Diff of the two buildlogs: -- --- b1/build.log 2025-02-01 21:19:33.934276907 +0000 +++ b2/build.log 2025-02-01 22:21:16.830913998 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 6 15:35:08 -12 2026 -I: pbuilder-time-stamp: 1772854508 +I: Current time: Sun Feb 2 11:19:37 +14 2025 +I: pbuilder-time-stamp: 1738444777 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3914048/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/83875/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Feb 1 21:20 /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/83875/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/83875/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 parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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 parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a22cd34a16bc4f6982256defba687b1a' - 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='3914048' - PS1='# ' - PS2='> ' + INVOCATION_ID=32ac575b9ca34378bd52b90d35fd9492 + 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=83875 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.pHuWPLr5/pbuilderrc_QheZ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pHuWPLr5/b1 --logfile b1/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.pHuWPLr5/pbuilderrc_OChp --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pHuWPLr5/b2 --logfile b2/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3914048/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/83875/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ Get: 31 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] -Fetched 22.8 MB in 0s (137 MB/s) +Fetched 22.8 MB in 1s (23.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19848 files and directories currently installed.) @@ -289,7 +321,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+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 > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/83875/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/83875/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+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 > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -360,7 +396,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j42 + make -j20 make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' @@ -401,9 +437,9 @@ Single-end simulation -Total CPU time used: 0.040076 +Total CPU time used: 0.124415 -The random seed for the run: 1772854551 +The random seed for the run: 1738444971 Parameters Settings number of flow cycles: 100 @@ -434,9 +470,9 @@ Paired-end simulation -Total CPU time used: 0.031987 +Total CPU time used: 0.104451 -The random seed for the run: 1772854551 +The random seed for the run: 1738444972 Parameters Settings number of flow cycles: 100 @@ -472,9 +508,9 @@ Paired-end simulation -Total CPU time used: 0.034671 +Total CPU time used: 0.10871 -The random seed for the run: 1772854551 +The random seed for the run: 1738444972 Parameters Settings number of flow cycles: 200 @@ -510,9 +546,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 6.63356 +Total CPU time used: 21.7001 -The random seed for the run: 1772854551 +The random seed for the run: 1738444973 Parameters Settings number of flow cycles: 100 @@ -543,9 +579,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 5.23005 +Total CPU time used: 18.7329 -The random seed for the run: 1772854558 +The random seed for the run: 1738445022 Parameters Settings number of flow cycles: 100 @@ -578,7 +614,7 @@ Single-end simulation -Total CPU time used: 0.045979 +Total CPU time used: 0.117188 The random seed for the run: 777 @@ -611,7 +647,7 @@ Single-end simulation -Total CPU time used: 0.041101 +Total CPU time used: 0.127714 The random seed for the run: 777 @@ -645,9 +681,9 @@ Single-end simulation -Total CPU time used: 0.065112 +Total CPU time used: 0.21555 -The random seed for the run: 1772854564 +The random seed for the run: 1738445063 Parameters Settings fold of read coverage: 10X @@ -677,9 +713,9 @@ Single-end simulation -Total CPU time used: 0.087682 +Total CPU time used: 0.219141 -The random seed for the run: 1772854564 +The random seed for the run: 1738445063 Parameters Settings fold of read coverage: 20X @@ -707,9 +743,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.110603 +Total CPU time used: 0.327166 -The random seed for the run: 1772854564 +The random seed for the run: 1738445064 Parameters Settings fold of read coverage: 20X @@ -747,7 +783,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.058064 +Total CPU time used: 0.134177 The random seed for the run: 777 @@ -785,7 +821,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.049966 +Total CPU time used: 0.120231 The random seed for the run: 777 @@ -828,9 +864,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 0.167673 +Total CPU time used: 0.445156 -The random seed for the run: 1772854564 +The random seed for the run: 1738445065 Parameters Settings fold of read coverage: 50X @@ -864,9 +900,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 172.378 +Total CPU time used: 554.276 -The random seed for the run: 1772854565 +The random seed for the run: 1738445066 Parameters Settings # reads per amplion: 100 @@ -896,9 +932,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 94.0046 +Total CPU time used: 266.892 -The random seed for the run: 1772854764 +The random seed for the run: 1738447076 Parameters Settings # read pairs per amplion: 80 @@ -929,9 +965,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 60.8178 +Total CPU time used: 203.127 -The random seed for the run: 1772854871 +The random seed for the run: 1738447740 Parameters Settings # read pairs per amplion: 50 @@ -963,9 +999,9 @@ Single-end Simulation -Total CPU time used: 0.040486 +Total CPU time used: 0.136646 -The random seed for the run: 1772854932 +The random seed for the run: 1738448359 Parameters used during run Read Length: 35 @@ -997,9 +1033,9 @@ Single-end Simulation -Total CPU time used: 0.03298 +Total CPU time used: 0.120769 -The random seed for the run: 1772854932 +The random seed for the run: 1738448359 Parameters used during run Read Length: 50 @@ -1031,9 +1067,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.023472 +Total CPU time used: 0.054381 -The random seed for the run: 1772854932 +The random seed for the run: 1738448360 Parameters used during run Read Length: 150 @@ -1070,9 +1106,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.038933 +Total CPU time used: 0.136331 -The random seed for the run: 1772854932 +The random seed for the run: 1738448360 Parameters used during run Read Length: 100 @@ -1109,9 +1145,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.026545 +Total CPU time used: 0.086861 -The random seed for the run: 1772854932 +The random seed for the run: 1738448360 Parameters used during run Read Length: 100 @@ -1148,9 +1184,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 0.241077 +Total CPU time used: 0.841242 -The random seed for the run: 1772854932 +The random seed for the run: 1738448360 Parameters used during run Read Length: 100 @@ -1182,9 +1218,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 0.298824 +Total CPU time used: 0.940163 -The random seed for the run: 1772854932 +The random seed for the run: 1738448363 Parameters used during run Read Length: 100 @@ -1219,9 +1255,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 0.437117 +Total CPU time used: 1.40869 -The random seed for the run: 1772854933 +The random seed for the run: 1738448366 Parameters used during run Read Length: 100 @@ -1256,7 +1292,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.025366 +Total CPU time used: 0.083588 The random seed for the run: 777 @@ -1295,7 +1331,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.025261 +Total CPU time used: 0.081899 The random seed for the run: 777 @@ -1334,9 +1370,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.029869 +Total CPU time used: 0.098772 -The random seed for the run: 1772854933 +The random seed for the run: 1738448372 Parameters used during run Read Length: 100 @@ -1375,9 +1411,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.026707 +Total CPU time used: 0.098777 -The random seed for the run: 1772854933 +The random seed for the run: 1738448373 Parameters used during run Read Length: 75 @@ -1410,14 +1446,14 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j42 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j20 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' -make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' +make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' - /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' + /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_install-arch @@ -1480,12 +1516,14 @@ 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/83875/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/83875/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/3914048 and its subdirectories -I: Current time: Fri Mar 6 15:42:31 -12 2026 -I: pbuilder-time-stamp: 1772854951 +I: removing directory /srv/workspace/pbuilder/83875 and its subdirectories +I: Current time: Sun Feb 2 12:21:15 +14 2025 +I: pbuilder-time-stamp: 1738448475