Diff of the two buildlogs: -- --- b1/build.log 2025-02-12 17:50:18.003020762 +0000 +++ b2/build.log 2025-02-12 18:12:49.406252314 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 12 05:26:53 -12 2025 -I: pbuilder-time-stamp: 1739381213 +I: Current time: Wed Mar 18 14:13:20 +14 2026 +I: pbuilder-time-stamp: 1773792800 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -48,52 +48,84 @@ dpkg-source: info: applying graphviz_compat.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/985633/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1136662/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 Mar 18 00:13 /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/1136662/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1136662/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='a6710a5eee334a9494e479628c4f3805' - 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='985633' - PS1='# ' - PS2='> ' + INVOCATION_ID=7123f840900948a3ac0673ce23a62033 + 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=1136662 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.0RS1S3io/pbuilderrc_pmin --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.0RS1S3io/b1 --logfile b1/build.log snakemake_7.32.4-7.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.0RS1S3io/pbuilderrc_dGdn --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.0RS1S3io/b2 --logfile b2/build.log snakemake_7.32.4-7.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/985633/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1136662/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -640,7 +672,7 @@ Get: 407 http://deb.debian.org/debian trixie/main arm64 r-cran-shiny all 1.10.0+dfsg-1 [3139 kB] Get: 408 http://deb.debian.org/debian trixie/main arm64 r-cran-rmarkdown all 2.29+dfsg-1 [1473 kB] Get: 409 http://deb.debian.org/debian trixie/main arm64 stress arm64 1.0.7-1+b1 [21.8 kB] -Fetched 238 MB in 3s (90.4 MB/s) +Fetched 238 MB in 1s (165 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (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 ... 19921 files and directories currently installed.) @@ -1947,8 +1979,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Feb 12 17:29:01 UTC 2025. -Universal Time is now: Wed Feb 12 17:29:01 UTC 2025. +Local time is now: Wed Mar 18 00:14:34 UTC 2026. +Universal Time is now: Wed Mar 18 00:14:34 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... @@ -2356,7 +2388,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snakemake-7.32.4/ && 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 > ../snakemake_7.32.4-7_source.changes +I: user script /srv/workspace/pbuilder/1136662/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1136662/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snakemake-7.32.4/ && 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 > ../snakemake_7.32.4-7_source.changes dpkg-buildpackage: info: source package snakemake dpkg-buildpackage: info: source version 7.32.4-7 dpkg-buildpackage: info: source distribution unstable @@ -2682,7 +2718,7 @@ Copying snakemake.egg-info to build/bdist.linux-aarch64/wheel/./snakemake-7.32.4.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/snakemake-7.32.4.dist-info/WHEEL -creating '/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/.tmp-aswwoqiy/snakemake-7.32.4-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it +creating '/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/.tmp-u11j6tas/snakemake-7.32.4-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'snakemake/__init__.py' adding 'snakemake/__main__.py' adding 'snakemake/_version.py' @@ -3381,13 +3417,19 @@ .pybuild/cpython3_3.13_snakemake/build/tests/tests.py::test_checkpoint_allowed_rules PASSED [ 86%] .pybuild/cpython3_3.13_snakemake/build/tests/tests.py::test_modules_ruledeps_inheritance PASSED [ 86%] .pybuild/cpython3_3.13_snakemake/build/tests/tests.py::test_issue1331 Timeout (0:01:00)! -Thread 0x0000ffff53fff180 (most recent call first): +Thread 0x0000ffff867cf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff6cf9f180 (most recent call first): +Thread 0x0000ffff877ef180 (most recent call first): + File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.13/threading.py", line 992 in run + File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner + File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap + +Thread 0x0000ffff9fdff180 (most recent call first): File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py", line 679 in run_group_job File "/usr/lib/python3.13/concurrent/futures/thread.py", line 59 in run File "/usr/lib/python3.13/concurrent/futures/thread.py", line 93 in _worker @@ -3395,103 +3437,85 @@ File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff7cb3e180 (most recent call first): - File "/usr/lib/python3.13/subprocess.py", line 2026 in _try_wait - File "/usr/lib/python3.13/subprocess.py", line 