Diff of the two buildlogs: -- --- b1/build.log 2024-07-14 17:01:35.809936667 +0000 +++ b2/build.log 2024-07-14 17:03:29.541102356 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jul 14 04:57:06 -12 2024 -I: pbuilder-time-stamp: 1720976226 +I: Current time: Sun Aug 17 13:24:36 +14 2025 +I: pbuilder-time-stamp: 1755386676 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ 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.TFmkratR/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 25 20:32:25 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.ASPko_fD/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 @@ -32,135 +32,166 @@ dpkg-source: info: applying cross I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3009372/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1165399/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 17 13:24 /bin/sh -> /bin/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/1165399/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1165399/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=42 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8aa149b543df44cb9c8ef8b6ef458fc9' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3009372' - PS1='# ' - PS2='> ' + INVOCATION_ID=d4279a8036994635b13091c5fedf73b6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=1165399 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5g8fHZ21/pbuilderrc_4Hw1 --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5g8fHZ21/b1 --logfile b1/build.log gmap_2021-02-22+ds-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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/r-b-build.5g8fHZ21/pbuilderrc_mdm7 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5g8fHZ21/b2 --logfile b2/build.log gmap_2021-02-22+ds-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 22:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 22:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 22:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 22:09 more - -rwsr-xr-x 1 root root 55528 Mar 27 22:09 mount - -rwxr-xr-x 1 root root 18664 Mar 27 22:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 6 21:26 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 22:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 21:59 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 22:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 22:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3009372/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 2024 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 2024 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 2024 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 2024 more + -rwsr-xr-x 1 root root 55528 Mar 29 2024 mount + -rwxr-xr-x 1 root root 18664 Mar 29 2024 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Aug 17 13:24 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 2024 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 2024 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 2024 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1165399/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -237,7 +268,7 @@ Get: 33 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 18.7 MB in 0s (54.1 MB/s) +Fetched 18.7 MB in 2s (9052 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 ... 19711 files and directories currently installed.) @@ -393,7 +424,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gmap-2021-02-22+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gmap_2021-02-22+ds-1_source.changes +I: user script /srv/workspace/pbuilder/1165399/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1165399/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 @@ -586,7 +621,7 @@ checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no -checking for avx2 support... no +checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no @@ -599,6 +634,8 @@ checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes +checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes +checking for immintrin.h header file... yes checking gmapdb... /var/cache/gmap checking MAX_STACK_READLENGTH... 300 checking for zlib support... enabled @@ -655,11 +692,11 @@ checking standard linker flags to be used... checking pthread compiler flags to be used... -pthread checking popcnt flags to be used... -mpopcnt -checking compile level... sse42 -checking SSE4.2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 +checking compile level... avx2 +checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 make[1]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds' dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds' Making all in src make[2]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds/src' @@ -683,6 +720,30 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.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); @@ -702,8 +763,7 @@ 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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.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); @@ -724,11 +784,47 @@ 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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.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); @@ -754,6 +850,7 @@ access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'copy_limited_from_file': access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -770,6 +867,7 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -779,12 +877,12 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.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] @@ -871,20 +969,13 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c 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.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); - | ^~~~~~~~~ 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] @@ -893,6 +984,69 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +access.c: In function 'copy_memory_from_file': +access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c +In file included from iit-read.c:12: +iit-read.c: In function 'IIT_read_divint': +littleendian.h: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) @@ -943,6 +1097,7 @@ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c 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)); @@ -965,6 +1120,7 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -979,6 +1135,7 @@ 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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) @@ -992,130 +1149,10 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c -access.c: In function 'copy_memory_from_file': -access.c:532:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 532 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:537:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 537 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:543:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 543 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:548:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 548 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:554:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 554 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:559:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 559 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:565:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 565 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c: In function 'copy_limited_from_file': -access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:598:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 598 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:604:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 604 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:606:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 606 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:612:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 612 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:614:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 614 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:620:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 620 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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] @@ -1192,7 +1229,7 @@ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 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)); @@ -1217,7 +1254,21 @@ 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.