Diff of the two buildlogs: -- --- b1/build.log 2024-12-14 05:55:24.712654315 +0000 +++ b2/build.log 2024-12-14 06:19:09.775955985 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 15 23:53:09 -12 2026 -I: pbuilder-time-stamp: 1768564389 +I: Current time: Sat Jan 17 02:18:27 +14 2026 +I: pbuilder-time-stamp: 1768565907 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -50,52 +50,84 @@ dpkg-source: info: applying no_pkg_resources.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2441984/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2512146/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 Jan 16 12:18 /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/2512146/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2512146/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='1897e3f75cb9430787a42536551fd1a0' - 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='2441984' - PS1='# ' - PS2='> ' + INVOCATION_ID=ade9ab7029884d1b867cae6d38cae971 + 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=2512146 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.FJTr3vHe/pbuilderrc_e1zg --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.FJTr3vHe/b1 --logfile b1/build.log snakemake_7.32.4-6.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.FJTr3vHe/pbuilderrc_uaoO --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.FJTr3vHe/b2 --logfile b2/build.log snakemake_7.32.4-6.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 codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2441984/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2512146/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -1894,8 +1926,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 16 11:54:28 UTC 2026. -Universal Time is now: Fri Jan 16 11:54:28 UTC 2026. +Local time is now: Fri Jan 16 12:19:20 UTC 2026. +Universal Time is now: Fri Jan 16 12:19:20 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... @@ -2296,7 +2328,11 @@ 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_7.32.4-6_source.changes +I: user script /srv/workspace/pbuilder/2512146/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2512146/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_7.32.4-6_source.changes dpkg-buildpackage: info: source package snakemake dpkg-buildpackage: info: source version 7.32.4-6 dpkg-buildpackage: info: source distribution unstable @@ -2622,7 +2658,7 @@ 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_3.12_snakemake/.tmp-3ccoehdz/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_3.12_snakemake/.tmp-ax_m5p1e/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' @@ -3227,7 +3263,7 @@ .pybuild/cpython3_3.12_snakemake/build/tests/tests.py::test_group_job_resources_with_pipe PASSED [ 55%] .pybuild/cpython3_3.12_snakemake/build/tests/tests.py::test_group_job_resources_with_pipe_with_too_much_constraint PASSED [ 55%] .pybuild/cpython3_3.12_snakemake/build/tests/tests.py::test_multicomp_group_jobs Timeout (0:01:00)! -Thread 0x0000ffff317af180 (most recent call first): +Thread 0x0000ffff50f9f180 (most recent call first): File "/usr/lib/python3.12/selectors.py", line 468 in select File "/usr/lib/python3.12/asyncio/base_events.py", line 1954 in _run_once File "/usr/lib/python3.12/asyncio/base_events.py", line 640 in run_forever @@ -3239,7 +3275,7 @@ File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff497af180 (most recent call first): +Thread 0x0000ffff6afdf180 (most recent call first): File "/usr/lib/python3.12/selectors.py", line 468 in select File "/usr/lib/python3.12/asyncio/base_events.py", line 1954 in _run_once File "/usr/lib/python3.12/asyncio/base_events.py", line 640 in run_forever @@ -3251,121 +3287,115 @@ File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff31fbf180 (most recent call first): +Thread 0x0000ffff517af180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff327cf180 (most recent call first): +Thread 0x0000ffff51fbf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff32fdf180 (most recent call first): +Thread 0x0000ffff527cf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff337ef180 (most recent call first): +Thread 0x0000ffff52fdf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff33fff180 (most recent call first): +Thread 0x0000ffff537ef180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff48f9f180 (most recent call first): +Thread 0x0000ffff53fff180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff49fbf180 (most recent call first): +Thread 0x0000ffff68f9f180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff78def180 (most recent call first): - File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker - File "/usr/lib/python3.12/threading.py", line 1012 in run - File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner - File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap - -Thread 0x0000ffff4a7cf180 (most recent call first): +Thread 0x0000ffff6a7cf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff4afdf180 (most recent call first): +Thread 0x0000ffff69fbf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff4b7ef180 (most recent call first): +Thread 