Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 10:02:46.351222162 +0000 +++ b2/build.log 2024-01-07 10:06:58.496688930 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 21:58:07 -12 2024 -I: pbuilder-time-stamp: 1704621487 +I: Current time: Sun Feb 9 06:25:53 +14 2025 +I: pbuilder-time-stamp: 1739031953 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -31,49 +31,81 @@ dpkg-source: info: applying join-threads-for-concurrency.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2249886/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1406593/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 Feb 8 16:26 /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/1406593/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1406593/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=15 ' - DISTRIBUTION='bookworm' - 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]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='289309995ca94c6f8f18f55baad96eba' - 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='2249886' - PS1='# ' - PS2='> ' + INVOCATION_ID=91af6a9912694dc5a69f82d404fcf3d1 + 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=1406593 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.Cyjr8EcD/pbuilderrc_BPUt --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.Cyjr8EcD/b1 --logfile b1/build.log macsyfinder_2.0-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.Cyjr8EcD/pbuilderrc_pPPV --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.Cyjr8EcD/b2 --logfile b2/build.log macsyfinder_2.0-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -131,15 +163,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 8 16:26 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -159,7 +191,7 @@ -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/2249886/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1406593/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -427,7 +459,7 @@ Get: 192 http://deb.debian.org/debian bookworm/main amd64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-extra all 2022.20230122-4 [19.2 MB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 texlive-plain-generic all 2022.20230122-4 [28.9 MB] -Fetched 211 MB in 20s (10.6 MB/s) +Fetched 211 MB in 2s (95.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18148 files and directories currently installed.) @@ -1057,8 +1089,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 7 09:59:05 UTC 2024. -Universal Time is now: Sun Jan 7 09:59:05 UTC 2024. +Local time is now: Sat Feb 8 16:26:30 UTC 2025. +Universal Time is now: Sat Feb 8 16:26:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-5+b1) ... @@ -1258,7 +1290,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/macsyfinder-2.0/ && 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 > ../macsyfinder_2.0-2_source.changes +I: user script /srv/workspace/pbuilder/1406593/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/1406593/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/macsyfinder-2.0/ && 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 > ../macsyfinder_2.0-2_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.0-2 dpkg-buildpackage: info: source distribution unstable @@ -1522,10 +1558,10 @@ test_execute_hmm_wo_GA (test_Profile.TestProfile.test_execute_hmm_wo_GA) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) ok test_execute_hmmer_failed (test_Profile.TestProfile.test_execute_hmmer_failed) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) -an error occurred during Hmmer execution: command = "/tmp/hmmer_failed" --cpu 1 -o "/tmp/macsyfinder-20240106_22-01-03/hmmer_results/abc.search_hmm.out" -E 0.100000 "/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/profiles/abc.hmm" "/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240106_22-01-03/hmmer_results/abc.search_hmm.err +an error occurred during Hmmer execution: command = "/tmp/hmmer_failed" --cpu 1 -o "/tmp/macsyfinder-20250209_06-28-28/hmmer_results/abc.search_hmm.out" -E 0.100000 "/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/profiles/abc.hmm" "/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20250209_06-28-28/hmmer_results/abc.search_hmm.err ok test_execute_unknown_binary (test_Profile.TestProfile.test_execute_unknown_binary) ... GA bit thresholds unavailable on profile abc. Switch to e-value threshold (-E 0.100000) -an error occurred during Hmmer execution: command = "Nimportnaoik" --cpu 1 -o "/tmp/macsyfinder-20240106_22-01-03/hmmer_results/abc.search_hmm.out" -E 0.100000 "/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/profiles/abc.hmm" "/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20240106_22-01-03/hmmer_results/abc.search_hmm.err +an error occurred during Hmmer execution: command = "Nimportnaoik" --cpu 1 -o "/tmp/macsyfinder-20250209_06-28-28/hmmer_results/abc.search_hmm.out" -E 0.100000 "/build/reproducible-path/macsyfinder-2.0/tests/data/models/foo/profiles/abc.hmm" "/build/reproducible-path/macsyfinder-2.0/tests/data/base/test_1.fasta" : return code = 127 check /tmp/macsyfinder-20250209_06-28-28/hmmer_results/abc.search_hmm.err ok test_ga_threshold (test_Profile.TestProfile.test_ga_threshold) ... bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''. GA score will not used for gene 'bad_GA'. @@ -1788,38 +1824,38 @@ /build/reproducible-path/macsyfinder-2.0/tests/test_macsy_gembase_split.py:59: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='utf-8'> for h in logger.handlers[:]: ResourceWarning: Enable tracemalloc to get the object allocation traceback -/usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpvamnyxik/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='utf-8'> +/usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpgmrjqs42/macsyfinder_test_split/base/macsy_gembase_split.