Diff of the two buildlogs: -- --- b1/build.log 2024-07-11 18:15:12.017819123 +0000 +++ b2/build.log 2024-07-11 18:18:14.798072797 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 11 06:10:50 -12 2024 -I: pbuilder-time-stamp: 1720721450 +I: Current time: Thu Aug 14 14:38:15 +14 2025 +I: pbuilder-time-stamp: 1755131895 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 [./progressivemauve_1.2.0+4713+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.W_xUPdP8/trustedkeys.kbx': General error -gpgv: Signature made Tue Dec 1 08:10:27 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.kVEwj50I/trustedkeys.kbx': General error +gpgv: Signature made Wed Dec 2 10:10:27 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,135 +35,166 @@ dpkg-source: info: applying fix_FTBFS_boost1.67.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1894930/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2871938/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 14 14:38 /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/2871938/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2871938/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='7a6df56ca448456ebffa8e864788e2b4' - 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='1894930' - PS1='# ' - PS2='> ' + INVOCATION_ID=67ed96ab7786406dbedd6d5d46ec47b6 + 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=2871938 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.9gxkfz6k/pbuilderrc_jNKo --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.9gxkfz6k/b1 --logfile b1/build.log progressivemauve_1.2.0+4713+dfsg-5.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.9gxkfz6k/pbuilderrc_GmkQ --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.9gxkfz6k/b2 --logfile b2/build.log progressivemauve_1.2.0+4713+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 ionos1-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/1894930/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 14 14:38 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/2871938/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -273,7 +304,7 @@ Get: 54 http://deb.debian.org/debian bullseye/main amd64 libmems-dev amd64 1.6.0+4725-9+b1 [970 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libpkgconf3 amd64 1.7.4~git20210206+dcf529b-3 [35.2 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 pkgconf amd64 1.7.4~git20210206+dcf529b-3 [41.9 kB] -Fetched 43.4 MB in 3s (16.6 MB/s) +Fetched 43.4 MB in 2s (23.7 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 ... 19711 files and directories currently installed.) @@ -517,7 +548,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/ && 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 > ../progressivemauve_1.2.0+4713+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/2871938/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/2871938/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/ && 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 > ../progressivemauve_1.2.0+4713+dfsg-5_source.changes dpkg-buildpackage: info: source package progressivemauve dpkg-buildpackage: info: source version 1.2.0+4713+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -625,7 +660,7 @@ config.status: creating src/config.h config.status: executing depfiles commands dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' @@ -652,6 +687,13 @@ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o projectAndStrip.o projectAndStrip.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o backbone_global_to_local.o backbone_global_to_local.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp +g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp In file included from /usr/include/c++/10/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, @@ -664,23 +706,26 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from mauveAligner.cpp:30: + from /usr/include/libMems/Backbone.h:24, + from bbAnalyze.cpp:4: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -mauveAligner.cpp:413:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 413 | cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; - | ^~~~~~~~ -mauveAligner.cpp:413:70: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 413 | cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; - | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toRawSequence toRawSequence.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE In file included from /usr/include/c++/10/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from /usr/include/libMems/ProgressiveAligner.h:21, - from alignmentProjector.cpp:18: + from /usr/include/libMems/Backbone.h:24, + from backbone_global_to_local.cpp:2: +/usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +In file included from /usr/include/c++/10/ext/hash_map:60, + from /usr/include/libMems/HomologyHMM/dptables.h:43, + from /usr/include/libMems/HomologyHMM/homology.h:27, + from /usr/include/libMems/Islands.h:25, + from randomGeneSample.cpp:18: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -702,7 +747,8 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from projectAndStrip.cpp:18: + from /usr/include/libMems/Backbone.h:24, + from bbFilter.cpp:1: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -710,7 +756,7 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from toMultiFastA.cpp:2: + from mauveAligner.cpp:30: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -718,16 +764,21 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from createBackboneMFA.cpp:2: + from projectAndStrip.cpp:18: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp +mauveAligner.cpp:413:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 413 | cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; + | ^~~~~~~~ +mauveAligner.cpp:413:70: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 