_code_copy.patch dpkg-source: info: applying cross I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/21864/tmp/hooks/D01_modify_environment starting debug: Running on virt32a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/21864/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/21864/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=7ac2b1acd08b4947989aad95db714342 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=21864 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.hXGGWQw6Cs/pbuilderrc_6ZN8 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.hXGGWQw6Cs/b2 --logfile b2/build.log --extrapackages usrmerge gmap_2021-02-22+ds-1.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-2 (2021-07-20) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 30 19:27 sh -> bash lrwxrwxrwx 1 root root 4 Jul 26 23:24 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/21864/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), help2man, libbz2-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbz2-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 18.1 MB of archives. After unpacking 64.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf liblocale-gettext-perl armhf 1.07-4+b1 [18.3 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf help2man armhf 1.48.1 [190 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libbz2-dev armhf 1.0.8-4 [29.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Fetched 18.1 MB in 3s (6322 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_armhf.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../05-liblocale-gettext-perl_1.07-4+b1_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../24-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../26-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package help2man. Preparing to unpack .../32-help2man_1.48.1_armhf.deb ... Unpacking help2man (1.48.1) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../33-libbz2-dev_1.0.8-4_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-4) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../34-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libbz2-dev:armhf (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 1s (48.4 kB/s) Selecting previously unselected package libnumber-compare-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21399 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Name or service not known I: Running cd /build/gmap-2021-02-22+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gmap_2021-02-22+ds-1_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2021-02-22+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:106: installing 'config/compile' configure.ac:87: installing 'config/config.guess' configure.ac:87: installing 'config/config.sub' configure.ac:111: installing 'config/install-sh' configure.ac:111: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing 'config/depcomp' src/Makefile.am:901: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or src/Makefile.am:901: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:592: warning: variable 'dist_uniqscan_SOURCES' is defined but no program or src/Makefile.am:592: library has 'uniqscan' as canonical name (possible typo) src/Makefile.am:647: warning: variable 'dist_uniqscanl_SOURCES' is defined but no program or src/Makefile.am:647: library has 'uniqscanl' as canonical name (possible typo) src/Makefile.am:900: warning: variable 'iit_pileup_LDADD' is defined but no program or src/Makefile.am:900: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:590: warning: variable 'uniqscan_LDADD' 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_LDADD' is defined but no program or src/Makefile.am:645: library has 'uniqscanl' as canonical name (possible typo) src/Makefile.am:899: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or src/Makefile.am:899: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:589: warning: variable 'uniqscan_LDFLAGS' is defined but no program or src/Makefile.am:589: library has 'uniqscan' as canonical name (possible typo) src/Makefile.am:644: warning: variable 'uniqscanl_LDFLAGS' is defined but no program or src/Makefile.am:644: library has 'uniqscanl' as canonical name (possible typo) parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gmap-2021-02-22+ds' dh_auto_configure -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap checking package version... 2021-02-22 loading default site script ./config.site checking CFLAGS... -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf 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... 64 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/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 for C compiler vendor... gnu checking for rint in -lm... yes 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required 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 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... 4 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether alloca is enabled... not specified so 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -mpopcnt... no configure: WARNING: Your compiler does not support -mpopcnt checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking for bsr instruction in assembly... yes checking compiler is defective and requires an immediate in sse2 shift commands... yes checking for _mm_extract_epi64... no checking for _mm_popcnt_u64... no checking for whether simd is enabled... not specified so enabled by default checking for sse2 support... no checking for ssse3 support... no checking for sse4.1 support... no checking for sse4.2 support... no checking for popcnt support... no checking for bmi1 support... no checking for avx2 support... no checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no 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_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.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 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 configure: WARNING: WARNING: Your C compiler does not know how to handle a particular form of the SSE2 shift commands, and must be somewhat old (probably gcc 4.1 or gcc 4.2). The configure script has therefore substituted alternate C code that your compiler can handle. However, for optimal performance, you may want to obtain a more recent C compiler and build the code with that. checking standard compiler and flags to be used... gcc -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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... checking compile level... none make[1]: Leaving directory '/build/gmap-2021-02-22+ds' dh_auto_build make -j4 make[1]: Entering directory '/build/gmap-2021-02-22+ds' Making all in src make[2]: Entering directory '/build/gmap-2021-02-22+ds/src' make all-am make[3]: Entering directory '/build/gmap-2021-02-22+ds/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-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=/build/gmap-2021-02-22+ds=. -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 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c regiondb.c: In function 'Regiondb_get_filenames': regiondb.c:1644:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 1644 