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] @@ -1226,8 +1277,8 @@ 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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo './'`tableint.c iit-read.c: In function 'IIT_read': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1260,13 +1311,11 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1295,6 +1344,7 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1328,22 +1378,15 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c indexdb.c: In function 'positions_read_multiple': +In file included from regiondb-write.c:19: +regiondb-write.c: In function 'Region_read': indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1356,12 +1399,6 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 @@ -1369,14 +1406,29 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 +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); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -1393,30 +1445,25 @@ 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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -1467,13 +1514,15 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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] @@ -1482,12 +1531,16 @@ iit-read-univ.c:1065:2: note: in expansion of macro 'FREAD_UINT' 1065 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +indexdb.c: In function 'positions_read_multiple': 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); | ^~~~~~~~~ +indexdb.c:1935:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1935 | read(positions_fd,buffer,4); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1574,7 +1627,8 @@ 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/reproducible-path/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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 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] @@ -1583,6 +1637,7 @@ 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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) @@ -1619,6 +1674,14 @@ 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 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); + | ^~~~~~~~~~~ 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] @@ -1661,6 +1724,7 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -1682,34 +1746,10 @@ 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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 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); @@ -1729,7 +1769,7 @@ 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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -1750,17 +1790,11 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -1786,6 +1820,7 @@ access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -1811,6 +1846,8 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 @@ -1822,27 +1859,11 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -1859,17 +1880,36 @@ bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +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': 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -1920,15 +1960,46 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 +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); + | ^~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': +bigendian.c: In function 'Bigendian_write_char': 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); | ^~~~~~~~~~ +bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1997,6 +2068,14 @@ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~ 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)); @@ -2013,6 +2092,14 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~ 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] @@ -2021,21 +2108,18 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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 -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) @@ -2114,7 +2198,6 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -2136,58 +2219,16 @@ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -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': -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: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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.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); @@ -2238,9 +2279,12 @@ 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 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.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] @@ -2274,7 +2318,6 @@ 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2342,7 +2385,48 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.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); + | ^~~~~~~~~~~~~~ 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] @@ -2351,6 +2435,7 @@ 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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.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) @@ -2429,6 +2514,7 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c 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] @@ -2438,6 +2524,7 @@ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2450,56 +2537,6 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -2507,6 +2544,9 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -2557,8 +2597,11 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.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] @@ -2567,8 +2610,7 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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] @@ -2669,8 +2711,9 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-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] @@ -2715,6 +2758,7 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c 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] @@ -2778,21 +2822,14 @@ 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snpindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c +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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c @@ -2820,10 +2857,12 @@ 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.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); @@ -2836,15 +2875,20 @@ bigendian.c:367:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 367 | write(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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c 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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 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); @@ -2895,12 +2939,20 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 +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); + | ^~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2999,23 +3051,19 @@ 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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); | ^~~~~~~~~ -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); - | ^~~~~~~~~~~ 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) @@ -3023,6 +3071,7 @@ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | 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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c 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); @@ -3039,7 +3088,6 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c 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); @@ -3116,22 +3164,14 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c 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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.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] @@ -3146,9 +3186,6 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c @@ -3164,7 +3201,6 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.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); @@ -3184,6 +3220,8 @@ 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.