0x0000ffff697af180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff68b9e180 (most recent call first): +Thread 0x0000ffff8b7ef180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff4bfff180 (most recent call first): +Thread 0x0000ffff6bfff180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff69fbf180 (most recent call first): +Thread 0x0000ffff6b7ef180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6a7cf180 (most recent call first): +Thread 0x0000ffff897af180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6afdf180 (most recent call first): +Thread 0x0000ffff89fbf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6b7ef180 (most recent call first): +Thread 0x0000ffff8a7cf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6bfff180 (most recent call first): +Thread 0x0000ffff8afdf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff7962f180 (most recent call first): +Thread 0x0000ffff8bfff180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff80dbc740 (most recent call first): +Thread 0x0000ffff97b65740 (most recent call first): File "/usr/lib/python3.12/threading.py", line 355 in wait File "/usr/lib/python3.12/threading.py", line 507 in acquire File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/scheduler.py", line 546 in schedule @@ -3501,13 +3531,57 @@ .pybuild/cpython3_3.12_snakemake/build/tests/tests.py::test_checkpoint_allowed_rules PASSED [ 86%] .pybuild/cpython3_3.12_snakemake/build/tests/tests.py::test_modules_ruledeps_inheritance PASSED [ 87%] .pybuild/cpython3_3.12_snakemake/build/tests/tests.py::test_issue1331 Timeout (0:01:00)! -Thread 0x0000ffff0efdf180 (most recent call first): +Thread 0x0000ffff2ffff180 (most recent call first): + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff9164f180 (most recent call first): + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff2efdf180 (most recent call first): + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff6bfff180 (most recent call first): + File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/executors/__init__.py", line 679 in run_group_job + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 59 in run + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 93 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff8b7ef180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff497af180 (most recent call first): +Thread 0x0000ffff2f7ef180 (most recent call first): + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff2e7cf180 (most recent call first): + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff6b7ef180 (most recent call first): + File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker + File "/usr/lib/python3.12/threading.py", line 1012 in run + File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner + File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap + +Thread 0x0000ffff6afdf180 (most recent call first): File "/usr/lib/python3.12/selectors.py", line 468 in select File "/usr/lib/python3.12/asyncio/base_events.py", line 1954 in _run_once File "/usr/lib/python3.12/asyncio/base_events.py", line 640 in run_forever @@ -3519,115 +3593,101 @@ File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff31fbf180 (most recent call first): +Thread 0x0000ffff517af180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff327cf180 (most recent call first): +Thread 0x0000ffff51fbf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff32fdf180 (most recent call first): +Thread 0x0000ffff527cf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff337ef180 (most recent call first): +Thread 0x0000ffff52fdf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff33fff180 (most recent call first): +Thread 0x0000ffff537ef180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff48f9f180 (most recent call first): +Thread 0x0000ffff53fff180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff49fbf180 (most recent call first): +Thread 0x0000ffff68f9f180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff78def180 (most recent call first): +Thread 0x0000ffff6a7cf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff4a7cf180 (most recent call first): +Thread 0x0000ffff69fbf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff4b7ef180 (most recent call first): +Thread 0x0000ffff697af180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff4bfff180 (most recent call first): +Thread 0x0000ffff897af180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6a7cf180 (most recent call first): +Thread 0x0000ffff89fbf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6afdf180 (most recent call first): +Thread 0x0000ffff8a7cf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6b7ef180 (most recent call first): +Thread 0x0000ffff8afdf180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff6bfff180 (most recent call first): +Thread 0x0000ffff8bfff180 (most recent call first): File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker File "/usr/lib/python3.12/threading.py", line 1012 in run File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap -Thread 0x0000ffff7962f180 (most recent call first): - File "/usr/lib/python3.12/concurrent/futures/thread.py", line 