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 1645 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c In file included from regiondb-write.c:19: regiondb-write.c: In function 'Region_read': littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:478:3: note: in expansion of macro 'FREAD_USHORTS' 478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp); | ^~~~~~~~~~~~~ littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:479:3: note: in expansion of macro 'FREAD_USHORTS' 479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp); | ^~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo './'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c bigendian.c: In function 'Bigendian_write_char': bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_store-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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_get-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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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 access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function 'Bigendian_write_char': bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_char': littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_char': bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c In file included from regiondb-write.c:19: regiondb-write.c: In function 'Region_read': littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:478:3: note: in expansion of macro 'FREAD_USHORTS' 478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp); | ^~~~~~~~~~~~~ littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:479:3: note: in expansion of macro 'FREAD_USHORTS' 479 | FREAD_USHORTS(buffer->positions,REGION_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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c In file included from regiondb-write.c:19: regiondb-write.c: In function 'Region_read': littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:478:3: note: in expansion of macro 'FREAD_USHORTS' 478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp); | ^~~~~~~~~~~~~ littleendian.h:22:31: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:479:3: note: in expansion of macro 'FREAD_USHORTS' 479 | FREAD_USHORTS(buffer->positions,REGION_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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | 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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ samheader.c: In function 'SAM_header_change_HD_tosorted': samheader.c:153:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:158:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-getline.o `test -f 'getline.c' || echo './'`getline.c samread.c: In function 'Samread_flag_duplicate': samread.c:1186:29: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 1186 | sprintf(newflag_string,"%u",flag | DUPLICATE_READ); | ^ In file included from /usr/include/stdio.h:867, from samread.c:6: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 11 bytes into a destination of size 10 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 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -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=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-except.o `test -f 'except.c' || echo './'`except.c sam_sort.c: In function 'process_no_dedup': sam_sort.c:1160:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1160 | fgets(line,linelen+1,fp_sam); /* Will read linelen characters with '\n' and then '\0' */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c: In function 'print_results': sam_sort.c:1012:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1012 | fgets(line,linelen+1,fp_sam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c:1029:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1029 | fgets(line,linelen+1,fp_sam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c: In function 'read_sam_files_for_hashseq': sam_sort.c:1369:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1369 | fgets(line,linelen+1,fp_sam); /* Will read linelen characters with '\n' and then '\0' */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function 'SAM_header_change_HD_tosorted': samheader.c:153:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:158:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c In file included from compress-write.c:21: compress-write.c: In function 'Compress_cat': littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro 'FREAD_UINTS' 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple_large': indexdb.c:1879:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1879 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1883:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1883 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function 'SAM_header_change_HD_tosorted': samheader.c:153:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:158:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function 'Transcriptome_new': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:5: note: in expansion of macro 'FREAD_INT' 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c regiondb.c: In function 'Regiondb_get_filenames': regiondb.c:1644:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 1644 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 1645 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-cigar.o `test -f 'cigar.c' || echo './'`cigar.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo './'`junction.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo './'`method.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-ladder.o `test -f 'ladder.c' || echo './'`ladder.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo './'`concordance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo './'`listpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-intersect.o `test -f 'intersect.c' || echo './'`intersect.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-terminal.o `test -f 'terminal.c' || echo './'`terminal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function 'SAM_header_change_HD_tosorted': samheader.c:153:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:158:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function 'Bigendian_write_char': bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo './'`access.