Diff of the two buildlogs: -- --- b1/build.log 2025-09-30 07:59:46.336249683 +0000 +++ b2/build.log 2025-09-30 08:21:06.765612637 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 2 01:48:13 -12 2026 -I: pbuilder-time-stamp: 1793627293 +I: Current time: Tue Sep 30 21:59:47 +14 2025 +I: pbuilder-time-stamp: 1759219187 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -48,53 +48,85 @@ 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/3036897/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1233404/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Sep 30 08:00 /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/1233404/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1233404/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='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c2ae536a4ab244bd8ba74f29e970d3bc' - 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='3036897' - PS1='# ' - PS2='> ' + INVOCATION_ID=f9ceabc53e7d46eebf3522cb915cb3ca + 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=1233404 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.ETz5Zugq/pbuilderrc_627Z --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ETz5Zugq/b1 --logfile b1/build.log snakemake_7.32.4-7.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - 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.ETz5Zugq/pbuilderrc_JbDn --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ETz5Zugq/b2 --logfile b2/build.log snakemake_7.32.4-7.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + 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 ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3036897/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1233404/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -107,7 +139,7 @@ Depends: ca-certificates, cwltool, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, environment-modules, glpk-utils, imagemagick, python3, python3-platformdirs, python3-biopython, python3-boto3, python3-botocore, python3-configargparse, python3-connection-pool, python3-datrie, python3-docutils, python3-dropbox, python3-flask, python3-git, python3-jinja2 (>= 3.0~), python3-jsonschema, python3-nbformat, python3-packaging, python3-pandas, python3-psutil, python3-pulp (>= 2.0~), python3-pygments, python3-pytest, python3-pytools, python3-ratelimiter, python3-recommonmark, python3-requests, python3-requests-mock, python3-retry, python3-pytest-mock, python3-rpy2, python3-setuptools, python3-smart-open (>= 3.0~), python3-sphinx (>= 3.0~), python3-sphinx-argparse, python3-sphinx-bootstrap-theme, python3-sphinx-rtd-theme, python3-stopit, python3-tabulate, python3-throttler, python3-toposort, python3-wrapt, python3-yaml, python3-yte, r-cran-rmarkdown, stress dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19919 files and directories currently installed.) +(Reading database ... 19898 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -643,10 +675,10 @@ Get: 409 http://deb.debian.org/debian forky/main amd64 r-cran-shiny all 1.10.0+dfsg-2 [3139 kB] Get: 410 http://deb.debian.org/debian forky/main amd64 r-cran-rmarkdown all 2.29+dfsg-1 [1473 kB] Get: 411 http://deb.debian.org/debian forky/main amd64 stress amd64 1.0.7-1 [21.9 kB] -Fetched 248 MB in 10s (24.6 MB/s) +Fetched 248 MB in 8s (33.0 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 ... 19919 files and directories currently installed.) +(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 ... 19898 files and directories currently installed.) Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libexpat1:amd64. @@ -794,7 +826,7 @@ Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. -(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 ... 21542 files and directories currently installed.) +(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 ... 21521 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. @@ -827,7 +859,7 @@ Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. -(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 ... 22552 files and directories currently installed.) +(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 ... 22531 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. @@ -1958,8 +1990,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Nov 2 13:53:39 UTC 2026. -Universal Time is now: Mon Nov 2 13:53:39 UTC 2026. +Local time is now: Tue Sep 30 08:01:31 UTC 2025. +Universal Time is now: Tue Sep 30 08:01:31 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17030-1) ... @@ -2367,7 +2399,11 @@ 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/1233404/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1233404/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 @@ -2410,142 +2446,142 @@ running build running build_py creating build/lib/snakemake -copying snakemake/interfaces.py -> build/lib/snakemake copying snakemake/profiles.py -> build/lib/snakemake -copying snakemake/io.py -> build/lib/snakemake -copying snakemake/target_jobs.py -> build/lib/snakemake -copying snakemake/path_modifier.py -> build/lib/snakemake -copying snakemake/script.py -> build/lib/snakemake -copying snakemake/logging.py -> build/lib/snakemake -copying snakemake/__main__.py -> build/lib/snakemake +copying snakemake/__init__.py -> build/lib/snakemake +copying snakemake/stats.py -> build/lib/snakemake +copying snakemake/checkpoints.py -> build/lib/snakemake +copying snakemake/modules.py -> build/lib/snakemake +copying snakemake/sourcecache.py -> build/lib/snakemake +copying snakemake/benchmark.py -> build/lib/snakemake +copying snakemake/jobs.py -> build/lib/snakemake +copying snakemake/ruleinfo.py -> build/lib/snakemake +copying snakemake/_version.py -> build/lib/snakemake copying snakemake/wrapper.py -> build/lib/snakemake -copying snakemake/decorators.py -> build/lib/snakemake -copying snakemake/utils.py -> build/lib/snakemake copying snakemake/persistence.py -> build/lib/snakemake -copying snakemake/gui.py -> build/lib/snakemake -copying snakemake/cwl.py -> build/lib/snakemake copying snakemake/parser.py -> build/lib/snakemake -copying snakemake/ruleinfo.py -> build/lib/snakemake copying snakemake/scheduler.py -> build/lib/snakemake +copying snakemake/path_modifier.py -> build/lib/snakemake copying snakemake/dag.py -> build/lib/snakemake -copying snakemake/output_index.py -> build/lib/snakemake -copying snakemake/_version.py -> build/lib/snakemake -copying snakemake/__init__.py -> build/lib/snakemake -copying snakemake/workflow.py -> build/lib/snakemake +copying snakemake/decorators.py -> build/lib/snakemake +copying snakemake/io.py -> build/lib/snakemake copying snakemake/notebook.py -> build/lib/snakemake -copying snakemake/exceptions.py -> build/lib/snakemake -copying snakemake/benchmark.py -> build/lib/snakemake -copying snakemake/shell.py -> build/lib/snakemake -copying snakemake/checkpoints.py -> build/lib/snakemake -copying snakemake/stats.py -> build/lib/snakemake +copying snakemake/workflow.py -> build/lib/snakemake copying snakemake/rules.py -> build/lib/snakemake +copying snakemake/__main__.py -> build/lib/snakemake +copying snakemake/interfaces.py -> build/lib/snakemake copying snakemake/resources.py -> build/lib/snakemake -copying snakemake/modules.py -> build/lib/snakemake -copying snakemake/sourcecache.py -> build/lib/snakemake -copying snakemake/jobs.py -> build/lib/snakemake -creating build/lib/snakemake/template_rendering -copying snakemake/template_rendering/jinja2.py -> build/lib/snakemake/template_rendering -copying snakemake/template_rendering/__init__.py -> build/lib/snakemake/template_rendering -copying snakemake/template_rendering/yte.py -> build/lib/snakemake/template_rendering -creating build/lib/snakemake/executors -copying snakemake/executors/ga4gh_tes.py -> build/lib/snakemake/executors -copying snakemake/executors/common.py -> build/lib/snakemake/executors -copying snakemake/executors/azure_batch.py -> build/lib/snakemake/executors -copying snakemake/executors/__init__.py -> build/lib/snakemake/executors -copying snakemake/executors/google_lifesciences.py -> build/lib/snakemake/executors -copying snakemake/executors/google_lifesciences_helper.py -> build/lib/snakemake/executors -copying snakemake/executors/flux.py -> build/lib/snakemake/executors +copying snakemake/output_index.py -> build/lib/snakemake +copying snakemake/logging.py -> build/lib/snakemake +copying snakemake/target_jobs.py -> build/lib/snakemake +copying snakemake/utils.py -> build/lib/snakemake +copying snakemake/cwl.py -> build/lib/snakemake +copying snakemake/script.py -> build/lib/snakemake +copying snakemake/gui.py -> build/lib/snakemake +copying snakemake/shell.py -> build/lib/snakemake +copying snakemake/exceptions.py -> build/lib/snakemake creating build/lib/snakemake/linting -copying snakemake/linting/snakefiles.py -> build/lib/snakemake/linting -copying snakemake/linting/links.py -> build/lib/snakemake/linting copying snakemake/linting/__init__.py -> build/lib/snakemake/linting +copying snakemake/linting/snakefiles.py -> build/lib/snakemake/linting copying snakemake/linting/rules.py -> build/lib/snakemake/linting -creating build/lib/snakemake/deployment -copying snakemake/deployment/env_modules.py -> build/lib/snakemake/deployment -copying snakemake/deployment/containerize.py -> build/lib/snakemake/deployment -copying snakemake/deployment/conda.py -> build/lib/snakemake/deployment -copying snakemake/deployment/__init__.py -> build/lib/snakemake/deployment -copying snakemake/deployment/singularity.py -> build/lib/snakemake/deployment -creating build/lib/snakemake/unit_tests -copying snakemake/unit_tests/__init__.py -> build/lib/snakemake/unit_tests -creating build/lib/snakemake/common -copying snakemake/common/tbdstring.py -> build/lib/snakemake/common -copying snakemake/common/__init__.py -> build/lib/snakemake/common -creating build/lib/snakemake/caching -copying snakemake/caching/local.py -> build/lib/snakemake/caching -copying snakemake/caching/__init__.py -> build/lib/snakemake/caching -copying snakemake/caching/remote.py -> build/lib/snakemake/caching -copying snakemake/caching/hash.py -> build/lib/snakemake/caching -creating build/lib/snakemake/report -copying snakemake/report/rulegraph_spec.py -> build/lib/snakemake/report -copying snakemake/report/__init__.py -> build/lib/snakemake/report +copying snakemake/linting/links.py -> build/lib/snakemake/linting creating build/lib/snakemake/remote -copying snakemake/remote/AzBlob.py -> build/lib/snakemake/remote +copying snakemake/remote/__init__.py -> build/lib/snakemake/remote +copying snakemake/remote/EGA.py -> build/lib/snakemake/remote +copying snakemake/remote/HTTP.py -> build/lib/snakemake/remote copying snakemake/remote/NCBI.py -> build/lib/snakemake/remote copying snakemake/remote/gfal.py -> build/lib/snakemake/remote -copying snakemake/remote/S3.py -> build/lib/snakemake/remote +copying snakemake/remote/GS.py -> build/lib/snakemake/remote +copying snakemake/remote/AzBlob.py -> build/lib/snakemake/remote copying snakemake/remote/XRootD.py -> build/lib/snakemake/remote -copying snakemake/remote/S3Mocked.py -> build/lib/snakemake/remote -copying snakemake/remote/HTTP.py -> build/lib/snakemake/remote -copying snakemake/remote/SFTP.py -> build/lib/snakemake/remote +copying snakemake/remote/FTP.py -> build/lib/snakemake/remote copying snakemake/remote/dropbox.py -> build/lib/snakemake/remote -copying snakemake/remote/GS.py -> build/lib/snakemake/remote copying snakemake/remote/zenodo.py -> build/lib/snakemake/remote -copying snakemake/remote/FTP.py -> build/lib/snakemake/remote +copying snakemake/remote/SFTP.py -> build/lib/snakemake/remote +copying snakemake/remote/S3.py -> build/lib/snakemake/remote copying snakemake/remote/iRODS.py -> build/lib/snakemake/remote -copying snakemake/remote/__init__.py -> build/lib/snakemake/remote -copying snakemake/remote/EGA.py -> build/lib/snakemake/remote copying snakemake/remote/webdav.py -> build/lib/snakemake/remote copying snakemake/remote/gridftp.py -> build/lib/snakemake/remote +copying snakemake/remote/S3Mocked.py -> build/lib/snakemake/remote +creating build/lib/snakemake/executors +copying snakemake/executors/__init__.py -> build/lib/snakemake/executors +copying snakemake/executors/ga4gh_tes.py -> build/lib/snakemake/executors +copying snakemake/executors/flux.py -> build/lib/snakemake/executors +copying snakemake/executors/common.py -> build/lib/snakemake/executors +copying snakemake/executors/google_lifesciences_helper.py -> build/lib/snakemake/executors +copying snakemake/executors/google_lifesciences.py -> build/lib/snakemake/executors +copying snakemake/executors/azure_batch.py -> build/lib/snakemake/executors +creating build/lib/snakemake/report +copying snakemake/report/__init__.py -> build/lib/snakemake/report +copying snakemake/report/rulegraph_spec.py -> build/lib/snakemake/report +creating build/lib/snakemake/unit_tests +copying snakemake/unit_tests/__init__.py -> build/lib/snakemake/unit_tests +creating build/lib/snakemake/common +copying snakemake/common/__init__.py -> build/lib/snakemake/common +copying snakemake/common/tbdstring.py -> build/lib/snakemake/common +creating build/lib/snakemake/caching +copying snakemake/caching/__init__.py -> build/lib/snakemake/caching +copying snakemake/caching/local.py -> build/lib/snakemake/caching +copying snakemake/caching/hash.py -> build/lib/snakemake/caching +copying snakemake/caching/remote.py -> build/lib/snakemake/caching +creating build/lib/snakemake/deployment +copying snakemake/deployment/__init__.py -> build/lib/snakemake/deployment +copying snakemake/deployment/containerize.py -> build/lib/snakemake/deployment +copying snakemake/deployment/env_modules.py -> build/lib/snakemake/deployment +copying snakemake/deployment/conda.py -> build/lib/snakemake/deployment +copying snakemake/deployment/singularity.py -> build/lib/snakemake/deployment +creating build/lib/snakemake/template_rendering +copying snakemake/template_rendering/__init__.py -> build/lib/snakemake/template_rendering +copying snakemake/template_rendering/jinja2.py -> build/lib/snakemake/template_rendering +copying snakemake/template_rendering/yte.py -> build/lib/snakemake/template_rendering creating build/lib/snakemake/executors/slurm copying snakemake/executors/slurm/__init__.py -> build/lib/snakemake/executors/slurm copying snakemake/executors/slurm/slurm_jobstep.py -> build/lib/snakemake/executors/slurm copying snakemake/executors/slurm/slurm_submit.py -> build/lib/snakemake/executors/slurm -creating build/lib/snakemake/unit_tests/templates -copying snakemake/unit_tests/templates/__init__.py -> build/lib/snakemake/unit_tests/templates creating build/lib/snakemake/report/data -copying snakemake/report/data/rulegraph.py -> build/lib/snakemake/report/data -copying snakemake/report/data/common.py -> build/lib/snakemake/report/data -copying snakemake/report/data/categories.py -> build/lib/snakemake/report/data -copying snakemake/report/data/runtimes.py -> build/lib/snakemake/report/data -copying snakemake/report/data/results.py -> build/lib/snakemake/report/data copying snakemake/report/data/__init__.py -> build/lib/snakemake/report/data copying snakemake/report/data/timeline.py -> build/lib/snakemake/report/data +copying snakemake/report/data/runtimes.py -> build/lib/snakemake/report/data copying snakemake/report/data/packages.py -> build/lib/snakemake/report/data +copying snakemake/report/data/common.py -> build/lib/snakemake/report/data copying snakemake/report/data/rules.py -> build/lib/snakemake/report/data +copying snakemake/report/data/results.py -> build/lib/snakemake/report/data +copying snakemake/report/data/rulegraph.py -> build/lib/snakemake/report/data +copying snakemake/report/data/categories.py -> build/lib/snakemake/report/data creating build/lib/snakemake/report/template copying snakemake/report/template/__init__.py -> build/lib/snakemake/report/template creating build/lib/snakemake/report/template/components copying snakemake/report/template/components/__init__.py -> build/lib/snakemake/report/template/components +creating build/lib/snakemake/unit_tests/templates +copying snakemake/unit_tests/templates/__init__.py -> build/lib/snakemake/unit_tests/templates copying snakemake/report.css -> build/lib/snakemake copying snakemake/gui.html -> build/lib/snakemake copying snakemake/executors/jobscript.sh -> build/lib/snakemake/executors -copying snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/lib/snakemake/unit_tests/templates -copying snakemake/unit_tests/templates/common.py.jinja2 -> build/lib/snakemake/unit_tests/templates copying snakemake/report/template/style.css -> build/lib/snakemake/report/template copying snakemake/report/template/index.html.jinja2 -> build/lib/snakemake/report/template copying snakemake/report/template/logo.svg -> build/lib/snakemake/report/template -copying snakemake/report/template/components/menu.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/result_info.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/breadcrumbs.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/report_info.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/icon.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/stats.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/list_heading.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/button.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/category.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/content.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/abstract_menu.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/navbar.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/result_view_button.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/rule_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/rule_graph.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/report_info.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/icon.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/list_item.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/breadcrumbs.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/result_info.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/button.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/menu.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/abstract_results.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/list_heading.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/subcategory.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/category.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/common.js -> build/lib/snakemake/report/template/components +copying snakemake/report/template/components/list_item.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/search_results.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/abstract_menu.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/content.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/app.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/abstract_results.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/subcategory.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/rule_info.js -> build/lib/snakemake/report/template/components -copying snakemake/report/template/components/result_view_button.js -> build/lib/snakemake/report/template/components +copying snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/lib/snakemake/unit_tests/templates +copying snakemake/unit_tests/templates/common.py.jinja2 -> build/lib/snakemake/unit_tests/templates UPDATING build/lib/snakemake/_version.py set build/lib/snakemake/_version.py to '7.32.4' installing to build/bdist.linux-x86_64/wheel @@ -2553,142 +2589,142 @@ running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/snakemake -creating build/bdist.linux-x86_64/wheel/snakemake/template_rendering -copying build/lib/snakemake/template_rendering/jinja2.py -> build/bdist.linux-x86_64/wheel/./snakemake/template_rendering -copying build/lib/snakemake/template_rendering/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/template_rendering -copying build/lib/snakemake/template_rendering/yte.py -> build/bdist.linux-x86_64/wheel/./snakemake/template_rendering -copying build/lib/snakemake/interfaces.py -> build/bdist.linux-x86_64/wheel/./snakemake copying build/lib/snakemake/profiles.