Diff of the two buildlogs: -- --- b1/build.log 2024-04-28 12:32:02.648486238 +0000 +++ b2/build.log 2024-04-28 12:34:48.993383223 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 28 00:28:38 -12 2024 -I: pbuilder-time-stamp: 1714307318 +I: Current time: Mon Apr 29 02:32:06 +14 2024 +I: pbuilder-time-stamp: 1714307526 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying man-align-cols.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2855958/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2119148/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 28 12:32 /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/2119148/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2119148/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(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='052e1b1decd444878f0aaed037563bee' - 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='2855958' - PS1='# ' - PS2='> ' + INVOCATION_ID=30dd0ed55fd0478e9a0814bb4d33393b + 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=2119148 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.tykw7SgY/pbuilderrc_yrV0 --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.tykw7SgY/b1 --logfile b1/build.log kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.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.tykw7SgY/pbuilderrc_j2yH --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.tykw7SgY/b2 --logfile b2/build.log kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.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 codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2855958/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 23 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2119148/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -421,7 +453,7 @@ Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-pytest-xdist all 3.5.0-1 [42.1 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.11.4-6 [17.5 MB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-uritools all 4.0.1-1 [25.1 kB] -Fetched 104 MB in 1s (115 MB/s) +Fetched 104 MB in 1s (190 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). @@ -1017,8 +1049,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Apr 28 12:29:34 UTC 2024. -Universal Time is now: Sun Apr 28 12:29:34 UTC 2024. +Local time is now: Sun Apr 28 12:32:37 UTC 2024. +Universal Time is now: Sun Apr 28 12:32:37 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1) ... @@ -1192,7 +1224,11 @@ 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-2_source.changes +I: user script /srv/workspace/pbuilder/2119148/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2119148/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-2_source.changes dpkg-buildpackage: info: source package kineticstools dpkg-buildpackage: info: source version 0.6.1+git20220223.1326a4d+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1333,41 +1369,41 @@ scheduling tests via LoadScopeScheduling -test/test_integration.py::TestKineticsTools::test_help +test/test_summarize_modifications.py::TestSummarizeModifications::test_integration +test/test_outputs.py::TestOutputs::test_csv_output +[gw5] [ 5%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output +test/test_ReferenceUtils.py::TestReferenceUtils::test_bam +[gw0] [ 10%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_bam +[gw6] [ 15%] SKIPPED test/test_summarize_modifications.py::TestSummarizeModifications::test_integration +test/test_ipdModel.py::TestIpdModel::test_refLength +[gw2] [ 21%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength +test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig +[gw3] [ 26%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig +test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli +[gw3] [ 31%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli test/test_loader.py::test_basic -[gw2] [ 5%] PASSED test/test_loader.py::test_basic +[gw1] [ 36%] PASSED test/test_loader.py::test_basic test/test_loader.py::test_path -[gw2] [ 10%] PASSED test/test_loader.py::test_path +[gw1] [ 42%] PASSED test/test_loader.py::test_path test/test_loader.py::test_path_with_prefixed_chem -[gw2] [ 15%] PASSED test/test_loader.py::test_path_with_prefixed_chem +[gw1] [ 47%] PASSED test/test_loader.py::test_path_with_prefixed_chem test/test_loader.py::test_getResourcePathSpec -[gw2] [ 21%] PASSED test/test_loader.py::test_getResourcePathSpec -test/test_ipdModel.py::TestIpdModel::test_refLength -[gw1] [ 26%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength +[gw1] [ 52%] PASSED test/test_loader.py::test_getResourcePathSpec test/test_ipdModel.py::TestIpdModel::test_snippetFunc -[gw1] [ 31%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc +[gw2] [ 57%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow -test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig -[gw3] [ 36%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig -test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli -[gw3] [ 42%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli -[gw1] [ 47%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow -test/test_ReferenceUtils.py::TestReferenceUtils::test_bam -[gw0] [ 52%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_bam +[gw2] [ 63%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow +test/test_integration.py::TestKineticsTools::test_help +test/test_outputs.py::TestOutputs::test_bigwig +[gw5] [ 68%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset -[gw0] [ 57%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset -test/test_summarize_modifications.py::TestSummarizeModifications::test_integration -[gw5] [ 63%] SKIPPED test/test_summarize_modifications.py::TestSummarizeModifications::test_integration +[gw0] [ 73%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow -[gw0] [ 68%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow +[gw0] [ 78%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows -[gw0] [ 73%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows +[gw0] [ 84%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks -[gw0] [ 78%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks -test/test_outputs.py::TestOutputs::test_csv_output -[gw6] [ 84%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output -test/test_outputs.py::TestOutputs::test_bigwig -[gw6] [ 89%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig +[gw0] [ 89%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks [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 @@ -1380,10 +1416,10 @@ -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/nosetests.xml - ============================= slowest 20 durations ============================= -0.83s call test/test_integration.py::TestKineticsTools::test_help +0.78s call test/test_integration.py::TestKineticsTools::test_help (19 durations < 0.005s hidden. Use -vv to show these durations.) -================== 5 passed, 14 skipped, 12 warnings in 2.94s ================== +================== 5 passed, 14 skipped, 12 warnings 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 @@ -1478,8 +1514,8 @@ creating /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools creating /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/loader.cpython-311.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ -copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/ipdModel.cpython-311.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/sharedArray.cpython-311.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ +copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/ipdModel.cpython-311.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/ReferenceUtils.cpython-311.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__ copying /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tree_predict.cpython-311-aarch64-linux-gnu.so -> /build/reproducible-path/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools @@ -1579,10 +1615,10 @@ dpkg-gencontrol: warning: Depends field of package python3-kineticstools: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-kineticstools-dbgsym' in '../python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_arm64.deb'. -dpkg-deb: building package 'kineticstools-data' in '../kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2_all.deb'. dpkg-deb: building package 'kineticstools' in '../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_all.deb'. +dpkg-deb: building package 'kineticstools-data' in '../kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2_all.deb'. dpkg-deb: building package 'python3-kineticstools' in '../python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_arm64.deb'. +dpkg-deb: building package 'python3-kineticstools-dbgsym' in '../python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1590,12 +1626,14 @@ 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/2119148/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2119148/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/2855958 and its subdirectories -I: Current time: Sun Apr 28 00:32:01 -12 2024 -I: pbuilder-time-stamp: 1714307521 +I: removing directory /srv/workspace/pbuilder/2119148 and its subdirectories +I: Current time: Mon Apr 29 02:34:47 +14 2024 +I: pbuilder-time-stamp: 1714307687