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c access.c: In function 'Access_allocate_shared': access.c:888:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 888 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", | ~~^ | | | long unsigned int | %u 889 | filename,*len); | ~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap': access.c:1015:88: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1015 | fprintf(stderr,"Error in access.c (1): Got mmap failure on file %s with length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1016 | filename,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_offset': access.c:1087:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c:1087:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1087 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1088 | fd,offset,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} access.c: In function 'Access_mmap_and_preload': access.c:1320:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~ | | | size_t {aka unsigned int} access.c:1320:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1320 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ | | | long long int | %d 1321 | filename,*len,length,errno,strerror(errno)); | ~~~~~~ | | | size_t {aka unsigned int} 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1068:2: note: in expansion of macro 'FREAD_INT' 1068 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1069:2: note: in expansion of macro 'FREAD_INT' 1069 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1070:2: note: in expansion of macro 'FREAD_INT' 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1118:7: note: in expansion of macro 'FREAD_UINT8' 1118 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1119:7: note: in expansion of macro 'FREAD_UINT8' 1119 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1120:7: note: in expansion of macro 'FREAD_INT' 1120 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1129:7: note: in expansion of macro 'FREAD_UINT' 1129 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1131:7: note: in expansion of macro 'FREAD_UINT' 1131 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_words': littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1386:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1386 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1390:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1390 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1394:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1394 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1398 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1402:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | 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:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1275:3: note: in expansion of macro 'FREAD_UINT' 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function 'IIT_read': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_tree': iit-read.c:1760:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function 'read_intervals': iit-read.c:1889:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro 'FREAD_UINT8' 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function 'read_annotations': iit-read.c:2482:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro 'FREAD_INT' 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro 'FREAD_UINT8' 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function 'Transcriptome_new': littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:5: note: in expansion of macro 'FREAD_INT' 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:928:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 928 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 929 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int indexdb.c: In function 'positions_read_multiple_large': indexdb.c:1879:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1879 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1883:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1883 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb.c: In function 'Regiondb_get_filenames': regiondb.c:1644:85: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 1644 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", | ~~^ | | | long int | %d 1645 | idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); | ~~~ | | | int gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-cigar.o `test -f 'cigar.c' || echo './'`cigar.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-samprint.o `test -f 'samprint.c' || echo './'`samprint.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo './'`mapq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo './'`shortread.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-substring.o `test -f 'substring.c' || echo './'`substring.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo './'`junction.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo './'`method.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-ladder.o `test -f 'ladder.c' || echo './'`ladder.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo './'`concordance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo './'`listpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo './'`splice.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo './'`indel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-intersect.o `test -f 'intersect.c' || echo './'`intersect.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-terminal.o `test -f 'terminal.c' || echo './'`terminal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-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=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo './'`output.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function 'SAM_header_change_HD_tosorted': samheader.c:153:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:158:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 158 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c gcc -DMAIN=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-get-genome.o -lz -lbz2 -lm gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-regiondb.o gmapindex-regiondb-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 gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-iit_dump.o -lm gcc -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-snpindex.o -lz -lbz2 -lm gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-indexdb.o cmetindex-indexdb-write.o cmetindex-regiondb-write.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-cmetindex.o -lz -lbz2 -lm gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-indexdb.o atoiindex-indexdb-write.o atoiindex-regiondb-write.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-atoiindex.o -lz -lbz2 -lm gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-bzip2.o sam_sort-getline.o sam_sort-datadir.o sam_sort-sam_sort.o -lz -lbz2 -lm gcc -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-transcript.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-transcript.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genome128_hr.o gsnap_nosimd-genome128_consec.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-regiondb.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mdprint.o gsnap_nosimd-cigar.o gsnap_nosimd-samprint.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-substring.o gsnap_nosimd-junction.o gsnap_nosimd-transcript.o gsnap_nosimd-method.o gsnap_nosimd-stage3hr.o gsnap_nosimd-ladder.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-maxent.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-intersect.o gsnap_nosimd-kmer-search.o gsnap_nosimd-path-solve.o gsnap_nosimd-extension-search.o gsnap_nosimd-segment-search.o gsnap_nosimd-terminal.o gsnap_nosimd-distant-rna.o gsnap_nosimd-distant-dna.o gsnap_nosimd-uint8table_rh.o gsnap_nosimd-uinttable_rh.o gsnap_nosimd-stage1hr.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-outbuffer.