Diff of the two buildlogs: -- --- b1/build.log 2025-10-23 05:12:39.161551128 +0000 +++ b2/build.log 2025-10-23 05:16:35.537815710 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 22 17:09:56 -12 2025 -I: pbuilder-time-stamp: 1761196196 +I: Current time: Thu Nov 26 01:35:40 +14 2026 +I: pbuilder-time-stamp: 1795606540 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -22,53 +22,85 @@ dpkg-source: info: unpacking mapdamage_2.2.3+dfsg-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1892354/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2217962/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Nov 25 11:36 /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/2217962/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2217962/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=40 ' - 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=42 ' + 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='ac7474c316024685ba9b108efcdbaf1a' - 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='1892354' - PS1='# ' - PS2='> ' + INVOCATION_ID=d483c89edd4d4f83b397ca1d4ad966f0 + 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=2217962 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.xVrx8QUt/pbuilderrc_FzGo --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.xVrx8QUt/b1 --logfile b1/build.log mapdamage_2.2.3+dfsg-1.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.xVrx8QUt/pbuilderrc_ADUO --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.xVrx8QUt/b2 --logfile b2/build.log mapdamage_2.2.3+dfsg-1.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-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 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1892354/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2217962/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -320,7 +352,7 @@ Get: 193 http://deb.debian.org/debian forky/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 194 http://deb.debian.org/debian forky/main amd64 r-cran-inline all 0.3.21-1 [132 kB] Get: 195 http://deb.debian.org/debian forky/main amd64 seqtk amd64 1.4-2 [34.6 kB] -Fetched 127 MB in 4s (31.9 MB/s) +Fetched 127 MB in 4s (30.5 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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.) @@ -963,8 +995,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Oct 23 05:11:56 UTC 2025. -Universal Time is now: Thu Oct 23 05:11:56 UTC 2025. +Local time is now: Wed Nov 25 11:37:52 UTC 2026. +Universal Time is now: Wed Nov 25 11:37:52 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-15) ... @@ -1150,7 +1182,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/mapdamage-2.2.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mapdamage_2.2.3+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2217962/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2217962/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mapdamage-2.2.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mapdamage_2.2.3+dfsg-1_source.changes dpkg-buildpackage: info: source package mapdamage dpkg-buildpackage: info: source version 2.2.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1187,15 +1223,15 @@ * Building wheel... No `packages` or `py_modules` configuration, performing automatic discovery. `flat-layout` detected -- analysing . -discovered packages -- ['mapdamage', 'mapdamage.seqtk', 'mapdamage.Rscripts', 'mapdamage.tests', 'mapdamage.Rscripts.stats', 'mapdamage.tests.probs'] +discovered packages -- ['mapdamage', 'mapdamage.tests', 'mapdamage.Rscripts', 'mapdamage.seqtk', 'mapdamage.tests.probs', 'mapdamage.Rscripts.stats'] /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). - By 2026-Feb-18, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** @@ -1206,18 +1242,18 @@ running build running build_py creating build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/parseoptions.py -> build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/align.py -> build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/composition.py -> build/lib.linux-x86_64-cpython-313/mapdamage copying mapdamage/version.py -> build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/mp_test.py -> build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/__init__.py -> build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/tables.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/seq.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/composition.py -> build/lib.linux-x86_64-cpython-313/mapdamage copying mapdamage/rscript.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/align.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/__init__.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/parseoptions.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/mp_test.py -> build/lib.linux-x86_64-cpython-313/mapdamage copying mapdamage/rescale.py -> build/lib.linux-x86_64-cpython-313/mapdamage +copying mapdamage/tables.py -> build/lib.linux-x86_64-cpython-313/mapdamage copying mapdamage/main.py -> build/lib.linux-x86_64-cpython-313/mapdamage copying mapdamage/__main__.py -> build/lib.linux-x86_64-cpython-313/mapdamage -copying mapdamage/seq.py -> build/lib.linux-x86_64-cpython-313/mapdamage running egg_info creating mapdamage.egg-info writing mapdamage.egg-info/PKG-INFO @@ -1234,21 +1270,20 @@ copying mapdamage/Rscripts/lengths.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts copying mapdamage/Rscripts/mapDamage.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts creating build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats -copying mapdamage/Rscripts/stats/data.