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/io.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/target_jobs.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/stats.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/checkpoints.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/modules.py -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/linting +copying build/lib/snakemake/linting/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting +copying build/lib/snakemake/linting/snakefiles.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting +copying build/lib/snakemake/linting/rules.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting +copying build/lib/snakemake/linting/links.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting +copying build/lib/snakemake/sourcecache.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/benchmark.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/jobs.py -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/remote +copying build/lib/snakemake/remote/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/EGA.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/HTTP.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/NCBI.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/gfal.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/GS.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/AzBlob.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/XRootD.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/FTP.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/dropbox.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/zenodo.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/SFTP.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/S3.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/iRODS.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/webdav.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/gridftp.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/remote/S3Mocked.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote +copying build/lib/snakemake/ruleinfo.py -> build/bdist.linux-x86_64/wheel/./snakemake creating build/bdist.linux-x86_64/wheel/snakemake/executors -copying build/lib/snakemake/executors/ga4gh_tes.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors +copying build/lib/snakemake/executors/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors copying build/lib/snakemake/executors/jobscript.sh -> build/bdist.linux-x86_64/wheel/./snakemake/executors +copying build/lib/snakemake/executors/ga4gh_tes.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors +copying build/lib/snakemake/executors/flux.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors copying build/lib/snakemake/executors/common.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors creating build/bdist.linux-x86_64/wheel/snakemake/executors/slurm copying build/lib/snakemake/executors/slurm/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors/slurm copying build/lib/snakemake/executors/slurm/slurm_jobstep.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors/slurm copying build/lib/snakemake/executors/slurm/slurm_submit.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors/slurm -copying build/lib/snakemake/executors/azure_batch.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors -copying build/lib/snakemake/executors/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors -copying build/lib/snakemake/executors/google_lifesciences.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors copying build/lib/snakemake/executors/google_lifesciences_helper.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors -copying build/lib/snakemake/executors/flux.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors -copying build/lib/snakemake/path_modifier.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/script.py -> build/bdist.linux-x86_64/wheel/./snakemake -creating build/bdist.linux-x86_64/wheel/snakemake/linting -copying build/lib/snakemake/linting/snakefiles.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting -copying build/lib/snakemake/linting/links.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting -copying build/lib/snakemake/linting/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting -copying build/lib/snakemake/linting/rules.py -> build/bdist.linux-x86_64/wheel/./snakemake/linting -copying build/lib/snakemake/logging.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/__main__.py -> build/bdist.linux-x86_64/wheel/./snakemake -creating build/bdist.linux-x86_64/wheel/snakemake/deployment -copying build/lib/snakemake/deployment/env_modules.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment -copying build/lib/snakemake/deployment/containerize.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment -copying build/lib/snakemake/deployment/conda.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment -copying build/lib/snakemake/deployment/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment -copying build/lib/snakemake/deployment/singularity.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment -creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests -copying build/lib/snakemake/unit_tests/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests -creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates -copying build/lib/snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests/templates -copying build/lib/snakemake/unit_tests/templates/common.py.jinja2 -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests/templates -copying build/lib/snakemake/unit_tests/templates/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests/templates -copying build/lib/snakemake/wrapper.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/decorators.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/utils.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/persistence.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/gui.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/cwl.py -> build/bdist.linux-x86_64/wheel/./snakemake -creating build/bdist.linux-x86_64/wheel/snakemake/common -copying build/lib/snakemake/common/tbdstring.py -> build/bdist.linux-x86_64/wheel/./snakemake/common -copying build/lib/snakemake/common/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/common -copying build/lib/snakemake/parser.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/ruleinfo.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/scheduler.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/report.css -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/gui.html -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/dag.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/output_index.