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok -test_functional_split_out_error (test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... /tmp/tmplhqvkrd7/macsyfinder_test_split/base is not a directory +test_functional_split_out_error (test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... /tmp/tmp1zh26hhi/macsyfinder_test_split/base is not a directory ok -test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... /tmp/tmpuqcewd44/macsyfinder_test_split/base is not writable -Cannot create /tmp/tmpuqcewd44/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmpuqcewd44/macsyfinder_test_split/base' +test_functional_split_out_not_writable (test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... /tmp/tmpu5b9qzz4/macsyfinder_test_split/base is not writable +Cannot create /tmp/tmpu5b9qzz4/macsyfinder_test_split/base : [Errno 13] Permission denied: '/tmp/tmpu5b9qzz4/macsyfinder_test_split/base' ok -test_functional_merge (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv' -Merging 'best_solution.tsv' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_best_solution.tsv' -Merging 'all_systems.tsv' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_all_systems.tsv' -Merging 'best_solution_multisystems.tsv' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv' -Merging 'best_solution_loners.tsv' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv' -Merging 'rejected_candidates.tsv' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv' -Merging 'all_systems.txt' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_all_systems.txt' -Merging 'rejected_candidates.txt' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt' -Merging 'best_solution_summary' in to '/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv' -/usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp4zxni76p/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> +test_functional_merge (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging 'all_best_solutions.tsv' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv' +Merging 'best_solution.tsv' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_best_solution.tsv' +Merging 'all_systems.tsv' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_all_systems.tsv' +Merging 'best_solution_multisystems.tsv' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv' +Merging 'best_solution_loners.tsv' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv' +Merging 'rejected_candidates.tsv' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv' +Merging 'all_systems.txt' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_all_systems.txt' +Merging 'rejected_candidates.txt' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt' +Merging 'best_solution_summary' in to '/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/merged_best_solution_summary.tsv' +/usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmplnkgyl2m/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok -test_functional_merge_one_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpc9b6s8rm/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> +test_functional_merge_one_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbrw_jhz8/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok -test_functional_merge_out_error (test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... /tmp/tmpnduncc0r/macsyfinder_test_merge/merged_results is not a directory +test_functional_merge_out_error (test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... /tmp/tmpubqzp8kz/macsyfinder_test_merge/merged_results is not a directory ok -test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... /tmp/tmpowgry7i_/macsyfinder_test_merge/merged_results is not writable -Cannot create /tmp/tmpowgry7i_/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmpowgry7i_/macsyfinder_test_merge/merged_results' +test_functional_merge_out_not_writable (test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... /tmp/tmpse8arbse/macsyfinder_test_merge/merged_results is not writable +Cannot create /tmp/tmpse8arbse/macsyfinder_test_merge/merged_results : [Errno 13] Permission denied: '/tmp/tmpse8arbse/macsyfinder_test_merge/merged_results' ok -test_functional_merge_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpi3cn00zc/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> +test_functional_merge_results_empty (test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp50f2moi8/macsyfinder_test_merge/merged_results/macsy_merge_results.out' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok @@ -1855,7 +1891,7 @@ test_build_argparser (test_macsydata.TestMacsydata.test_build_argparser) ... ok test_check (test_macsydata.TestMacsydata.test_check) ... If everyone were like you, I'd be out of business To push the models in organization: - cd /tmp/tmp0lb8mmss/fake_1 + cd /tmp/tmpz1zlijpc/fake_1 Transform the models into a git repository git init . git add . @@ -1880,10 +1916,10 @@ test_cite (test_macsydata.TestMacsydata.test_cite) ... Models 'nimportnaoik' not found locally. ok test_cmd_name (test_macsydata.TestMacsydata.test_cmd_name) ... ok -test_definition_all_def (test_macsydata.TestMacsydata.test_definition_all_def) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpa7_d151_/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> +test_definition_all_def (test_macsydata.TestMacsydata.test_definition_all_def) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp5nwu5942/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback -/build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpa7_d151_/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> +/build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp5nwu5942/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok @@ -1893,22 +1929,22 @@ ok test_definition_bad_subfamily (test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... 