90 in _worker - File "/usr/lib/python3.12/threading.py", line 1012 in run - File "/usr/lib/python3.12/threading.py", line 1075 in _bootstrap_inner - File "/usr/lib/python3.12/threading.py", line 1032 in _bootstrap - -Thread 0x0000ffff80dbc740 (most recent call first): - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/rules.py", line 1242 in get_wildcards - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 1707 in new_job - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 1985 in file2jobs - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 1894 in collect_potential_dependencies - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 978 in update_ - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 885 in update - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 1000 in update_ - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 885 in update - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 1000 in update_ - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 885 in update - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/dag.py", line 214 in init - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/workflow.py", line 895 in execute +Thread 0x0000ffff97b65740 (most recent call first): + File "/usr/lib/python3.12/threading.py", line 355 in wait + File "/usr/lib/python3.12/threading.py", line 507 in acquire + File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/scheduler.py", line 546 in schedule + File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/workflow.py", line 1242 in execute File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/snakemake/__init__.py", line 792 in snakemake File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/tests/common.py", line 234 in run File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/tests/tests.py", line 1856 in test_issue1331 @@ -3718,10 +3778,10 @@ warnings.warn( tests/tests.py::test_glpk_solver - :888: DeprecationWarning: This process (pid=2509782) is multi-threaded, use of fork() may lead to deadlocks in the child. + :888: DeprecationWarning: This process (pid=2545523) 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 -= 256 passed, 46 skipped, 92 deselected, 1 xfailed, 21 warnings in 1212.09s (0:20:12) = += 256 passed, 46 skipped, 92 deselected, 1 xfailed, 21 warnings in 1212.64s (0:20:12) = I: pybuild pybuild:334: rm -fr /build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/bin /build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.12_snakemake/build/tests make[1]: Leaving directory '/build/reproducible-path/snakemake-7.32.4' create-stamp debian/debhelper-build-stamp @@ -3753,8 +3813,8 @@ dpkg-gencontrol: warning: package snakemake-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'snakemake-doc' in '../snakemake-doc_7.32.4-6_all.deb'. dpkg-deb: building package 'snakemake' in '../snakemake_7.32.4-6_all.deb'. +dpkg-deb: building package 'snakemake-doc' in '../snakemake-doc_7.32.4-6_all.deb'. dpkg-genbuildinfo --build=binary -O../snakemake_7.32.4-6_arm64.buildinfo dpkg-genchanges --build=binary -O../snakemake_7.32.4-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3762,24 +3822,26 @@ 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/2512146/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2512146/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 W: Stray processes left from build: -* system-pbuilder-build-snakemake_7.32.4\x2d6-2441984.slice - Slice /system/pbuilder/build/snakemake_7.32.4-6/2441984 +* system-pbuilder-build-snakemake_7.32.4\x2d6-2512146.slice - Slice /system/pbuilder/build/snakemake_7.32.4-6/2512146 Loaded: loaded - Active: active since Thu 2026-01-15 23:53:14 -12; 25min ago + Active: active since Sat 2026-01-17 02:18:33 +14; 23min ago Tasks: 1 Memory: 1.6G - CPU: 5min 25.147s - CGroup: /system.slice/system-pbuilder.slice/system-pbuilder-build.slice/system-pbuilder-build-snakemake_7.32.4\x2d6.slice/system-pbuilder-build-snakemake_7.32.4\x2d6-2441984.slice - `-run-r456517a4359a4ea9825ee0f9245a2f39.scope - `-2721705 /usr/bin/bash -c "set -euo pipefail; grep 1 < test.1.txt > test.1.out" + CPU: 7min 8.247s + CGroup: /system.slice/system-pbuilder.slice/system-pbuilder-build.slice/system-pbuilder-build-snakemake_7.32.4\x2d6.slice/system-pbuilder-build-snakemake_7.32.4\x2d6-2512146.slice + `-run-rf215203e8ac4416ba7451af2afcbb68b.scope + `-2662533 /usr/bin/bash -c "set -euo pipefail; grep 1 < test.1.txt > test.1.out" -Jan 15 23:53:14 codethink01-arm64 systemd[1]: Created slice system-pbuilder-build-snakemake_7.32.4\x2d6-2441984.slice - Slice /system/pbuilder/build/snakemake_7.32.4-6/2441984. +Jan 17 02:18:33 codethink03-arm64 systemd[1]: Created slice system-pbuilder-build-snakemake_7.32.4\x2d6-2512146.slice - Slice /system/pbuilder/build/snakemake_7.32.4-6/2512146. I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2441984 and its subdirectories -I: Current time: Fri Jan 16 00:18:23 -12 2026 -I: pbuilder-time-stamp: 1768565903 +I: removing directory /srv/workspace/pbuilder/2512146 and its subdirectories +I: Current time: Sat Jan 17 02:42:08 +14 2026 +I: pbuilder-time-stamp: 1768567328