2068 in _wait - File "/usr/lib/python3.13/subprocess.py", line 1276 in wait - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/shell.py", line 284 in __new__ - File "/tmp/snakemake-p4o83e4r/Snakefile", line 56 in __rule_align - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py", line 2656 in run_wrapper - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py", line 699 in cached_or_run - File "/usr/lib/python3.13/concurrent/futures/thread.py", line 59 in run - File "/usr/lib/python3.13/concurrent/futures/thread.py", line 93 in _worker +Thread 0x0000ffff6afdf180 (most recent call first): + File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff30fae180 (most recent call first): - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py", line 679 in run_group_job - File "/usr/lib/python3.13/concurrent/futures/thread.py", line 59 in run - File "/usr/lib/python3.13/concurrent/futures/thread.py", line 93 in _worker +Thread 0x0000ffff857af180 (most recent call first): + File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff6dfbf180 (most recent call first): - File "/usr/lib/python3.13/subprocess.py", line 2026 in _try_wait - File "/usr/lib/python3.13/subprocess.py", line 2068 in _wait - File "/usr/lib/python3.13/subprocess.py", line 1276 in wait - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/shell.py", line 284 in __new__ - File "/tmp/snakemake-p4o83e4r/Snakefile", line 76 in __rule_sort - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py", line 2656 in run_wrapper - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/executors/__init__.py", line 699 in cached_or_run - File "/usr/lib/python3.13/concurrent/futures/thread.py", line 59 in run - File "/usr/lib/python3.13/concurrent/futures/thread.py", line 93 in _worker +Thread 0x0000ffff6b7ef180 (most recent call first): + File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff50f9f180 (most recent call first): +Thread 0x0000ffff46fdf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff51fbf180 (most recent call first): +Thread 0x0000ffff477ef180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff337ef180 (most recent call first): +Thread 0x0000ffff69fbf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff537ef180 (most recent call first): +Thread 0x0000ffff68f9f180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff33fff180 (most recent call first): +Thread 0x0000ffff697af180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff517af180 (most recent call first): +Thread 0x0000ffff86fdf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff6ffff180 (most recent call first): +Thread 0x0000ffff9cf9f180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff7d64e180 (most recent call first): +Thread 0x0000ffff9dfbf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff7de5e180 (most recent call first): +Thread 0x0000ffff9efdf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff7f17f180 (most recent call first): +Thread 0x0000ffff9e7cf180 (most recent call first): File "/usr/lib/python3.13/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.13/threading.py", line 992 in run File "/usr/lib/python3.13/threading.py", line 1041 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1012 in _bootstrap -Thread 0x0000ffff8b533740 (most recent call first): +Thread 0x0000ffffac22d740 (most recent call first): File "/usr/lib/python3.13/threading.py", line 359 in wait File "/usr/lib/python3.13/threading.py", line 511 in acquire File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/scheduler.py", line 546 in schedule @@ -3586,10 +3610,10 @@ warnings.warn( tests/tests.py::test_glpk_solver - :890: DeprecationWarning: This process (pid=1073107) is multi-threaded, use of fork() may lead to deadlocks in the child. + :890: DeprecationWarning: This process (pid=1251685) is multi-threaded, use of fork() may lead to deadlocks in the child. -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -= 249 passed, 46 skipped, 99 deselected, 1 xfailed, 21 warnings in 1137.40s (0:18:57) = += 249 passed, 46 skipped, 99 deselected, 1 xfailed, 21 warnings in 1130.61s (0:18:50) = I: pybuild pybuild:334: rm -fr /build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/bin /build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/tests make[1]: Leaving directory '/build/reproducible-path/snakemake-7.32.4' create-stamp debian/debhelper-build-stamp @@ -3630,12 +3654,14 @@ 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/1136662/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1136662/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/985633 and its subdirectories -I: Current time: Wed Feb 12 05:50:16 -12 2025 -I: pbuilder-time-stamp: 1739382616 +I: removing directory /srv/workspace/pbuilder/1136662 and its subdirectories +I: Current time: Wed Mar 18 14:35:47 +14 2026 +I: pbuilder-time-stamp: 1773794147