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -pthread -DTARGET=\"arm-unknown-linux-gnueabihf\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -fdebug-prefix-map=/build/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genome128_hr.o gsnapl_nosimd-genome128_consec.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-merge-diagonals-heap.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-regiondb.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mdprint.o gsnapl_nosimd-cigar.o gsnapl_nosimd-samprint.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-substring.o gsnapl_nosimd-junction.o gsnapl_nosimd-transcript.o gsnapl_nosimd-method.o gsnapl_nosimd-stage3hr.o gsnapl_nosimd-ladder.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-maxent.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-intersect.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-segment-search.o gsnapl_nosimd-terminal.o gsnapl_nosimd-distant-rna.o gsnapl_nosimd-distant-dna.o gsnapl_nosimd-uint8table_rh.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm make[3]: Leaving directory '/build/gmap-2021-02-22+ds/src' make[2]: Leaving directory '/build/gmap-2021-02-22+ds/src' Making all in util make[2]: Entering directory '/build/gmap-2021-02-22+ds/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes chmod +x gtf_splicesites chmod +x psl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_introns chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[2]: Leaving directory '/build/gmap-2021-02-22+ds/util' Making all in tests make[2]: Entering directory '/build/gmap-2021-02-22+ds/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/gmap-2021-02-22+ds/tests' make[2]: Entering directory '/build/gmap-2021-02-22+ds' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/gmap-2021-02-22+ds' make[1]: Leaving directory '/build/gmap-2021-02-22+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/gmap-2021-02-22+ds' dh_auto_test --no-parallel make -j1 check VERBOSE=1 make[2]: Entering directory '/build/gmap-2021-02-22+ds' Making check in src make[3]: Entering directory '/build/gmap-2021-02-22+ds/src' make[3]: Leaving directory '/build/gmap-2021-02-22+ds/src' Making check in util make[3]: Entering directory '/build/gmap-2021-02-22+ds/util' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/gmap-2021-02-22+ds/util' Making check in tests make[3]: Entering directory '/build/gmap-2021-02-22+ds/tests' make check-TESTS make[4]: Entering directory '/build/gmap-2021-02-22+ds/tests' make[5]: Entering directory '/build/gmap-2021-02-22+ds/tests' PASS: align.test PASS: coords1.test PASS: setup1.test PASS: iit.test ============================================================================ Testsuite summary for gmap 2021-02-22 ============================================================================ # TOTAL: 4 # PASS: 4 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/gmap-2021-02-22+ds/tests' make[4]: Leaving directory '/build/gmap-2021-02-22+ds/tests' make[3]: Leaving directory '/build/gmap-2021-02-22+ds/tests' make[3]: Entering directory '/build/gmap-2021-02-22+ds' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/gmap-2021-02-22+ds' make[2]: Leaving directory '/build/gmap-2021-02-22+ds' make[1]: Leaving directory '/build/gmap-2021-02-22+ds' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/gmap-2021-02-22+ds' mkdir -p /build/gmap-2021-02-22+ds/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string=2021-02-22+ds-1 --name='Genomic Mapping and Alignment Program' \ /build/gmap-2021-02-22+ds/src/gmap |debian/filter.pl >/build/gmap-2021-02-22+ds/debian/gmap/usr/share/man/man1/gmap.1 /usr/bin/help2man --no-info --version-string=2021-02-22+ds-1 --name='Genomic Short-read Nucleotide Alignment Program' \ /build/gmap-2021-02-22+ds/src/gsnap |debian/filter.pl >/build/gmap-2021-02-22+ds/debian/gmap/usr/share/man/man1/gsnap.1 /usr/bin/help2man --no-info --version-string=2021-02-22+ds-1 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/gmap-2021-02-22+ds/util/gmap_build |debian/filter.pl >/build/gmap-2021-02-22+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install make -j4 install DESTDIR=/build/gmap-2021-02-22\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-2021-02-22+ds' Making install in src make[3]: Entering directory '/build/gmap-2021-02-22+ds/src' make[4]: Entering directory '/build/gmap-2021-02-22+ds/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-2021-02-22+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex sam_sort gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd '/build/gmap-2021-02-22+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-2021-02-22+ds/src' make[3]: Leaving directory '/build/gmap-2021-02-22+ds/src' Making install in util make[3]: Entering directory '/build/gmap-2021-02-22+ds/util' make[4]: Entering directory '/build/gmap-2021-02-22+ds/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-2021-02-22+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat 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 '/build/gmap-2021-02-22+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-2021-02-22+ds/util' make[3]: Leaving directory '/build/gmap-2021-02-22+ds/util' Making install in tests make[3]: Entering directory '/build/gmap-2021-02-22+ds/tests' make[4]: Entering directory '/build/gmap-2021-02-22+ds/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 '/build/gmap-2021-02-22+ds/tests' make[3]: Leaving directory '/build/gmap-2021-02-22+ds/tests' make[3]: Entering directory '/build/gmap-2021-02-22+ds' make[4]: Entering directory '/build/gmap-2021-02-22+ds' make[4]: Nothing to be done for 'install-exec-am'. /bin/sh /build/gmap-2021-02-22+ds/config/install-sh -d /build/gmap-2021-02-22+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-2021-02-22+ds' make[3]: Leaving directory '/build/gmap-2021-02-22+ds' make[2]: Leaving directory '/build/gmap-2021-02-22+ds' make[1]: Leaving directory '/build/gmap-2021-02-22+ds' debian/rules override_dh_install make[1]: Entering directory '/build/gmap-2021-02-22+ds' mkdir -p debian/gmap/usr/bin dh_install for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \ cd /build/gmap-2021-02-22+ds/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 '/build/gmap-2021-02-22+ds' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/gmap-2021-02-22+ds' mkdir /build/gmap-2021-02-22+ds/debian/gmap/usr/share/doc/gmap/examples find tests/ -type f -print0 | xargs -0r sed -i \ -e 's@/build/gmap-2021-02-22+ds@«buildpath»@g' \ -e 's@\#! /bin/bash@\#! /bin/sh@g' tar --sort=name \ --mtime="@1614323733" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ --exclude='*/align.log' \ --exclude='*/Makefile' \ --exclude='*/Makefile.in' \ -cJf /build/gmap-2021-02-22+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests make[1]: Leaving directory '/build/gmap-2021-02-22+ds' dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gmap' in '../gmap_2021-02-22+ds-1_armhf.deb'. dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2021-02-22+ds-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gmap_2021-02-22+ds-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/21864/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/21864/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/21864 and its subdirectories I: Current time: Fri Jul 30 19:37:12 +14 2021 I: pbuilder-time-stamp: 1627623432