Diff of the two buildlogs: -- --- b1/build.log 2025-11-03 06:04:59.697228047 +0000 +++ b2/build.log 2025-11-03 06:06:15.561318261 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 6 00:26:18 -12 2026 -I: pbuilder-time-stamp: 1796559978 +I: Current time: Mon Nov 3 20:05:01 +14 2025 +I: pbuilder-time-stamp: 1762149901 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ dpkg-source: info: applying xfail_command_tests.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/120426/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/177478/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 3 06:05 /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/177478/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/177478/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='8a505dfc22dd439ca39c3e21c022801a' - 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='120426' - PS1='# ' - PS2='> ' + INVOCATION_ID=036ca703391a4a889fb991984ddded48 + 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=177478 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.PQHIzLJT/pbuilderrc_GUjB --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PQHIzLJT/b1 --logfile b1/build.log paleomix_1.3.10-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.PQHIzLJT/pbuilderrc_ZQ17 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PQHIzLJT/b2 --logfile b2/build.log paleomix_1.3.10-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/120426/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/177478/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -434,7 +466,7 @@ Get: 298 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml.clib arm64 0.2.12+ds-1+b1 [117 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 python3-setproctitle arm64 1.3.7-1 [18.5 kB] -Fetched 226 MB in 1s (162 MB/s) +Fetched 226 MB in 1s (224 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19968 files and directories currently installed.) @@ -1418,8 +1450,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 6 12:27:00 UTC 2026. -Universal Time is now: Sun Dec 6 12:27:00 UTC 2026. +Local time is now: Mon Nov 3 06:05:35 UTC 2025. +Universal Time is now: Mon Nov 3 06:05:35 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1862,7 +1894,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/paleomix-1.3.10/ && 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 > ../paleomix_1.3.10-1_source.changes +I: user script /srv/workspace/pbuilder/177478/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/177478/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/paleomix-1.3.10/ && 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 > ../paleomix_1.3.10-1_source.changes dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.3.10-1 dpkg-buildpackage: info: source distribution unstable @@ -2628,63 +2664,6 @@ creating /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/paleomix-1.3.10' -PATH=/build/reproducible-path/paleomix-1.3.10/bin/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test -I: pybuild pybuild:308: cp -a README.rst /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build; -I: pybuild base:311: cd /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build; python3.13 -m pytest tests -============================= test session starts ============================== -platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -rootdir: /build/reproducible-path/paleomix-1.3.10 -configfile: setup.cfg -plugins: typeguard-4.4.4 -collected 1500 items - -tests/atomiccmd_test/builder_test.py ................................... [ 2%] -...................................................... [ 5%] -tests/atomiccmd_test/command_test.py ................................... [ 8%] -........................................................................ [ 13%] -................ [ 14%] -tests/atomiccmd_test/pprint_test.py .................................... [ 16%] -.. [ 16%] -tests/atomiccmd_test/sets_test.py ...................................... [ 19%] -............ [ 20%] -tests/common_tests/bedtools_test.py ............................... [ 22%] -tests/common_tests/fileutils_test.py ................................... [ 24%] -...................................................................... [ 29%] -tests/common_tests/formats_tests/fasta_test.py ......................... [ 30%] -............. [ 31%] -tests/common_tests/formats_tests/fastq_test.py ......................... [ 33%] -........... [ 34%] -tests/common_tests/formats_tests/msa_test.py ........................... [ 35%] -................... [ 37%] -tests/common_tests/formats_tests/newick_test.py ........................ [ 38%] -........................................................................ [ 43%] -...... [ 43%] -tests/common_tests/formats_tests/phylip_test.py ........ [ 44%] -tests/common_tests/makefile_test.py .................................... [ 46%] -........................................................................ [ 51%] -........................................................................ [ 56%] -........................................................................ [ 61%] -........................................................................ [ 66%] -............................... [ 68%] -tests/common_tests/sampling_test.py ........................ [ 69%] -tests/common_tests/sequences_test.py ................................... [ 72%] -............... [ 73%] -tests/common_tests/text_test.py ....................................... [ 75%] -tests/common_tests/utilities_test.py ................................... [ 77%] -........................................................................ [ 82%] -.. [ 82%] -tests/common_tests/versions_test.py .................................... [ 85%] -............................................................ [ 89%] -tests/node_test.py ..................................................... [ 92%] -....................................... [ 95%] -tests/nodegraph_test.py ......... [ 96%] -tests/tools_test/factory_test.py xXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [ 98%] -XXXXXXXXXXXXXXXXXXX.. [100%] - -================= 1442 passed, 1 xfailed, 57 xpassed in 16.76s ================= -make[1]: Leaving directory '/build/reproducible-path/paleomix-1.3.10' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -3228,59 +3207,15 @@ check.warn(importable) running install_lib creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/README.rst -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/__pycache__/pipeline.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/__pycache__/main.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/__pycache__/nodegraph.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/__pycache__/node.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/__pycache__/yaml.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/__pycache__/sets.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/__pycache__/pprint.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/__pycache__/command.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/__pycache__/builder.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/builder.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/command.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/pprint.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/atomiccmd/sets.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/atomiccmd creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/vcfwrap.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/vcffilter.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/timer.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/bamfiles.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/argparse.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/rtools.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/resources.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/logging.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/system.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/text.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/sampling.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/makefile.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/sequences.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/testing.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/bedtools.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/versions.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/procs.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/utilities.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/fileutils.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/phylip.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/_graph.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/newick.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/msa.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/fastq.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/fasta.