Diff of the two buildlogs: -- --- b1/build.log 2024-03-26 20:36:04.745375586 +0000 +++ b2/build.log 2024-03-26 20:39:13.393354841 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 28 14:57:33 -12 2025 -I: pbuilder-time-stamp: 1745895453 +I: Current time: Wed Mar 27 10:36:07 +14 2024 +I: pbuilder-time-stamp: 1711485367 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -18,8 +18,8 @@ I: copying [./freebayes_1.3.5-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.08cUKVN8/trustedkeys.kbx': General error -gpgv: Signature made Tue Feb 9 22:31:15 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.x_A6xy54/trustedkeys.kbx': General error +gpgv: Signature made Thu Feb 11 00:31:15 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,137 +29,168 @@ dpkg-source: info: unpacking freebayes_1.3.5-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/59584/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1417/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Mar 27 10:36 /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/1417/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1417/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=22 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='b784289d83384f52a9fc20ef5cd359a3' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='59584' - PS1='# ' - PS2='> ' + INVOCATION_ID=147d6732414749cc891515c6e81a3909 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=1417 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.gPUBmDnb/pbuilderrc_08Sr --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.gPUBmDnb/b1 --logfile b1/build.log freebayes_1.3.5-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.gPUBmDnb/pbuilderrc_bs0j --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.gPUBmDnb/b2 --logfile b2/build.log freebayes_1.3.5-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin total 5772 - -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Jan 20 2022 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 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 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 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Jan 20 2022 more - -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount - -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 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 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Apr 9 08:02 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Jan 20 2022 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 598488 Jan 19 2024 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Jan 20 2022 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/59584/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1367848 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Jan 21 2022 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 71928 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 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 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Jan 21 2022 more + -rwsr-xr-x 1 root root 50720 Jan 21 2022 mount + -rwxr-xr-x 1 root root 13856 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 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 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Mar 27 10:36 sh -> /bin/bash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Jan 21 2022 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 598488 Jan 20 23:59 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Jan 21 2022 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Jan 21 2022 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/1417/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -424,7 +455,7 @@ Get: 201 http://deb.debian.org/debian bullseye/main i386 parallel all 20161222-1.1 [306 kB] Get: 202 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 203 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] -Fetched 113 MB in 2s (59.5 MB/s) +Fetched 113 MB in 4s (31.9 MB/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 ... 19731 files and directories currently installed.) @@ -1278,7 +1309,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/freebayes-1.3.5/ && 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 > ../freebayes_1.3.5-1_source.changes +I: user script /srv/workspace/pbuilder/1417/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1417/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/freebayes-1.3.5/ && 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 > ../freebayes_1.3.5-1_source.changes dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.5-1 dpkg-buildpackage: info: source distribution unstable @@ -1340,24 +1375,31 @@ Option optimization is: 0 [default: 3] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson -O--builddir=build - cd build && LC_ALL=C.UTF-8 ninja -j22 -v -[1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp -[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp -[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp -[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp -[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp -[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp -[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp -[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp -[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp -[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp -[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp -[12/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp -[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp -[14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp -[15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp -[16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp -[17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp + cd build && LC_ALL=C.UTF-8 ninja -j7 -v +[1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp +[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp +[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp +[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp +[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp +[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp +[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp +[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp +[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp +[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp +[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp +[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp +[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp +[14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp +../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: +../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] + 160 | switch (this->type) { + | ^ +../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] +[15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp +[16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp +[17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp +[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp +[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, @@ -1404,17 +1446,10 @@ ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] -[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp -[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp -[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp -../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: -../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] - 160 | switch (this->type) { - | ^ -../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] -[21/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp -[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp -[23/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp +[20/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp +[21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp +[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp +[23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp [24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -msse -mfpmath=sse -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp [25/27] rm -f libfreebayes_common.a && gcc-ar csrD libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/reproducible-path/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/liblzma.so -pthread /usr/lib/i386-linux-gnu/libhts.so /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/libvcflib.so /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/libsmithwaterman.so /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/libdisorder.so /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/libfastahack.so /usr/lib/i386-linux-gnu/libseqlib.so /usr/lib/libbwa.a -ltabixpp -Wl,--end-group @@ -1426,9 +1461,18 @@ mkdir -p test/test-simple-bash ln -s -t test/test-simple-bash /build/reproducible-path/freebayes-1.3.5/debian/test-simple-bash/* dh_auto_test -- -v --timeout-multiplier 100 - cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=22 meson test -v --timeout-multiplier 100 + cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=7 meson test -v --timeout-multiplier 100 ninja: Entering directory `/build/reproducible-path/freebayes-1.3.5/build' ninja: no work to do. +t/03_reference_bases.t .. +1..3 +ok 1 - freebayes rejects invalid reference +ok 2 - freebayes does not put uppercase IUPAC bases in VCFs +ok 3 - freebayes does not put lowercase IUPAC bases in VCFs +ok +All tests successful. +Files=1, Tests=3, 1 wallclock secs ( 0.06 usr 0.00 sys + 0.10 cusr 0.00 csys = 0.16 CPU) +Result: PASS t/00_region_and_target_handling.t .. 1..12 ok 1 - ref:4-5 ref:6-7 are empty @@ -1445,16 +1489,7 @@ ok 12 - region outside of bounds error ok All tests successful. -Files=1, Tests=12, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.12 cusr 0.06 csys = 0.20 CPU) -Result: PASS -t/03_reference_bases.t .. -1..3 -ok 1 - freebayes rejects invalid reference -ok 2 - freebayes does not put uppercase IUPAC bases in VCFs -ok 3 - freebayes does not put lowercase IUPAC bases in VCFs -ok -All tests successful. -Files=1, Tests=3, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.04 cusr 0.02 csys = 0.08 CPU) +Files=1, Tests=12, 1 wallclock secs ( 0.04 usr 0.00 sys + 0.24 cusr 0.08 csys = 0.36 CPU) Result: PASS t/02_multi_bam.t .. 1..7 @@ -1467,7 +1502,7 @@ ok 7 - freebayes rejects two BAMs with the same name ok All tests successful. -Files=1, Tests=7, 2 wallclock secs ( 0.02 usr 0.02 sys + 0.10 cusr 0.10 csys = 0.24 CPU) +Files=1, Tests=7, 2 wallclock secs ( 0.04 usr 0.02 sys + 0.26 cusr 0.12 csys = 0.44 CPU) Result: PASS t/01b_call_variants.t .. 1..10 @@ -1483,12 +1518,12 @@ ok 10 - freebayes correctly uses CNV map with multiple entries ok All tests successful. -Files=1, Tests=10, 5 wallclock secs ( 0.02 usr 0.00 sys + 4.72 cusr 0.40 csys = 5.14 CPU) +Files=1, Tests=10, 17 wallclock secs ( 0.06 usr 0.02 sys + 9.80 cusr 0.42 csys = 10.30 CPU) Result: PASS [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 -t/01_call_variants.t: line 107: 69312 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null +t/01_call_variants.t: Zeile 107: 16554 Abgebrochen freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null t/01_call_variants.t .. 1..16 ok 1 - variant calling recovers most of the GiAB variants in a test region @@ -1509,13 +1544,13 @@ ok 16 - ! ok All tests successful. -Files=1, Tests=16, 12 wallclock secs ( 0.02 usr 0.02 sys + 10.66 cusr 6.40 csys = 17.10 CPU) +Files=1, Tests=16, 32 wallclock secs ( 0.04 usr 0.00 sys + 16.14 cusr 3.16 csys = 19.34 CPU) Result: PASS -1/5 T00 OK 0.63s -2/5 T01 OK 12.65s -3/5 T01b OK 5.51s -4/5 T02 OK 2.94s -5/5 T03 OK 0.92s +1/5 T00 OK 1.79s +2/5 T01 OK 32.13s +3/5 T01b OK 17.19s +4/5 T02 OK 1.90s +5/5 T03 OK 0.95s Ok: 5 @@ -1554,8 +1589,8 @@ dh_gencontrol -O--buildsystem=meson -O--builddir=build dh_md5sums -O--buildsystem=meson -O--builddir=build dh_builddeb -O--buildsystem=meson -O--builddir=build -dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.5-1_i386.deb'. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.5-1_i386.deb'. +dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.5-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../freebayes_1.3.5-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1563,12 +1598,14 @@ 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/1417/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1417/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/59584 and its subdirectories -I: Current time: Mon Apr 28 14:59:03 -12 2025 -I: pbuilder-time-stamp: 1745895543 +I: removing directory /srv/workspace/pbuilder/1417 and its subdirectories +I: Current time: Wed Mar 27 10:39:12 +14 2024 +I: pbuilder-time-stamp: 1711485552