Diff of the two buildlogs: -- --- b1/build.log 2025-03-06 04:34:37.952573047 +0000 +++ b2/build.log 2025-03-06 04:37:19.733257414 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 5 16:29:44 -12 2025 -I: pbuilder-time-stamp: 1741235384 +I: Current time: Thu Apr 9 00:57:41 +14 2026 +I: pbuilder-time-stamp: 1775645861 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying remove-pkg-resources.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/532406/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3185854/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Apr 8 10:57 /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/3185854/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3185854/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='9f1e74baf7de48068576863d64252feb' - 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='532406' - PS1='# ' - PS2='> ' + INVOCATION_ID=b85afe4543d042ae9b21c5894d592e59 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3185854 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.AvyobFhq/pbuilderrc_OGhS --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.AvyobFhq/b1 --logfile b1/build.log kineticstools_0.6.1+git20220223.1326a4d+dfsg-6.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.AvyobFhq/pbuilderrc_B0jM --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.AvyobFhq/b2 --logfile b2/build.log kineticstools_0.6.1+git20220223.1326a4d+dfsg-6.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/532406/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3185854/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -311,7 +343,7 @@ Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-4+b1 [15.8 MB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-uritools all 4.0.3-1 [28.6 kB] -Fetched 90.9 MB in 1s (95.6 MB/s) +Fetched 90.9 MB in 1s (157 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19914 files and directories currently installed.) @@ -881,8 +913,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Mar 6 04:30:54 UTC 2025. -Universal Time is now: Thu Mar 6 04:30:54 UTC 2025. +Local time is now: Wed Apr 8 10:58:10 UTC 2026. +Universal Time is now: Wed Apr 8 10:58:10 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... @@ -1044,7 +1076,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+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 > ../kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/3185854/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3185854/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+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 > ../kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_source.changes dpkg-buildpackage: info: source package kineticstools dpkg-buildpackage: info: source version 0.6.1+git20220223.1326a4d+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -1189,52 +1225,51 @@ scheduling tests via LoadScopeScheduling -test/test_summarize_modifications.py::TestSummarizeModifications::test_integration -[gw6] [ 5%] SKIPPED test/test_summarize_modifications.py::TestSummarizeModifications::test_integration +test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig +test/test_ipdModel.py::TestIpdModel::test_refLength test/test_loader.py::test_basic -[gw1] [ 10%] PASSED test/test_loader.py::test_basic -test/test_loader.py::test_path -[gw1] [ 15%] PASSED test/test_loader.py::test_path -test/test_loader.py::test_path_with_prefixed_chem -[gw1] [ 21%] PASSED test/test_loader.py::test_path_with_prefixed_chem -test/test_loader.py::test_getResourcePathSpec -[gw1] [ 26%] PASSED test/test_loader.py::test_getResourcePathSpec test/test_ReferenceUtils.py::TestReferenceUtils::test_bam -[gw0] [ 31%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_bam +[gw0] [ 5%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_bam +test/test_outputs.py::TestOutputs::test_csv_output +[gw5] [ 10%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output +test/test_outputs.py::TestOutputs::test_bigwig +[gw5] [ 15%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig +[gw2] [ 21%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength +test/test_ipdModel.py::TestIpdModel::test_snippetFunc +test/test_summarize_modifications.py::TestSummarizeModifications::test_integration +[gw6] [ 26%] SKIPPED test/test_summarize_modifications.py::TestSummarizeModifications::test_integration test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset -[gw0] [ 36%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset +[gw0] [ 31%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow -[gw0] [ 42%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow +[gw0] [ 36%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows +[gw0] [ 42%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows +test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks +[gw0] [ 47%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks +[gw1] [ 52%] PASSED test/test_loader.py::test_basic +test/test_loader.py::test_path +[gw1] [ 57%] PASSED test/test_loader.py::test_path +test/test_loader.py::test_path_with_prefixed_chem +[gw1] [ 63%] PASSED test/test_loader.py::test_path_with_prefixed_chem +test/test_loader.py::test_getResourcePathSpec +[gw1] [ 68%] PASSED test/test_loader.py::test_getResourcePathSpec test/test_integration.py::TestKineticsTools::test_help -test/test_outputs.py::TestOutputs::test_csv_output -[gw5] [ 47%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output -test/test_outputs.py::TestOutputs::test_bigwig -[gw5] [ 52%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig -test/test_ipdModel.py::TestIpdModel::test_refLength -[gw2] [ 57%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength -test/test_ipdModel.py::TestIpdModel::test_snippetFunc -[gw2] [ 63%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc -test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow -[gw2] [ 68%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow -test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig [gw3] [ 73%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli [gw3] [ 78%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli -[gw0] [ 84%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows -test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks -[gw0] [ 89%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks +[gw2] [ 84%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc +test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow +[gw2] [ 89%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow [gw4] [ 94%] PASSED test/test_integration.py::TestKineticsTools::test_help test/test_integration.py::TestKineticsTools::test_ecoli_first_50k [gw4] [100%] SKIPPED test/test_integration.py::TestKineticsTools::test_ecoli_first_50k - generated xml file: /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/nosetests.xml - ============================= slowest 20 durations ============================= -1.52s call test/test_integration.py::TestKineticsTools::test_help -0.01s teardown test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig +0.89s call test/test_integration.py::TestKineticsTools::test_help -(18 durations < 0.005s hidden. Use -vv to show these durations.) -======================== 5 passed, 14 skipped in 4.70s ========================= +(19 durations < 0.005s hidden. Use -vv to show these durations.) +======================== 5 passed, 14 skipped in 2.52s ========================= make[1]: Leaving directory '/build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -1325,8 +1360,8 @@ creating /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools creating /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/__pycache__/loader.cpython-313.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ -copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/__pycache__/ipdModel.cpython-313.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/__pycache__/sharedArray.cpython-313.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ +copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/__pycache__/ipdModel.cpython-313.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/__pycache__/ReferenceUtils.cpython-313.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.13_kineticstools/build/kineticsTools/tree_predict.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.13/dist-packages/kineticsTools @@ -1429,9 +1464,9 @@ dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'kineticstools-data' in '../kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-6_all.deb'. -dpkg-deb: building package 'python3-kineticstools-dbgsym' in '../python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-6_arm64.deb'. -dpkg-deb: building package 'python3-kineticstools' in '../python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_arm64.deb'. dpkg-deb: building package 'kineticstools' in '../kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_all.deb'. +dpkg-deb: building package 'python3-kineticstools' in '../python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_arm64.deb'. +dpkg-deb: building package 'python3-kineticstools-dbgsym' in '../python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1439,12 +1474,14 @@ 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/3185854/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3185854/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/532406 and its subdirectories -I: Current time: Wed Mar 5 16:34:36 -12 2025 -I: pbuilder-time-stamp: 1741235676 +I: removing directory /srv/workspace/pbuilder/3185854 and its subdirectories +I: Current time: Thu Apr 9 01:00:18 +14 2026 +I: pbuilder-time-stamp: 1775646018