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/executors/google_lifesciences.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors +copying build/lib/snakemake/executors/azure_batch.py -> build/bdist.linux-x86_64/wheel/./snakemake/executors copying build/lib/snakemake/_version.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake -creating build/bdist.linux-x86_64/wheel/snakemake/caching -copying build/lib/snakemake/caching/local.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching -copying build/lib/snakemake/caching/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching -copying build/lib/snakemake/caching/remote.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching -copying build/lib/snakemake/caching/hash.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching -copying build/lib/snakemake/workflow.py -> build/bdist.linux-x86_64/wheel/./snakemake creating build/bdist.linux-x86_64/wheel/snakemake/report +copying build/lib/snakemake/report/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/report +copying build/lib/snakemake/report/rulegraph_spec.py -> build/bdist.linux-x86_64/wheel/./snakemake/report creating build/bdist.linux-x86_64/wheel/snakemake/report/data -copying build/lib/snakemake/report/data/rulegraph.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data -copying build/lib/snakemake/report/data/common.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data -copying build/lib/snakemake/report/data/categories.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data -copying build/lib/snakemake/report/data/runtimes.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data -copying build/lib/snakemake/report/data/results.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data copying build/lib/snakemake/report/data/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data copying build/lib/snakemake/report/data/timeline.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data +copying build/lib/snakemake/report/data/runtimes.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data copying build/lib/snakemake/report/data/packages.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data +copying build/lib/snakemake/report/data/common.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data copying build/lib/snakemake/report/data/rules.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data +copying build/lib/snakemake/report/data/results.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data +copying build/lib/snakemake/report/data/rulegraph.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data +copying build/lib/snakemake/report/data/categories.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/data creating build/bdist.linux-x86_64/wheel/snakemake/report/template -copying build/lib/snakemake/report/template/style.css -> build/bdist.linux-x86_64/wheel/./snakemake/report/template +copying build/lib/snakemake/report/template/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/template copying build/lib/snakemake/report/template/logo.svg -> build/bdist.linux-x86_64/wheel/./snakemake/report/template +copying build/lib/snakemake/report/template/index.html.jinja2 -> build/bdist.linux-x86_64/wheel/./snakemake/report/template creating build/bdist.linux-x86_64/wheel/snakemake/report/template/components -copying build/lib/snakemake/report/template/components/menu.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/result_info.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/breadcrumbs.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/stats.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/list_heading.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/button.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/category.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/navbar.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/rule_graph.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components copying build/lib/snakemake/report/template/components/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components copying build/lib/snakemake/report/template/components/report_info.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components copying build/lib/snakemake/report/template/components/icon.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/list_item.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/common.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/search_results.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/abstract_menu.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/stats.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components copying build/lib/snakemake/report/template/components/content.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/app.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/abstract_menu.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/navbar.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/result_view_button.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/rule_info.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/rule_graph.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/breadcrumbs.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/result_info.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/button.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/menu.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components copying build/lib/snakemake/report/template/components/abstract_results.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/list_heading.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components copying build/lib/snakemake/report/template/components/subcategory.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/rule_info.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/components/result_view_button.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components -copying build/lib/snakemake/report/template/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/report/template -copying build/lib/snakemake/report/template/index.html.jinja2 -> build/bdist.linux-x86_64/wheel/./snakemake/report/template -copying build/lib/snakemake/report/rulegraph_spec.py -> build/bdist.linux-x86_64/wheel/./snakemake/report -copying build/lib/snakemake/report/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/report +copying build/lib/snakemake/report/template/components/category.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/common.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/list_item.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/search_results.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/components/app.js -> build/bdist.linux-x86_64/wheel/./snakemake/report/template/components +copying build/lib/snakemake/report/template/style.css -> build/bdist.linux-x86_64/wheel/./snakemake/report/template +copying build/lib/snakemake/wrapper.