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/_common.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/_common.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/formats/_graph.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common/formats @@ -3310,24 +3245,6 @@ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/vcfwrap.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/common/versions.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/common creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/newick.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/examl.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/phylip.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/raxml.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/formats.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/mafft.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/sequences.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/bedtools.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/commands.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/mapdamage.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/picard.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/adapterremoval.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/validation.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/bowtie2.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/bwa.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/samtools.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/adapterremoval.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/bedtools.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes @@ -3346,29 +3263,8 @@ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/sequences.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/nodes/validation.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/nodes creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/trim_pipeline.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/mkfile.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/config.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/nodes.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/makefile.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/pipeline.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/paths.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/summary.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/statistics.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/target.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/prefix.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/sample.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/library.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/lane.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/reads.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/lane.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/parts/library.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam/parts @@ -3387,19 +3283,7 @@ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/pipeline.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/bam/trim_pipeline.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/bam creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/__pycache__/makefile.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/__pycache__/config.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/__pycache__/mkfile.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/__pycache__/example.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/__pycache__/pipeline.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/__pycache__/phylo.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/__pycache__/msa.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/__pycache__/genotype.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/genotype.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/parts/msa.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo/parts @@ -3411,24 +3295,7 @@ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/mkfile.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/phylo/pipeline.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/phylo creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/build_tped.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/build_mito.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/build_db.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/common.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/database.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/config.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/pipeline.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/summary.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/admixture.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/report.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/nuclear.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/mitochondria.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/common.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/admixture.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/pipelines/zonkey/parts/common.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/pipelines/zonkey/parts @@ -3511,23 +3378,7 @@ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/resources/examples/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/resources/examples copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/resources/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/resources creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/rscript.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/validate_fastq.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/vcf_to_fasta.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/vcf_filter.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/rmdup_collapsed.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/dupcheck.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/depths.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/coverage.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/cleanup.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/factory.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/__pycache__ creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats -creating /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/bam_stats/__pycache__/common.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/bam_stats/__pycache__/coverage.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats/__pycache__ -copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/bam_stats/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/bam_stats/__init__.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/bam_stats/common.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats copying /build/reproducible-path/paleomix-1.3.10/.pybuild/cpython3_3.13/build/paleomix/tools/bam_stats/coverage.py -> /build/reproducible-path/paleomix-1.3.10/debian/paleomix/usr/lib/python3.13/dist-packages/paleomix/tools/bam_stats @@ -3685,15 +3536,17 @@ # sure all files are really copied rsync -a -v tests debian/paleomix/usr/share/doc/paleomix sending incremental file list +tests/ tests/atomiccmd_test/ tests/common_tests/ tests/common_tests/formats_tests/ tests/data/ tests/data/empty_file_1 tests/data/empty_file_2 +tests/tools_test/ -sent 931 bytes received 76 bytes 2,014.00 bytes/sec -total size is 335,102 speedup is 332.77 +sent 1,016 bytes received 160 bytes 2,352.00 bytes/sec +total size is 335,102 speedup is 284.95 # test runner is seeking for paleomix modules in source - we use inside the installed package ### sed -i 's:(find paleomix -mindepth 1:(find /usr/lib/python*/dist-packages/paleomix -mindepth 1:' debian/*/usr/share/doc/*/tests/run #echo "====== Also empty files belong to the docs ======" @@ -3735,7 +3588,7 @@ D: dh_python3 pydist:175: trying to find dependency for setproctitle>=1.1.0 (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps -D: dh_python3 depends:253: D={'python3-pysam', 'python3-ruamel.yaml', 'python3:any', 'python3-configargparse', 'python3-setproctitle', 'python3-coloredlogs'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:253: D={'python3:any', 'python3-ruamel.yaml', 'python3-coloredlogs', 'python3-setproctitle', 'python3-pysam', 'python3-configargparse'}; R=[]; S=[]; E=[], B=[]; RT=[] make[1]: Leaving directory '/build/reproducible-path/paleomix-1.3.10' dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild @@ -3771,12 +3624,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/177478/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/177478/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/120426 and its subdirectories -I: Current time: Sun Dec 6 00:27:58 -12 2026 -I: pbuilder-time-stamp: 1796560078 +I: removing directory /srv/workspace/pbuilder/177478 and its subdirectories +I: Current time: Mon Nov 3 20:06:14 +14 2025 +I: pbuilder-time-stamp: 1762149974