413 | cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; + | ^~~~~~~~ In file included from /usr/include/c++/10/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from addUnalignedIntervals.cpp:2: + from getOrthologList.cpp:18: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -743,30 +794,15 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from randomGeneSample.cpp:18: -/usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -In file included from /usr/include/c++/10/ext/hash_map:60, - from /usr/include/libMems/HomologyHMM/dptables.h:43, - from /usr/include/libMems/HomologyHMM/homology.h:27, - from /usr/include/libMems/Islands.h:25, - from getOrthologList.cpp:18: + from createBackboneMFA.cpp:2: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -projectAndStrip.cpp: In function 'int main(int, char**)': -projectAndStrip.cpp:65:60: warning: conversion from 'long unsigned int' to '__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] - 65 | not_ids[seq_ids[i]] = (std::numeric_limits<size_t>::max)(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp In file included from /usr/include/c++/10/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from /usr/include/libMems/Backbone.h:24, - from bbFilter.cpp:1: + from toMultiFastA.cpp:2: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ @@ -774,57 +810,56 @@ from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from /usr/include/libMems/Backbone.h:24, - from bbAnalyze.cpp:4: + from /usr/include/libMems/ProgressiveAligner.h:21, + from xmfa2maf.cpp:2: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o backbone_global_to_local.o backbone_global_to_local.cpp In file included from /usr/include/c++/10/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from /usr/include/libMems/Backbone.h:24, - from backbone_global_to_local.cpp:2: + from /usr/include/libMems/ProgressiveAligner.h:21, + from alignmentProjector.cpp:18: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp -g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniqueMerCount uniqueMerCount.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toRawSequence toRawSequence.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE In file included from /usr/include/c++/10/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, - from /usr/include/libMems/ProgressiveAligner.h:21, - from xmfa2maf.cpp:2: + from addUnalignedIntervals.cpp:2: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mfa2xmfa mfa2xmfa.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toMultiFastA toMultiFastA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniqueMerCount uniqueMerCount.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +projectAndStrip.cpp: In function 'int main(int, char**)': +projectAndStrip.cpp:65:60: warning: conversion from 'long unsigned int' to '__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] + 65 | not_ids[seq_ids[i]] = (std::numeric_limits<size_t>::max)(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniquifyTrees uniquifyTrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toGrimmFormat toGrimmFormat.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mauveToXMFA mauveToXMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbFilter bbFilter.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toMultiFastA toMultiFastA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o addUnalignedIntervals addUnalignedIntervals.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripGapColumns stripGapColumns.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o scoreAlignment scoreAlignment.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getAlignmentWindows getAlignmentWindows.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o scoreAlignment scoreAlignment.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wl,-z,relro -Wl,-z,now -o mauveAligner mauveAligner.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o alignmentProjector alignmentProjector.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE +g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o progressiveMauve progressiveMauve.o UniqueMatchFinder.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE -g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbAnalyze bbAnalyze.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -fdebug-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o repeatoire repeatoire.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE make[3]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' @@ -834,7 +869,7 @@ make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' dh_auto_test - make -j20 check VERBOSE=1 + make -j42 check VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' @@ -846,7 +881,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j20 install DESTDIR=/build/reproducible-path/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' @@ -880,8 +915,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'progressivemauve' in '../progressivemauve_1.2.0+4713+dfsg-5_amd64.deb'. dpkg-deb: building package 'progressivemauve-dbgsym' in '../progressivemauve-dbgsym_1.2.0+4713+dfsg-5_amd64.deb'. +dpkg-deb: building package 'progressivemauve' in '../progressivemauve_1.2.0+4713+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../progressivemauve_1.2.0+4713+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -889,12 +924,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2871938/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2871938/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/1894930 and its subdirectories -I: Current time: Thu Jul 11 06:15:10 -12 2024 -I: pbuilder-time-stamp: 1720721710 +I: removing directory /srv/workspace/pbuilder/2871938 and its subdirectories +I: Current time: Thu Aug 14 14:41:13 +14 2025 +I: pbuilder-time-stamp: 1755132073