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); @@ -3204,12 +3242,17 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -3260,9 +3303,9 @@ 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 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] @@ -3296,6 +3339,8 @@ 1070 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function 'read_intervals_univ': +In file included from compress-write.c:21: +compress-write.c: In function 'Compress_cat': 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3332,6 +3377,12 @@ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ +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); + | ^~~~~~~~~~~ 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) @@ -3363,19 +3414,11 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 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] @@ -3384,6 +3427,7 @@ 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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.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) @@ -3391,6 +3435,8 @@ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c 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); @@ -3483,18 +3529,7 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.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] @@ -3509,9 +3544,11 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c +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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c @@ -3535,6 +3572,7 @@ littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | 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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c 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); @@ -3546,7 +3584,10 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-access.o `test -f 'access.c' || echo './'`access.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.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); @@ -3567,12 +3608,10 @@ 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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-access.o `test -f 'access.c' || echo './'`access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -3598,6 +3637,7 @@ access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -3623,118 +3663,10 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-list.o `test -f 'list.c' || echo './'`list.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] @@ -3835,18 +3767,124 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trindex-trindex.o `test -f 'trindex.c' || echo './'`trindex.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/reproducible-path/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 +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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); + | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -3866,7 +3904,7 @@ 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/reproducible-path/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/reproducible-path/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 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); @@ -3887,15 +3925,12 @@ 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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); @@ -3946,7 +3981,30 @@ 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/reproducible-path/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/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -4023,6 +4081,7 @@ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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)); @@ -4039,26 +4098,30 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sam_sort.c: In function 'process_no_dedup': In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_words_debug': +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' */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/reproducible-path/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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' */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] @@ -4067,6 +4130,25 @@ iit-read.c:2588:5: note: in expansion of macro 'FREAD_INT' 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~ 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) @@ -4090,6 +4172,7 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4166,52 +4249,9 @@ 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/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 bigendian.c: In function 'Bigendian_write_char': +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -4231,11 +4271,12 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4286,24 +4327,12 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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/x86_64-linux-gnu/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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -4404,6 +4433,11 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -4419,6 +4453,7 @@ iit-read.c:3103:5: note: in expansion of macro 'FREAD_INT' 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4511,11 +4546,11 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -4524,24 +4559,26 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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/x86_64-linux-gnu/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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -4580,6 +4617,10 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4587,10 +4628,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -4627,6 +4664,7 @@ 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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4643,15 +4681,12 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4677,7 +4712,6 @@ access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4703,120 +4737,17 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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': In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_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.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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4829,7 +4760,6 @@ iit-read-univ.c:1067:2: note: in expansion of macro 'FREAD_INT' 1067 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4917,14 +4847,6 @@ 1275 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -4933,7 +4855,125 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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); + | ^~~~~~~~~~~ +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); + | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4941,9 +4981,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -4985,7 +5022,6 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -4993,6 +5029,7 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -5027,8 +5064,6 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -5049,12 +5084,16 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -5105,7 +5144,12 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -5198,6 +5242,7 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -5206,11 +5251,8 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -5219,10 +5261,7 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -5330,19 +5369,17 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -5388,6 +5425,7 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -5395,7 +5433,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -5456,6 +5493,9 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -5506,8 +5546,11 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -5577,7 +5620,7 @@ iit-read-univ.c:1133:7: note: in expansion of macro 'FREAD_INT' 1133 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) @@ -5609,9 +5652,18 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 +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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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] @@ -5620,6 +5672,7 @@ 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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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) @@ -5719,27 +5772,15 @@ iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -5747,10 +5788,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 @@ -5795,6 +5832,8 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 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); @@ -5802,19 +5841,37 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-except.o `test -f 'except.c' || echo './'`except.