Diff of the two buildlogs: -- --- b1/build.log 2024-01-08 11:18:13.208133887 +0000 +++ b2/build.log 2024-01-08 11:29:49.622262846 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 7 23:11:33 -12 2024 -I: pbuilder-time-stamp: 1704712293 +I: Current time: Tue Jan 9 01:18:18 +14 2024 +I: pbuilder-time-stamp: 1704712698 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -29,49 +29,81 @@ dpkg-source: info: applying fix_problematic_comparison.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1438734/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3113567/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 8 11:18 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3113567/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3113567/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='443b7e38221e4b7fb67a60ee19ca30c5' - 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='1438734' - PS1='# ' - PS2='> ' + INVOCATION_ID=76e3cf3343de4f09872be9e23d9da446 + 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=3113567 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.G87X5jDZ/pbuilderrc_7hqN --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G87X5jDZ/b1 --logfile b1/build.log tnseq-transit_3.2.7-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + 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.G87X5jDZ/pbuilderrc_sAhC --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G87X5jDZ/b2 --logfile b2/build.log tnseq-transit_3.2.7-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink04-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -131,7 +163,7 @@ -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 68392 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 8 11:18 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su @@ -157,7 +189,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/1438734/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3113567/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -373,7 +405,7 @@ Get: 156 http://deb.debian.org/debian bookworm/main arm64 python3-sklearn all 1.2.1+dfsg-1 [2103 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 python3-statsmodels-lib arm64 0.13.5+dfsg-7 [1128 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 python3-statsmodels all 0.13.5+dfsg-7 [4515 kB] -Fetched 128 MB in 1s (197 MB/s) +Fetched 128 MB in 1s (111 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 18171 files and directories currently installed.) @@ -886,8 +918,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 8 11:12:13 UTC 2024. -Universal Time is now: Mon Jan 8 11:12:13 UTC 2024. +Local time is now: Mon Jan 8 11:19:40 UTC 2024. +Universal Time is now: Mon Jan 8 11:19:40 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.0.0-1) ... @@ -1039,7 +1071,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tnseq-transit-3.2.7/ && 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 > ../tnseq-transit_3.2.7-1_source.changes +I: user script /srv/workspace/pbuilder/3113567/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/3113567/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tnseq-transit-3.2.7/ && 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 > ../tnseq-transit_3.2.7-1_source.changes dpkg-buildpackage: info: source package tnseq-transit dpkg-buildpackage: info: source version 3.2.7-1 dpkg-buildpackage: info: source distribution unstable @@ -1049,7 +1085,7 @@ debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt binnengegaan dh_auto_clean I: pybuild base:240: python3.11 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead @@ -1060,7 +1096,7 @@ 'build/scripts-3.11' does not exist -- can't clean it rm -rf tests_invalid_data rm -rf tnseq_transit.egg-info -make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -1068,7 +1104,7 @@ dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt binnengegaan mkdir -p tests_invalid_data mv tests/H37Rv.fna tests_invalid_data dh_auto_configure @@ -1076,7 +1112,7 @@ /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running config -make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt verlaten dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead @@ -1244,7 +1280,7 @@ copying src/pytransit/genomes/mc2_155_tamu.fna -> /build/reproducible-path/tnseq-transit-3.2.7/.pybuild/cpython3_3.11/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.prot_table -> /build/reproducible-path/tnseq-transit-3.2.7/.pybuild/cpython3_3.11/build/pytransit/genomes debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt binnengegaan dh_auto_test -- --system=custom --test-args="PYTHONPATH=tests {interpreter} -m unittest -v tests/*.py" I: pybuild base:240: PYTHONPATH=tests python3.11 -m unittest -v tests/*.py test_Binomial (tests.test_analysis_methods.TestMethods.test_Binomial) ... /build/reproducible-path/tnseq-transit-3.2.7/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.2.7/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> @@ -1477,7 +1513,7 @@ ResourceWarning: Enable tracemalloc to get the object allocation traceback [anova] Adding File: /build/reproducible-path/tnseq-transit-3.2.7/tests/testoutput.txt [anova] Finished Anova analysis -[anova] Time: 0.3s +[anova] Time: 0.8s Removing output file... @@ -1501,7 +1537,7 @@ test_resampling_adaptive (tests.test_analysis_methods.TestMethods.test_resampling_adaptive) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 34 -[resampling] Time: 10.05s +[resampling] Time: 28.32s [resampling] Finished resampling Method Removing output file... @@ -1522,8 +1558,8 @@ ResourceWarning: Enable tracemalloc to get the object allocation traceback [resampling] [resampling] Performing Benjamini-Hochberg Correction -[resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 9.26s +[resampling] Number of significant conditionally essential genes (Padj<0.05): 34 +[resampling] Time: 16.06s [resampling] Finished resampling Method Removing output file... @@ -1542,9 +1578,9 @@ test_resampling_histogram (tests.test_analysis_methods.TestMethods.test_resampling_histogram) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 10.62s +[resampling] Time: 19.46s [resampling] Finished resampling Method -36 +37 35 Removing output file... @@ -1562,8 +1598,8 @@ [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_multistrain (tests.test_analysis_methods.TestMethods.test_resampling_multistrain) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction -[resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 30.57s +[resampling] Number of significant conditionally essential genes (Padj<0.05): 36 +[resampling] Time: 48.23s [resampling] Finished resampling Method Removing histogram files Removing output file... @@ -1585,7 +1621,7 @@ test_utest (tests.test_analysis_methods.TestMethods.test_utest) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 45.83s +[resampling] Time: 60.82s [resampling] Finished resampling Method Removing histogram files Removing output file... @@ -1634,7 +1670,7 @@ test_resampling_Quantile (tests.test_norm_methods.TestNormMethods.test_resampling_Quantile) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 2.99s +[resampling] Time: 4.32s [resampling] Finished resampling Method Removing output file... @@ -1656,7 +1692,7 @@ test_resampling_TTR (tests.test_norm_methods.TestNormMethods.test_resampling_TTR) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 3.68s +[resampling] Time: 6.69s [resampling] Finished resampling Method Removing output file... @@ -1675,7 +1711,7 @@ test_resampling_TotReads (tests.test_norm_methods.TestNormMethods.test_resampling_TotReads) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 2.74s +[resampling] Time: 4.80s [resampling] Finished resampling Method Removing output file... @@ -1694,7 +1730,7 @@ test_resampling_ZINFNB (tests.test_norm_methods.TestNormMethods.test_resampling_ZINFNB) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 3.10s +[resampling] Time: 5.45s [resampling] Finished resampling Method Removing output file... @@ -1713,7 +1749,7 @@ test_resampling_nonorm (tests.test_norm_methods.TestNormMethods.test_resampling_nonorm) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 8.42s +[resampling] Time: 16.06s [resampling] Finished resampling Method Removing output file... @@ -1769,21 +1805,21 @@ [tn_preprocess] /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna b'[bwa_index] Pack FASTA... 0.03 sec' b'[bwa_index] Construct BWT for the packed sequence...' -b'[bwa_index] 2.12 seconds elapse.' +b'[bwa_index] 2.03 seconds elapse.' b'[bwa_index] Update BWT... 0.02 sec' b'[bwa_index] Pack forward-only FASTA... 0.02 sec' -b'[bwa_index] Construct SA from BWT and Occ... 1.28 sec' +b'[bwa_index] Construct SA from BWT and Occ... 1.18 sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna' -b'[main] Real time: 8.686 sec; CPU: 3.481 sec' +b'[main] Real time: 10.113 sec; CPU: 3.283 sec' b'' [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' -b'[M::mem_process_seqs] Processed 2500 reads in 0.203 CPU sec, 0.448 real sec' +b'[M::mem_process_seqs] Processed 2500 reads in 0.207 CPU sec, 0.714 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp.trimmed1' -b'[main] Real time: 0.488 sec; CPU: 0.213 sec' +b'[main] Real time: 0.781 sec; CPU: 0.217 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.2.7/tests/../src/pytpp/tpp_tools.py:387: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna' mode='r' encoding='UTF-8'> @@ -1821,10 +1857,10 @@ [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' -b'[M::mem_process_seqs] Processed 2500 reads in 0.212 CPU sec, 0.589 real sec' +b'[M::mem_process_seqs] Processed 2500 reads in 0.209 CPU sec, 0.493 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp.trimmed1' -b'[main] Real time: 0.618 sec; CPU: 0.221 sec' +b'[main] Real time: 0.520 sec; CPU: 0.218 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.2.7/tests/data/test-multicontig.fna [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.2.7/tests/test_tpp_temp_a.wig @@ -1837,13 +1873,13 @@ test_tpp_protocol_mme1 (tests.test_tpp.TestTPP.test_tpp_protocol_mme1) ... skipped 'requires local data file' ---------------------------------------------------------------------- -Ran 39 tests in 194.863s +Ran 39 tests in 348.447s OK (skipped=6) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 2.83s +[resampling] Time: 4.51s [resampling] Finished resampling Method Removing output file... @@ -1907,7 +1943,7 @@ tests.test_tpp.TestTPP.test_tpp_multicontig_auto_replicon_ids #################### # title: Tn-Seq Pre-Processor -# date: 01/07/2024 23:16:15 +# date: 01/09/2024 01:27:30 # command: python python3.11 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti @@ -1989,7 +2025,7 @@ tests.test_tpp.TestTPP.test_tpp_multicontig_empty_prefix #################### # title: Tn-Seq Pre-Processor -# date: 01/07/2024 23:16:19 +# date: 01/09/2024 01:27:33 # command: python python3.11 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti @@ -2065,7 +2101,7 @@ Removing tpp test file Removing tpp test file Removing tpp test file -make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2295,10 +2331,10 @@ Installing tpp script to /build/reproducible-path/tnseq-transit-3.2.7/debian/tnseq-transit/usr/bin Installing transit script to /build/reproducible-path/tnseq-transit-3.2.7/debian/tnseq-transit/usr/bin debian/rules override_dh_install -make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt binnengegaan dh_install mv debian/tnseq-transit/usr/bin/tpp debian/tnseq-transit/usr/bin/transit-tpp -make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.2.7' +make[1]: Map '/build/reproducible-path/tnseq-transit-3.2.7' wordt verlaten dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild @@ -2318,7 +2354,7 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'tnseq-transit' in '../tnseq-transit_3.2.7-1_arm64.deb'. +dpkg-deb: pakket 'tnseq-transit' wordt gebouwd in '../tnseq-transit_3.2.7-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../tnseq-transit_3.2.7-1_arm64.buildinfo dpkg-genchanges --build=binary -O../tnseq-transit_3.2.7-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2326,12 +2362,14 @@ 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/3113567/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3113567/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/1438734 and its subdirectories -I: Current time: Sun Jan 7 23:18:12 -12 2024 -I: pbuilder-time-stamp: 1704712692 +I: removing directory /srv/workspace/pbuilder/3113567 and its subdirectories +I: Current time: Tue Jan 9 01:29:48 +14 2024 +I: pbuilder-time-stamp: 1704713388