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/persistence.py -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests +copying build/lib/snakemake/unit_tests/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests +creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates +copying build/lib/snakemake/unit_tests/templates/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests/templates +copying build/lib/snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests/templates +copying build/lib/snakemake/unit_tests/templates/common.py.jinja2 -> build/bdist.linux-x86_64/wheel/./snakemake/unit_tests/templates +copying build/lib/snakemake/parser.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/scheduler.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/path_modifier.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/dag.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/decorators.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/io.py -> build/bdist.linux-x86_64/wheel/./snakemake copying build/lib/snakemake/notebook.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/exceptions.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/benchmark.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/shell.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/checkpoints.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/stats.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/report.css -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/workflow.py -> build/bdist.linux-x86_64/wheel/./snakemake copying build/lib/snakemake/rules.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/__main__.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/interfaces.py -> build/bdist.linux-x86_64/wheel/./snakemake copying build/lib/snakemake/resources.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/modules.py -> build/bdist.linux-x86_64/wheel/./snakemake -creating build/bdist.linux-x86_64/wheel/snakemake/remote -copying build/lib/snakemake/remote/AzBlob.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/NCBI.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/gfal.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/S3.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/XRootD.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/S3Mocked.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/HTTP.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/SFTP.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/dropbox.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/GS.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/zenodo.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/FTP.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/iRODS.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/EGA.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/webdav.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/remote/gridftp.py -> build/bdist.linux-x86_64/wheel/./snakemake/remote -copying build/lib/snakemake/sourcecache.py -> build/bdist.linux-x86_64/wheel/./snakemake -copying build/lib/snakemake/jobs.py -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/common +copying build/lib/snakemake/common/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/common +copying build/lib/snakemake/common/tbdstring.py -> build/bdist.linux-x86_64/wheel/./snakemake/common +copying build/lib/snakemake/output_index.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/logging.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/target_jobs.py -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/caching +copying build/lib/snakemake/caching/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching +copying build/lib/snakemake/caching/local.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching +copying build/lib/snakemake/caching/hash.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching +copying build/lib/snakemake/caching/remote.py -> build/bdist.linux-x86_64/wheel/./snakemake/caching +copying build/lib/snakemake/utils.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/cwl.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/script.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/gui.html -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/deployment +copying build/lib/snakemake/deployment/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment +copying build/lib/snakemake/deployment/containerize.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment +copying build/lib/snakemake/deployment/env_modules.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment +copying build/lib/snakemake/deployment/conda.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment +copying build/lib/snakemake/deployment/singularity.py -> build/bdist.linux-x86_64/wheel/./snakemake/deployment +copying build/lib/snakemake/gui.py -> build/bdist.linux-x86_64/wheel/./snakemake +copying build/lib/snakemake/shell.py -> build/bdist.linux-x86_64/wheel/./snakemake +creating build/bdist.linux-x86_64/wheel/snakemake/template_rendering +copying build/lib/snakemake/template_rendering/__init__.py -> build/bdist.linux-x86_64/wheel/./snakemake/template_rendering +copying build/lib/snakemake/template_rendering/jinja2.py -> build/bdist.linux-x86_64/wheel/./snakemake/template_rendering +copying build/lib/snakemake/template_rendering/yte.py -> build/bdist.linux-x86_64/wheel/./snakemake/template_rendering +copying build/lib/snakemake/exceptions.py -> build/bdist.linux-x86_64/wheel/./snakemake running install_egg_info running egg_info creating snakemake.egg-info @@ -2706,7 +2742,7 @@ Copying snakemake.egg-info to build/bdist.linux-x86_64/wheel/./snakemake-7.32.4.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/snakemake-7.32.4.dist-info/WHEEL -creating '/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/.tmp-5kybur0_/snakemake-7.32.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/.tmp-9vi_5u4h/snakemake-7.32.