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo './'`assert.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo './'`mem.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo './'`intlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-list.o `test -f 'list.c' || echo './'`list.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-except.o `test -f 'except.c' || echo './'`except.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-list.o `test -f 'list.c' || echo './'`list.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c bigendian.c: In function 'Bigendian_write_char': bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -5835,33 +5892,19 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo './'`interval.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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-access.o `test -f 'access.c' || echo './'`access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo './'`filestring.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-md5.o `test -f 'md5.c' || echo './'`md5.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-access.o `test -f 'access.c' || echo './'`access.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo './'`md5.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo './'`compress.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); @@ -5912,10 +5955,11 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-fopen.o `test -f 'fopen.c' || echo './'`fopen.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-sequence.o `test -f 'sequence.c' || echo './'`sequence.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-reader.o `test -f 'reader.c' || echo './'`reader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.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] @@ -6016,15 +6060,27 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': +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); + | ^~~~~~~~~~~ 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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.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) @@ -6075,6 +6131,7 @@ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c 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)); @@ -6124,76 +6181,56 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-compress.o `test -f 'compress.c' || echo './'`compress.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-genome.o `test -f 'genome.c' || echo './'`genome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-popcount.o `test -f 'popcount.c' || echo './'`popcount.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-oligo.o `test -f 'oligo.c' || echo './'`oligo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-block.o `test -f 'block.c' || echo './'`block.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo './'`chrom.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-block.o `test -f 'block.c' || echo './'`block.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-match.o `test -f 'match.c' || echo './'`match.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo './'`diag.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo './'`pair.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo './'`gregion.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-match.o `test -f 'match.c' || echo './'`match.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo './'`stage1.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo './'`diag.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo './'`cmet.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-atoi.o `test -f 'atoi.c' || echo './'`atoi.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-transcript.o `test -f 'transcript.c' || echo './'`transcript.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-intron.o `test -f 'intron.c' || echo './'`intron.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-maxent.o `test -f 'maxent.c' || echo './'`maxent.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo './'`pair.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo './'`stage2.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo './'`smooth.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo './'`translation.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-stage3.o `test -f 'stage3.c' || echo './'`stage3.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-request.o `test -f 'request.c' || echo './'`request.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-result.o `test -f 'result.c' || echo './'`result.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-output.o `test -f 'output.c' || echo './'`output.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-samheader.o `test -f 'samheader.c' || echo './'`samheader.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo './'`translation.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-request.o `test -f 'request.c' || echo './'`request.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-result.o `test -f 'result.c' || echo './'`result.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-output.o `test -f 'output.c' || echo './'`output.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.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); @@ -6201,19 +6238,22 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-chimera.o `test -f 'chimera.c' || echo './'`chimera.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-datadir.o `test -f 'datadir.c' || echo './'`datadir.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-parserange.o `test -f 'parserange.c' || echo './'`parserange.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-getline.o `test -f 'getline.c' || echo './'`getline.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse42-gmap.o `test -f 'gmap.c' || echo './'`gmap.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-except.o `test -f 'except.c' || echo './'`except.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-assert.o `test -f 'assert.c' || echo './'`assert.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-mem.o `test -f 'mem.c' || echo './'`mem.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-intlist.o `test -f 'intlist.c' || echo './'`intlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-list.o `test -f 'list.c' || echo './'`list.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-except.o `test -f 'except.c' || echo './'`except.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-list.o `test -f 'list.c' || echo './'`list.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo './'`interval.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); @@ -6233,11 +6273,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo './'`interval.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.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); @@ -6258,13 +6293,16 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-access.o `test -f 'access.c' || echo './'`access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-filestring.o `test -f 'filestring.c' || echo './'`filestring.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-md5.o `test -f 'md5.c' || echo './'`md5.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-access.o `test -f 'access.c' || echo './'`access.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo './'`md5.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c access.c: In function 'copy_memory_from_file': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6314,8 +6352,11 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-fopen.o `test -f 'fopen.c' || echo './'`fopen.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-sequence.o `test -f 'sequence.c' || echo './'`sequence.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.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] @@ -6392,8 +6433,6 @@ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from iit-read.c:12: -iit-read.c: In function 'IIT_read_divint': 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)); @@ -6404,12 +6443,6 @@ 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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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-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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6418,12 +6451,25 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_words_debug': +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo './'`dinucl_bits.