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats -copying mapdamage/Rscripts/stats/priorPropose.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats -copying mapdamage/Rscripts/stats/checkLibraries.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats copying mapdamage/Rscripts/stats/main.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats +copying mapdamage/Rscripts/stats/priorPropose.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats +copying mapdamage/Rscripts/stats/function.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats +copying mapdamage/Rscripts/stats/data.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats +copying mapdamage/Rscripts/stats/postConditonal.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats copying mapdamage/Rscripts/stats/start.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats +copying mapdamage/Rscripts/stats/checkLibraries.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats copying mapdamage/Rscripts/stats/runGeneral.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats -copying mapdamage/Rscripts/stats/postConditonal.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats -copying mapdamage/Rscripts/stats/function.R -> build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats -creating build/lib.linux-x86_64-cpython-313/mapdamage/tests -copying mapdamage/tests/test.rescaled.correct.sam -> build/lib.linux-x86_64-cpython-313/mapdamage/tests -copying mapdamage/tests/dnacomp.txt -> build/lib.linux-x86_64-cpython-313/mapdamage/tests -copying mapdamage/tests/fake1.fasta -> build/lib.linux-x86_64-cpython-313/mapdamage/tests -copying mapdamage/tests/test.bam -> build/lib.linux-x86_64-cpython-313/mapdamage/tests creating build/lib.linux-x86_64-cpython-313/mapdamage/tests/probs copying mapdamage/tests/probs/Stats_out_MCMC_correct_prob.csv -> build/lib.linux-x86_64-cpython-313/mapdamage/tests/probs +copying mapdamage/tests/test.bam -> build/lib.linux-x86_64-cpython-313/mapdamage/tests +copying mapdamage/tests/dnacomp.txt -> build/lib.linux-x86_64-cpython-313/mapdamage/tests +copying mapdamage/tests/test.rescaled.correct.sam -> build/lib.linux-x86_64-cpython-313/mapdamage/tests +copying mapdamage/tests/fake1.fasta -> build/lib.linux-x86_64-cpython-313/mapdamage/tests creating build/lib.linux-x86_64-cpython-313/mapdamage/seqtk copying mapdamage/seqtk/README.md -> build/lib.linux-x86_64-cpython-313/mapdamage/seqtk copying mapdamage/seqtk/kseq.h -> build/lib.linux-x86_64-cpython-313/mapdamage/seqtk @@ -1263,47 +1298,47 @@ running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/mapdamage -creating build/bdist.linux-x86_64/wheel/mapdamage/seqtk -copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk/kseq.h -> build/bdist.linux-x86_64/wheel/./mapdamage/seqtk -copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk/seqtk.c -> build/bdist.linux-x86_64/wheel/./mapdamage/seqtk -copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk/README.md -> build/bdist.linux-x86_64/wheel/./mapdamage/seqtk -copying build/lib.linux-x86_64-cpython-313/mapdamage/parseoptions.py -> build/bdist.linux-x86_64/wheel/./mapdamage -copying build/lib.linux-x86_64-cpython-313/mapdamage/align.py -> build/bdist.linux-x86_64/wheel/./mapdamage -copying build/lib.linux-x86_64-cpython-313/mapdamage/composition.py -> build/bdist.linux-x86_64/wheel/./mapdamage +creating build/bdist.linux-x86_64/wheel/mapdamage/tests +creating build/bdist.linux-x86_64/wheel/mapdamage/tests/probs +copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/probs/Stats_out_MCMC_correct_prob.csv -> build/bdist.linux-x86_64/wheel/./mapdamage/tests/probs +copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/test.bam -> build/bdist.linux-x86_64/wheel/./mapdamage/tests +copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/dnacomp.txt -> build/bdist.linux-x86_64/wheel/./mapdamage/tests +copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/test.rescaled.correct.sam -> build/bdist.linux-x86_64/wheel/./mapdamage/tests +copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/fake1.fasta -> build/bdist.linux-x86_64/wheel/./mapdamage/tests copying build/lib.linux-x86_64-cpython-313/mapdamage/version.py -> build/bdist.linux-x86_64/wheel/./mapdamage -copying build/lib.linux-x86_64-cpython-313/mapdamage/mp_test.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/seq.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/composition.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/rscript.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/align.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/__init__.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/parseoptions.py -> build/bdist.linux-x86_64/wheel/./mapdamage creating build/bdist.linux-x86_64/wheel/mapdamage/Rscripts copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/lengths.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts creating build/bdist.linux-x86_64/wheel/mapdamage/Rscripts/stats -copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/data.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats -copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/priorPropose.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats -copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/checkLibraries.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/main.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats +copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/priorPropose.