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'snakemake/__init__.py' adding 'snakemake/__main__.py' adding 'snakemake/_version.py' @@ -3008,9 +3044,9 @@ copying downloadable files... [100%] ../tests/test_report/expected-results/report.html copying static files... -Writing evaluated template result to /build/reproducible-path/snakemake-7.32.4/docs/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/snakemake-7.32.4/docs/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/snakemake-7.32.4/docs/_build/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/snakemake-7.32.4/docs/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/snakemake-7.32.4/docs/_build/html/_static/js/versions.js copying static files: done copying extra files... @@ -3144,7 +3180,7 @@ cachedir: .pytest_cache rootdir: /build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build configfile: pyproject.toml -plugins: requests_mock-1.12.1, mock-3.15.0, typeguard-4.4.4 +plugins: mock-3.15.0, typeguard-4.4.4, requests_mock-1.12.1 collecting ... collected 395 items / 99 deselected / 296 selected .pybuild/cpython3_3.13_snakemake/build/tests/test_expand.py::test_simple_expand PASSED [ 0%] @@ -3159,34 +3195,34 @@ .pybuild/cpython3_3.13_snakemake/build/tests/test_kubernetes.py::test_kubernetes_singularity SKIPPED [ 3%] .pybuild/cpython3_3.13_snakemake/build/tests/test_kubernetes.py::test_kubernetes_conda_singularity SKIPPED [ 3%] .pybuild/cpython3_3.13_snakemake/build/tests/test_kubernetes.py::test_issue1041 SKIPPED [ 4%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[iofile_by_index-positive] SKIPPED [ 4%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[iofile_by_index-negative] SKIPPED [ 4%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[envvars-positive] SKIPPED [ 5%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[envvars-negative] SKIPPED [ 5%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[absolute_paths-positive] SKIPPED [ 5%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[absolute_paths-negative] SKIPPED [ 6%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[singularity-positive] SKIPPED [ 6%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[singularity-negative] SKIPPED [ 6%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[dynamic-positive] SKIPPED [ 7%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[dynamic-negative] SKIPPED [ 7%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[missing_software_definition-positive] SKIPPED [ 7%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[missing_software_definition-negative] SKIPPED [ 8%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[params_prefix-positive] SKIPPED [ 8%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[params_prefix-negative] SKIPPED [ 8%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[path_add-positive] SKIPPED [ 9%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[path_add-negative] SKIPPED [ 9%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[params_prefix-positive] SKIPPED [ 4%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[params_prefix-negative] SKIPPED [ 4%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[log_directive-positive] SKIPPED [ 5%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[log_directive-negative] SKIPPED [ 5%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[long_run-positive] SKIPPED [ 5%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[long_run-negative] SKIPPED [ 6%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[envvars-positive] SKIPPED [ 6%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[envvars-negative] SKIPPED [ 6%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[tab_usage-positive] SKIPPED [ 7%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[tab_usage-negative] SKIPPED [ 7%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[absolute_paths-positive] SKIPPED [ 7%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[absolute_paths-negative] SKIPPED [ 8%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[singularity-positive] SKIPPED [ 8%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[singularity-negative] SKIPPED [ 8%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[mixed_func_and_rules-positive] SKIPPED [ 9%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[mixed_func_and_rules-negative] SKIPPED [ 9%] .pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[version-positive] SKIPPED [ 9%] .pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[version-negative] SKIPPED [ 10%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[log_directive-positive] SKIPPED [ 10%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[log_directive-negative] SKIPPED [ 10%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[long_run-positive] SKIPPED [ 11%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[long_run-negative] SKIPPED [ 11%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[not_used_params-positive] SKIPPED [ 11%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[not_used_params-negative] SKIPPED [ 12%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[tab_usage-positive] SKIPPED [ 12%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[tab_usage-negative] SKIPPED [ 12%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[mixed_func_and_rules-positive] SKIPPED [ 13%] -.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[mixed_func_and_rules-negative] SKIPPED [ 13%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[not_used_params-positive] SKIPPED [ 10%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[not_used_params-negative] SKIPPED [ 10%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[iofile_by_index-positive] SKIPPED [ 11%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[iofile_by_index-negative] SKIPPED [ 11%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[missing_software_definition-positive] SKIPPED [ 11%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[missing_software_definition-negative] SKIPPED [ 12%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[path_add-positive] SKIPPED [ 12%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[path_add-negative] SKIPPED [ 12%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[dynamic-positive] SKIPPED [ 13%] +.pybuild/cpython3_3.13_snakemake/build/tests/test_linting.py::test_lint[dynamic-negative] SKIPPED [ 13%] .pybuild/cpython3_3.13_snakemake/build/tests/test_persistence.py::TestCleanupContainers::test_one_unrequired_container_gets_removed PASSED [ 13%] .pybuild/cpython3_3.13_snakemake/build/tests/test_schema.py::test_config PASSED [ 14%] .pybuild/cpython3_3.13_snakemake/build/tests/test_schema.py::test_config_ref PASSED [ 14%] @@ -3405,12 +3441,12 @@ .