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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo './'`genome_canonical.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) @@ -6447,6 +6493,7 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c 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); @@ -6474,7 +6521,6 @@ iit-read.c:2150:5: note: in expansion of macro 'FREAD_UINT' 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-reader.o `test -f 'reader.c' || echo './'`reader.c 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)); @@ -6503,6 +6549,14 @@ 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 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); + | ^~~~~~~~~~~ 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] @@ -6511,8 +6565,8 @@ 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 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c iit-read.c: In function 'read_words_debug': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6525,27 +6579,36 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-compress.o `test -f 'compress.c' || echo './'`compress.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-genome.o `test -f 'genome.c' || echo './'`genome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-popcount.o `test -f 'popcount.c' || echo './'`popcount.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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo './'`oligo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-block.o `test -f 'block.c' || echo './'`block.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-block.o `test -f 'block.c' || echo './'`block.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-match.o `test -f 'match.c' || echo './'`match.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo './'`diag.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo './'`pair.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c 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); @@ -6553,54 +6616,25 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo './'`chrom.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo './'`gregion.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-match.o `test -f 'match.c' || echo './'`match.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo './'`stage1.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo './'`diag.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo './'`cmet.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo './'`atoi.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-transcript.o `test -f 'transcript.c' || echo './'`transcript.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo './'`intron.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo './'`maxent.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo './'`pair.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo './'`stage2.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo './'`smooth.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-translation.o `test -f 'translation.c' || echo './'`translation.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-stage3.o `test -f 'stage3.c' || echo './'`stage3.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-request.o `test -f 'request.c' || echo './'`request.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-result.o `test -f 'result.c' || echo './'`result.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-output.o `test -f 'output.c' || echo './'`output.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-samheader.o `test -f 'samheader.c' || echo './'`samheader.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo './'`chimera.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-datadir.o `test -f 'datadir.c' || echo './'`datadir.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-parserange.o `test -f 'parserange.c' || echo './'`parserange.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo './'`translation.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-request.o `test -f 'request.c' || echo './'`request.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-result.o `test -f 'result.c' || echo './'`result.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-output.o `test -f 'output.c' || echo './'`output.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.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); @@ -6608,16 +6642,22 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-getline.o `test -f 'getline.c' || echo './'`getline.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_sse42-gmap.o `test -f 'gmap.c' || echo './'`gmap.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-except.o `test -f 'except.c' || echo './'`except.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo './'`assert.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo './'`mem.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo './'`intlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-list.o `test -f 'list.c' || echo './'`list.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-except.o `test -f 'except.c' || echo './'`except.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-list.o `test -f 'list.c' || echo './'`list.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.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); @@ -6637,7 +6677,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-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); @@ -6658,12 +6697,15 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo './'`interval.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-access.o `test -f 'access.c' || echo './'`access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-filestring.o `test -f 'filestring.c' || echo './'`filestring.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-access.o `test -f 'access.c' || echo './'`access.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo './'`compress.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); @@ -6714,118 +6756,11 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-reader.o `test -f 'reader.c' || echo './'`reader.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-compress.o `test -f 'compress.c' || echo './'`compress.c -In file included from iit-read.c:12: -iit-read.c: In function 'IIT_read_divint': -littleendian.h: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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.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] @@ -6926,13 +6861,20 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-genome.o `test -f 'genome.c' || echo './'`genome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-popcount.o `test -f 'popcount.c' || echo './'`popcount.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c +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); + | ^~~~~~~~~ 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] @@ -6941,66 +6883,162 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo './'`oligo.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); + | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-substring.o `test -f 'substring.c' || echo './'`substring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo './'`junction.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-method.o `test -f 'method.c' || echo './'`method.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-cigar.o `test -f 'cigar.c' || echo './'`cigar.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-samprint.o `test -f 'samprint.c' || echo './'`samprint.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo './'`mapq.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo './'`fopen.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo './'`shortread.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-substring.o `test -f 'substring.c' || echo './'`substring.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo './'`junction.