Diff of the two buildlogs: -- --- b1/build.log 2025-03-02 01:30:53.059317925 +0000 +++ b2/build.log 2025-03-02 02:06:14.587788642 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 3 19:28:50 -12 2026 -I: pbuilder-time-stamp: 1775287730 +I: Current time: Sun Mar 2 15:30:56 +14 2025 +I: pbuilder-time-stamp: 1740879056 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/1322144/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2860088/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 Mar 2 01:31 /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/2860088/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2860088/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='70dc222b5ec04f9e97f8573ee1e83b6a' - 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='1322144' - PS1='# ' - PS2='> ' + INVOCATION_ID=bc970020473546bab17da404d942097d + 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=2860088 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.CYOJGPSo/pbuilderrc_TJIW --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CYOJGPSo/b1 --logfile b1/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+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.CYOJGPSo/pbuilderrc_Bbt2 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CYOJGPSo/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 ionos5-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 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/1322144/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2860088/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 unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] -Fetched 22.9 MB in 5s (5007 kB/s) +Fetched 22.9 MB in 0s (68.4 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 ... 19780 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/2860088/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2860088/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 @@ -363,7 +399,7 @@ 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' @@ -404,9 +440,9 @@ Single-end simulation -Total CPU time used: 0.0767 +Total CPU time used: 0.111969 -The random seed for the run: 1775287901 +The random seed for the run: 1740879173 Parameters Settings number of flow cycles: 100 @@ -437,9 +473,9 @@ Paired-end simulation -Total CPU time used: 0.05222 +Total CPU time used: 0.107471 -The random seed for the run: 1775287901 +The random seed for the run: 1740879174 Parameters Settings number of flow cycles: 100 @@ -475,9 +511,9 @@ Paired-end simulation -Total CPU time used: 0.063489 +Total CPU time used: 0.086295 -The random seed for the run: 1775287901 +The random seed for the run: 1740879174 Parameters Settings number of flow cycles: 200 @@ -513,9 +549,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 14.3902 +Total CPU time used: 19.3516 -The random seed for the run: 1775287901 +The random seed for the run: 1740879174 Parameters Settings number of flow cycles: 100 @@ -546,9 +582,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 11.035 +Total CPU time used: 16.4096 -The random seed for the run: 1775287943 +The random seed for the run: 1740879199 Parameters Settings number of flow cycles: 100 @@ -581,7 +617,7 @@ Single-end simulation -Total CPU time used: 0.071297 +Total CPU time used: 0.097785 The random seed for the run: 777 @@ -614,7 +650,7 @@ Single-end simulation -Total CPU time used: 0.074331 +Total CPU time used: 0.096205 The random seed for the run: 777 @@ -648,9 +684,9 @@ Single-end simulation -Total CPU time used: 0.112928 +Total CPU time used: 0.158649 -The random seed for the run: 1775287965 +The random seed for the run: 1740879226 Parameters Settings fold of read coverage: 10X @@ -680,9 +716,9 @@ Single-end simulation -Total CPU time used: 0.143653 +Total CPU time used: 0.193906 -The random seed for the run: 1775287965 +The random seed for the run: 1740879226 Parameters Settings fold of read coverage: 20X @@ -710,9 +746,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.194454 +Total CPU time used: 0.240109 -The random seed for the run: 1775287965 +The random seed for the run: 1740879226 Parameters Settings fold of read coverage: 20X @@ -750,7 +786,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.097303 +Total CPU time used: 0.131118 The random seed for the run: 777 @@ -788,7 +824,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.092593 +Total CPU time used: 0.130493 The random seed for the run: 777 @@ -831,9 +867,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 0.30381 +Total CPU time used: 0.354142 -The random seed for the run: 1775287968 +The random seed for the run: 1740879228 Parameters Settings fold of read coverage: 50X @@ -867,9 +903,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 316.124 +Total CPU time used: 517.269 -The random seed for the run: 1775287969 +The random seed for the run: 1740879229 Parameters Settings # reads per amplion: 100 @@ -899,9 +935,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 221.947 +Total CPU time used: 229.742 -The random seed for the run: 1775288440 +The random seed for the run: 1740880683 Parameters Settings # read pairs per amplion: 80 @@ -932,9 +968,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 161.331 +Total CPU time used: 156.184 -The random seed for the run: 1775288889 +The random seed for the run: 1740880958 Parameters Settings # read pairs per amplion: 50 @@ -966,9 +1002,9 @@ Single-end Simulation -Total CPU time used: 0.07254 +Total CPU time used: 0.14218 -The random seed for the run: 1775289171 +The random seed for the run: 1740881143 Parameters used during run Read Length: 35 @@ -1000,9 +1036,9 @@ Single-end Simulation -Total CPU time used: 0.055916 +Total CPU time used: 0.109661 -The random seed for the run: 1775289171 +The random seed for the run: 1740881143 Parameters used during run Read Length: 50 @@ -1034,9 +1070,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.036626 +Total CPU time used: 0.058544 -The random seed for the run: 1775289171 +The random seed for the run: 1740881143 Parameters used during run Read Length: 150 @@ -1073,9 +1109,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.06798 +Total CPU time used: 0.085042 -The random seed for the run: 1775289171 +The random seed for the run: 1740881143 Parameters used during run Read Length: 100 @@ -1112,9 +1148,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.046043 +Total CPU time used: 0.07949 -The random seed for the run: 1775289171 +The random seed for the run: 1740881143 Parameters used during run Read Length: 100 @@ -1151,9 +1187,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 0.407344 +Total CPU time used: 0.615474 -The random seed for the run: 1775289171 +The random seed for the run: 1740881143 Parameters used during run Read Length: 100 @@ -1185,9 +1221,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 2.87677 +Total CPU time used: 0.696632 -The random seed for the run: 1775289173 +The random seed for the run: 1740881144 Parameters used during run Read Length: 100 @@ -1222,9 +1258,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 0.741273 +Total CPU time used: 0.911978 -The random seed for the run: 1775289176 +The random seed for the run: 1740881145 Parameters used during run Read Length: 100 @@ -1259,7 +1295,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.045273 +Total CPU time used: 0.057111 The random seed for the run: 777 @@ -1298,7 +1334,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.044654 +Total CPU time used: 0.062154 The random seed for the run: 777 @@ -1337,9 +1373,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.053512 +Total CPU time used: 0.084697 -The random seed for the run: 1775289180 +The random seed for the run: 1740881146 Parameters used during run Read Length: 100 @@ -1378,9 +1414,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.046305 +Total CPU time used: 0.072977 -The random seed for the run: 1775289180 +The random seed for the run: 1740881147 Parameters used during run Read Length: 75 @@ -1413,12 +1449,12 @@ 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' - /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/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' make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' @@ -1473,9 +1509,9 @@ dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb +dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb'. -dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1483,12 +1519,14 @@ 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/2860088/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2860088/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/1322144 and its subdirectories -I: Current time: Fri Apr 3 19:53:48 -12 2026 -I: pbuilder-time-stamp: 1775289228 +I: removing directory /srv/workspace/pbuilder/2860088 and its subdirectories +I: Current time: Sun Mar 2 16:06:13 +14 2025 +I: pbuilder-time-stamp: 1740881173