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 0x00007f995f7fe6c0 (most recent call first): +Thread 0x00007f39577fe6c0 (most recent call first): File "/usr/lib/python3.13/subprocess.py", line 2024 in _try_wait File "/usr/lib/python3.13/subprocess.py", line 2066 in _wait File "/usr/lib/python3.13/subprocess.py", line 1280 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-y361dt49/Snakefile", line 76 in __rule_sort + File "/tmp/snakemake-n2oqhfex/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 @@ -3419,27 +3455,12 @@ File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f995dffb6c0 (most recent call first): - File "/usr/lib/python3.13/threading.py", line 363 in wait - File "/usr/lib/python3.13/threading.py", line 659 in wait - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/benchmark.py", line 184 in run - File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner - File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap - -Thread 0x00007f995effd6c0 (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 - File "/usr/lib/python3.13/threading.py", line 994 in run - File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner - File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap - -Thread 0x00007f99b57fa6c0 (most recent call first): +Thread 0x00007f39b920d6c0 (most recent call first): File "/usr/lib/python3.13/subprocess.py", line 2024 in _try_wait File "/usr/lib/python3.13/subprocess.py", line 2066 in _wait File "/usr/lib/python3.13/subprocess.py", line 1280 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-y361dt49/Snakefile", line 76 in __rule_sort + File "/tmp/snakemake-n2oqhfex/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 @@ -3448,34 +3469,34 @@ File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f9984ff96c0 (most recent call first): - File "/usr/lib/python3.13/subprocess.py", line 2024 in _try_wait - File "/usr/lib/python3.13/subprocess.py", line 2066 in _wait - File "/usr/lib/python3.13/subprocess.py", line 1280 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-y361dt49/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 +Thread 0x00007f39abfff6c0 (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 File "/usr/lib/python3.13/threading.py", line 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f995d7fa6c0 (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 +Thread 0x00007f39567fc6c0 (most recent call first): + File "/usr/lib/python3.13/subprocess.py", line 2024 in _try_wait + File "/usr/lib/python3.13/subprocess.py", line 2066 in _wait + File "/usr/lib/python3.13/subprocess.py", line 1280 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-n2oqhfex/Snakefile", line 34 in __rule_trimming + 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 File "/usr/lib/python3.13/threading.py", line 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f994b7fe6c0 (most recent call first): +Thread 0x00007f3957fff6c0 (most recent call first): File "/usr/lib/python3.13/subprocess.py", line 2024 in _try_wait File "/usr/lib/python3.13/subprocess.py", line 2066 in _wait File "/usr/lib/python3.13/subprocess.py", line 1280 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-y361dt49/Snakefile", line 56 in __rule_align + File "/tmp/snakemake-n2oqhfex/Snakefile", line 34 in __rule_trimming 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 @@ -3484,116 +3505,109 @@ File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f994affd6c0 (most recent call first): - File "/usr/lib/python3.13/threading.py", line 363 in wait - File "/usr/lib/python3.13/threading.py", line 659 in wait - File "/build/reproducible-path/snakemake-7.32.4/.pybuild/cpython3_3.13_snakemake/build/snakemake/benchmark.py", line 184 in run - File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner - File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap - -Thread 0x00007f999ffff6c0 (most recent call first): +Thread 0x00007f3965ffb6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99b4ff96c0 (most recent call first): +Thread 0x00007f3966ffd6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99877fe6c0 (most recent call first): +Thread 0x00007f398d7fa6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f9985ffb6c0 (most recent call first): +Thread 0x00007f3967fff6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99867fc6c0 (most recent call first): +Thread 0x00007f398cff96c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f999e7fc6c0 (most recent call first): +Thread 0x00007f398dffb6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f999cff96c0 (most recent call first): +Thread 0x00007f398e7fc6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f999f7fe6c0 (most recent call first): +Thread 0x00007f398effd6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f999effd6c0 (most recent call first): +Thread 0x00007f398f7fe6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99b6ffd6c0 (most recent call first): +Thread 0x00007f398ffff6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f999dffb6c0 (most recent call first): +Thread 0x00007f39a97fa6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f9987fff6c0 (most recent call first): +Thread 0x00007f39a9ffb6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99c56a66c0 (most recent call first): +Thread 0x00007f39ba50f6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99b5ffb6c0 (most recent call first): +Thread 0x00007f39aaffd6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99b67fc6c0 (most recent call first): +Thread 0x00007f39ab7fe6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99b77fe6c0 (most recent call first): +Thread 0x00007f39b9d0e6c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99c5ea76c0 (most recent call first): +Thread 0x00007f39bb6116c0 (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 994 in run File "/usr/lib/python3.13/threading.py", line 1043 in _bootstrap_inner File "/usr/lib/python3.13/threading.py", line 1014 in _bootstrap -Thread 0x00007f99ce043100 (most recent call first): +Thread 0x00007f39c77bf100 (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 @@ -3690,10 +3704,10 @@ warnings.warn( tests/tests.py::test_glpk_solver - :891: DeprecationWarning: This process (pid=3305293) is multi-threaded, use of fork() may lead to deadlocks in the child. + :891: DeprecationWarning: This process (pid=1253594) 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 1210.35s (0:20:10) = += 249 passed, 46 skipped, 99 deselected, 1 xfailed, 21 warnings in 1071.21s (0:17:51) = 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 @@ -3727,8 +3741,8 @@ 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_7.32.4-7_all.deb'. dpkg-deb: building package 'snakemake' in '../snakemake_7.32.4-7_all.deb'. +dpkg-deb: building package 'snakemake-doc' in '../snakemake-doc_7.32.4-7_all.deb'. dpkg-genbuildinfo --build=binary -O../snakemake_7.32.4-7_amd64.buildinfo dpkg-genchanges --build=binary -O../snakemake_7.32.4-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3736,12 +3750,14 @@ 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/1233404/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1233404/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/3036897 and its subdirectories -I: Current time: Mon Nov 2 02:22:44 -12 2026 -I: pbuilder-time-stamp: 1793629364 +I: removing directory /srv/workspace/pbuilder/1233404 and its subdirectories +I: Current time: Tue Sep 30 22:21:06 +14 2025 +I: pbuilder-time-stamp: 1759220466