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-transcript.o `test -f 'transcript.c' || echo './'`transcript.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-method.o `test -f 'method.c' || echo './'`method.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-ladder.o `test -f 'ladder.c' || echo './'`ladder.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-concordance.o `test -f 'concordance.c' || echo './'`concordance.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-maxent.o `test -f 'maxent.c' || echo './'`maxent.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo './'`listpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo './'`intron.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo './'`splice.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo './'`indel.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-intersect.o `test -f 'intersect.c' || echo './'`intersect.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-terminal.o `test -f 'terminal.c' || echo './'`terminal.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-request.o `test -f 'request.c' || echo './'`request.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-output.o `test -f 'output.c' || echo './'`output.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-samheader.o `test -f 'samheader.c' || echo './'`samheader.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-datadir.o `test -f 'datadir.c' || echo './'`datadir.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo './'`splice.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo './'`indel.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-request.o `test -f 'request.c' || echo './'`request.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-output.o `test -f 'output.c' || echo './'`output.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.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); @@ -7008,22 +7046,23 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-parserange.o `test -f 'parserange.c' || echo './'`parserange.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-getline.o `test -f 'getline.c' || echo './'`getline.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_sse42-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo './'`except.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo './'`assert.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-mem.o `test -f 'mem.c' || echo './'`mem.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo './'`intlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo './'`list.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo './'`except.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo './'`list.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo './'`interval.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); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c 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); @@ -7039,9 +7078,9 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo './'`interval.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo './'`access.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); @@ -7062,9 +7101,13 @@ bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo './'`access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-filestring.o `test -f 'filestring.c' || echo './'`filestring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo './'`compress.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); @@ -7090,6 +7133,7 @@ access.c:570:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 570 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c access.c: In function 'copy_limited_from_file': access.c:596:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 596 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -7115,17 +7159,10 @@ access.c:622:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 622 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo './'`reader.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo './'`compress.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo './'`genome.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function 'read_tree_univ': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-popcount.o `test -f 'popcount.c' || echo './'`popcount.c 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -7200,6 +7237,7 @@ iit-read-univ.c:1193:3: note: in expansion of macro 'FREAD_UINT' 1193 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c 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)); @@ -7224,10 +7262,20 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c In file included from iit-read.c:12: iit-read.c: In function 'IIT_read_divint': -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -7333,8 +7381,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.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] @@ -7343,70 +7389,67 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-substring.o `test -f 'substring.c' || echo './'`substring.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo './'`junction.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo './'`method.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c indexdb.c: In function 'positions_read_multiple_large': +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo './'`oligo.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-cigar.o `test -f 'cigar.c' || echo './'`cigar.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-samprint.o `test -f 'samprint.c' || echo './'`samprint.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo './'`mapq.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo './'`fopen.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo './'`shortread.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-substring.o `test -f 'substring.c' || echo './'`substring.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo './'`junction.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo './'`transcript.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo './'`method.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-ladder.o `test -f 'ladder.c' || echo './'`ladder.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo './'`concordance.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-maxent.o `test -f 'maxent.c' || echo './'`maxent.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-listpool.o `test -f 'listpool.c' || echo './'`listpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-intron.o `test -f 'intron.c' || echo './'`intron.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-splice.o `test -f 'splice.c' || echo './'`splice.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo './'`indel.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-intersect.o `test -f 'intersect.c' || echo './'`intersect.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-terminal.o `test -f 'terminal.c' || echo './'`terminal.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-request.o `test -f 'request.c' || echo './'`request.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-output.o `test -f 'output.c' || echo './'`output.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-samheader.o `test -f 'samheader.c' || echo './'`samheader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo './'`splice.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo './'`indel.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo './'`request.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo './'`output.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c +gcc -DMAIN=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm 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); @@ -7414,12 +7457,6 @@ 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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-datadir.o `test -f 'datadir.c' || echo './'`datadir.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo './'`parserange.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo './'`getline.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c -gcc -DMAIN=1 -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 @@ -7439,10 +7476,10 @@ gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/build/reproducible-path/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 -gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-transcript.