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats +copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/function.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats +copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/data.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats +copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/postConditonal.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/start.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats +copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/checkLibraries.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/runGeneral.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats -copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/postConditonal.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats -copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/stats/function.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts/stats copying build/lib.linux-x86_64-cpython-313/mapdamage/Rscripts/mapDamage.R -> build/bdist.linux-x86_64/wheel/./mapdamage/Rscripts -copying build/lib.linux-x86_64-cpython-313/mapdamage/__init__.py -> build/bdist.linux-x86_64/wheel/./mapdamage -creating build/bdist.linux-x86_64/wheel/mapdamage/tests -copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/test.rescaled.correct.sam -> build/bdist.linux-x86_64/wheel/./mapdamage/tests -copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/dnacomp.txt -> build/bdist.linux-x86_64/wheel/./mapdamage/tests -copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/fake1.fasta -> build/bdist.linux-x86_64/wheel/./mapdamage/tests -copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/test.bam -> build/bdist.linux-x86_64/wheel/./mapdamage/tests -creating build/bdist.linux-x86_64/wheel/mapdamage/tests/probs -copying build/lib.linux-x86_64-cpython-313/mapdamage/tests/probs/Stats_out_MCMC_correct_prob.csv -> build/bdist.linux-x86_64/wheel/./mapdamage/tests/probs -copying build/lib.linux-x86_64-cpython-313/mapdamage/tables.py -> build/bdist.linux-x86_64/wheel/./mapdamage -copying build/lib.linux-x86_64-cpython-313/mapdamage/rscript.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/mp_test.py -> build/bdist.linux-x86_64/wheel/./mapdamage copying build/lib.linux-x86_64-cpython-313/mapdamage/rescale.py -> build/bdist.linux-x86_64/wheel/./mapdamage +copying build/lib.linux-x86_64-cpython-313/mapdamage/tables.py -> build/bdist.linux-x86_64/wheel/./mapdamage copying build/lib.linux-x86_64-cpython-313/mapdamage/main.py -> build/bdist.linux-x86_64/wheel/./mapdamage -copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./mapdamage +creating build/bdist.linux-x86_64/wheel/mapdamage/seqtk +copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk/kseq.h -> build/bdist.linux-x86_64/wheel/./mapdamage/seqtk +copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk/README.md -> build/bdist.linux-x86_64/wheel/./mapdamage/seqtk +copying build/lib.linux-x86_64-cpython-313/mapdamage/seqtk/seqtk.c -> build/bdist.linux-x86_64/wheel/./mapdamage/seqtk copying build/lib.linux-x86_64-cpython-313/mapdamage/__main__.py -> build/bdist.linux-x86_64/wheel/./mapdamage -copying build/lib.linux-x86_64-cpython-313/mapdamage/seq.py -> build/bdist.linux-x86_64/wheel/./mapdamage running install_egg_info Copying mapdamage.egg-info to build/bdist.linux-x86_64/wheel/./mapdamage-2.2.3.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/mapdamage-2.2.3.dist-info/WHEEL -creating '/build/reproducible-path/mapdamage-2.2.3+dfsg/.pybuild/cpython3_3.13/.tmp-362qlp8q/mapdamage-2.2.3-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/mapdamage-2.2.3+dfsg/.pybuild/cpython3_3.13/.tmp-f9i1jplv/mapdamage-2.2.3-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'mapdamage/__init__.py' adding 'mapdamage/__main__.py' adding 'mapdamage/align.py' @@ -1349,7 +1384,7 @@ set -e \ ; for py3 in 3.13 \ ; do cd mapdamage \ -; PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reproducible-path/mapdamage-2.2.3+dfsg/.pybuild/cpython3_${py3}/scripts \ +; PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/reproducible-path/mapdamage-2.2.3+dfsg/.pybuild/cpython3_${py3}/scripts \ PYTHONPATH=/build/reproducible-path/mapdamage-2.2.3+dfsg/.pybuild/cpython3_3.13/build \ python3 mp_test.py \ ; done @@ -1364,7 +1399,7 @@ pdf tests/results/Fragmisincorporation_plot.pdf generated .. ---------------------------------------------------------------------- -Ran 2 tests in 4.127s +Ran 2 tests in 11.379s OK make[1]: Leaving directory '/build/reproducible-path/mapdamage-2.2.3+dfsg' @@ -1402,8 +1437,8 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'mapdamage-dbgsym' in '../mapdamage-dbgsym_2.2.3+dfsg-1_amd64.deb'. dpkg-deb: building package 'mapdamage' in '../mapdamage_2.2.3+dfsg-1_amd64.deb'. +dpkg-deb: building package 'mapdamage-dbgsym' in '../mapdamage-dbgsym_2.2.3+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mapdamage_2.2.3+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../mapdamage_2.2.3+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1411,12 +1446,14 @@ 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/2217962/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2217962/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/1892354 and its subdirectories -I: Current time: Wed Oct 22 17:12:38 -12 2025 -I: pbuilder-time-stamp: 1761196358 +I: removing directory /srv/workspace/pbuilder/2217962 and its subdirectories +I: Current time: Thu Nov 26 01:39:34 +14 2026 +I: pbuilder-time-stamp: 1795606774