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm -gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-transcript.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm -gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genome128_hr.o gsnap_sse42-genome128_consec.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-regiondb.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mdprint.o gsnap_sse42-cigar.o gsnap_sse42-samprint.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-substring.o gsnap_sse42-junction.o gsnap_sse42-transcript.o gsnap_sse42-method.o gsnap_sse42-stage3hr.o gsnap_sse42-ladder.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-maxent.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-knownsplicing.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-bitpack64-access.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-intersect.o gsnap_sse42-kmer-search.o gsnap_sse42-path-solve.o gsnap_sse42-extension-search.o gsnap_sse42-segment-search.o gsnap_sse42-terminal.o gsnap_sse42-distant-rna.o gsnap_sse42-distant-dna.o gsnap_sse42-uint8table_rh.o gsnap_sse42-uinttable_rh.o gsnap_sse42-stage1hr.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-outbuffer.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm -gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genome128_hr.o gsnapl_sse42-genome128_consec.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-merge-diagonals-heap.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-regiondb.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mdprint.o gsnapl_sse42-cigar.o gsnapl_sse42-samprint.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-substring.o gsnapl_sse42-junction.o gsnapl_sse42-transcript.o gsnapl_sse42-method.o gsnapl_sse42-stage3hr.o gsnapl_sse42-ladder.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-maxent.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-intersect.o gsnapl_sse42-intersect-large.o gsnapl_sse42-kmer-search.o gsnapl_sse42-path-solve.o gsnapl_sse42-extension-search.o gsnapl_sse42-segment-search.o gsnapl_sse42-terminal.o gsnapl_sse42-distant-rna.o gsnapl_sse42-distant-dna.o gsnapl_sse42-uint8table_rh.o gsnapl_sse42-stage1hr.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-outbuffer.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm +gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-transcript.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm +gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genome128_hr.o gsnap_avx2-genome128_consec.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-regiondb.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mdprint.o gsnap_avx2-cigar.o gsnap_avx2-samprint.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-substring.o gsnap_avx2-junction.o gsnap_avx2-transcript.o gsnap_avx2-method.o gsnap_avx2-stage3hr.o gsnap_avx2-ladder.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-maxent.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-knownsplicing.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-bitpack64-access.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-intersect.o gsnap_avx2-kmer-search.o gsnap_avx2-path-solve.o gsnap_avx2-extension-search.o gsnap_avx2-segment-search.o gsnap_avx2-terminal.o gsnap_avx2-distant-rna.o gsnap_avx2-distant-dna.o gsnap_avx2-uint8table_rh.o gsnap_avx2-uinttable_rh.o gsnap_avx2-stage1hr.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-outbuffer.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm +gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-transcript.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm +gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/gmap-2021-02-22+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genome128_hr.o gsnapl_avx2-genome128_consec.o gsnapl_avx2-dinucl_bits.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-merge-diagonals-heap.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-regiondb.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mdprint.o gsnapl_avx2-cigar.o gsnapl_avx2-samprint.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-substring.o gsnapl_avx2-junction.o gsnapl_avx2-transcript.o gsnapl_avx2-method.o gsnapl_avx2-stage3hr.o gsnapl_avx2-ladder.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-maxent.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-intersect.o gsnapl_avx2-intersect-large.o gsnapl_avx2-kmer-search.o gsnapl_avx2-path-solve.o gsnapl_avx2-extension-search.o gsnapl_avx2-segment-search.o gsnapl_avx2-terminal.o gsnapl_avx2-distant-rna.o gsnapl_avx2-distant-dna.o gsnapl_avx2-uint8table_rh.o gsnapl_avx2-stage1hr.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-outbuffer.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[3]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds/src' make[2]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds/src' Making all in util @@ -7452,36 +7489,36 @@ cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords -cp psl_splicesites.pl psl_splicesites -cp psl_introns.pl psl_introns -cp psl_genes.pl psl_genes -cp ensembl_genes.pl ensembl_genes -cp gtf_splicesites.pl gtf_splicesites -cp gtf_introns.pl gtf_introns -chmod +x gmap_build chmod +x gmap_process +chmod +x gmap_build chmod +x gmap_cat chmod +x md_coords chmod +x fa_coords +cp psl_splicesites.pl psl_splicesites +cp psl_introns.pl psl_introns +cp psl_genes.pl psl_genes +cp ensembl_genes.pl ensembl_genes chmod +x psl_splicesites +cp gtf_splicesites.pl gtf_splicesites chmod +x psl_introns chmod +x psl_genes +chmod +x ensembl_genes +cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites -chmod +x gtf_introns cp gtf_genes.pl gtf_genes -chmod +x ensembl_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites +chmod +x gtf_introns cp gff3_introns.pl gff3_introns -cp gff3_genes.pl gff3_genes -cp dbsnp_iit.pl dbsnp_iit -cp gvf_iit.pl gvf_iit chmod +x gtf_genes -cp vcf_iit.pl vcf_iit chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites +cp gff3_genes.pl gff3_genes chmod +x gff3_introns +cp dbsnp_iit.pl dbsnp_iit +cp gvf_iit.pl gvf_iit chmod +x gff3_genes +cp vcf_iit.pl vcf_iit chmod +x dbsnp_iit chmod +x gvf_iit chmod +x vcf_iit @@ -7546,14 +7583,14 @@ /usr/bin/help2man --no-info --version-string=2021-02-22+ds-1 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2021-02-22+ds/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2021-02-22+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install - make -j20 install DESTDIR=/build/reproducible-path/gmap-2021-02-22\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/gmap-2021-02-22\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds/src' make[4]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds/src' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/reproducible-path/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 gmap.sse42 gmapl.sse42 gsnap.sse42 gsnapl.sse42 '/build/reproducible-path/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 gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/reproducible-path/gmap-2021-02-22+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds/src' Making install in util @@ -7574,7 +7611,7 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds' make[4]: Entering directory '/build/reproducible-path/gmap-2021-02-22+ds' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2021-02-22+ds/config/install-sh -d /build/reproducible-path/gmap-2021-02-22+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2021-02-22+ds/config/install-sh -d /build/reproducible-path/gmap-2021-02-22+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds' make[3]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds' make[2]: Leaving directory '/build/reproducible-path/gmap-2021-02-22+ds' @@ -7631,12 +7668,14 @@ 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/1165399/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1165399/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/3009372 and its subdirectories -I: Current time: Sun Jul 14 05:01:34 -12 2024 -I: pbuilder-time-stamp: 1720976494 +I: removing directory /srv/workspace/pbuilder/1165399 and its subdirectories +I: Current time: Sun Aug 17 13:26:27 +14 2025 +I: pbuilder-time-stamp: 1755386787