'niportnaoik' not found in package 'fake_1'. ok -test_definition_models_dir (test_macsydata.TestMacsydata.test_definition_models_dir) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmptfymira8/model_dir/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> +test_definition_models_dir (test_macsydata.TestMacsydata.test_definition_models_dir) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmprh5fc5b0/model_dir/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback -/build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmptfymira8/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> +/build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmprh5fc5b0/model_dir/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok -test_definition_one_def (test_macsydata.TestMacsydata.test_definition_one_def) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbd8vv9er/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> +test_definition_one_def (test_macsydata.TestMacsydata.test_definition_one_def) ... /build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp4rx34nw2/fake_1/definitions/sub_fam_1/model_1.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback -/build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpbd8vv9er/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> +/build/reproducible-path/macsyfinder-2.0/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp4rx34nw2/fake_1/definitions/sub_fam_2/model_2.xml' mode='r' encoding='utf-8'> return open(path, 'r').read() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_download (test_macsydata.TestMacsydata.test_download) ... Downloading fake_1 1.0 -Successfully downloaded packaging fake_1 in /tmp/tmpct6jr3vg/fake_1-1.0.tar.gz +Successfully downloaded packaging fake_1 in /tmp/tmpd0zk526b/fake_1-1.0.tar.gz No version that satisfy requirements '>2.0' for 'fake_1'. Available versions: 1.0 Downloading fake_1 1.0 @@ -1921,56 +1957,56 @@ ok test_install_bad_target (test_macsydata.TestMacsydata.test_install_bad_target) ... ok test_install_installed_package_corrupted (test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmpuqc2xm4c/models +Installing fake_pack (0.0b2) in /tmp/tmpuzgm9po7/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. fake_pack locally installed is corrupted. -You can fix it by removing '/tmp/tmpuqc2xm4c/models/fake_pack'. +You can fix it by removing '/tmp/tmpuzgm9po7/models/fake_pack'. ok test_install_local (test_macsydata.TestMacsydata.test_install_local) ... Extracting fake_pack (3.0). -Installing fake_pack (3.0) in /tmp/tmpix2qlysw/models +Installing fake_pack (3.0) in /tmp/tmpwgmgjmak/models Cleaning. The models fake_pack (3.0) have been installed successfully. ok test_install_local_already_installed (test_macsydata.TestMacsydata.test_install_local_already_installed) ... Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmpdg2d6f3u/models +Installing fake_pack (0.0b2) in /tmp/tmpn8kn0d5s/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. -Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmpdg2d6f3u/models/fake_pack. +Requirement already satisfied: fake_pack==0.0b2 in /tmp/tmpn8kn0d5s/models/fake_pack. To force installation use option -f --force-reinstall. ok test_install_local_already_installed_force (test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmp2kjmw1fm/models +Installing fake_pack (0.0b2) in /tmp/tmpvgwgfi8o/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmp2kjmw1fm/models +Installing fake_pack (0.0b2) in /tmp/tmpvgwgfi8o/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. ok test_install_remote (test_macsydata.TestMacsydata.test_install_remote) ... Downloading fake_pack (0.0b2). Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmp17cib__c/models +Installing fake_pack (0.0b2) in /tmp/tmp0n70n1tb/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. ok -test_install_remote_already_in_local (test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmpr8qygd7h/models/fake_pack. +test_install_remote_already_in_local (test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... Requirement already satisfied: fake_pack>0.0b2 in /tmp/tmpnexsrhp9/models/fake_pack. To force installation use option -f --force-reinstall. ok test_install_remote_already_in_local_force (test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... Downloading fake_pack (0.0b2). Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmp7bmxxh1i/models +Installing fake_pack (0.0b2) in /tmp/tmpla7luer9/models Cleaning. The models fake_pack (0.0b2) have been installed successfully. ok test_install_remote_lower_in_local (test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... fake_pack (0.0b2) is already installed but 1.0 version is available. To install it please run 'macsydata install --upgrade fake_pack' ok -test_install_remote_permision_error (test_macsydata.TestMacsydata.test_install_remote_permision_error) ... /tmp/tmp84eap5oo/models is not readable: [Errno 13] Permission denied: '/tmp/tmp84eap5oo/models' : skip it. +test_install_remote_permision_error (test_macsydata.TestMacsydata.test_install_remote_permision_error) ... /tmp/tmpqdt3j3yg/models is not readable: [Errno 13] Permission denied: '/tmp/tmpqdt3j3yg/models' : skip it. Downloading fake_pack (0.0b2). Extracting fake_pack (0.0b2). -Installing fake_pack (0.0b2) in /tmp/tmp84eap5oo/models -/tmp/tmp84eap5oo/models is not writable: [Errno 13] Permission denied: '/tmp/tmp84eap5oo/models/fake_pack' +Installing fake_pack (0.0b2) in /tmp/tmpqdt3j3yg/models +/tmp/tmpqdt3j3yg/models is not writable: [Errno 13] Permission denied: '/tmp/tmpqdt3j3yg/models/fake_pack' Maybe you can use --user option to install in your HOME. ok test_install_remote_spec_not_found (test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... Could not find version that satisfied 'fake_pack>0.0b2' @@ -1979,14 +2015,14 @@ To downgrade to 0.0b1 use option -f --force-reinstall. ok test_install_target (test_macsydata.TestMacsydata.test_install_target) ... Extracting fake_pack (3.0). -Installing fake_pack (3.0) in /tmp/tmpn6t1plbn/target +Installing fake_pack (3.0) in /tmp/tmp38mn3huz/target Cleaning. The models fake_pack (3.0) have been installed successfully. ok test_list (test_macsydata.TestMacsydata.test_list) ... ok test_list_outdated (test_macsydata.TestMacsydata.test_list_outdated) ... ok test_list_uptodate (test_macsydata.TestMacsydata.test_list_uptodate) ... ok -test_list_verbose (test_macsydata.TestMacsydata.test_list_verbose) ... [Errno 2] No such file or directory: '/tmp/tmp84fua1co/models/fake_1/metadata.yml' +test_list_verbose (test_macsydata.TestMacsydata.test_list_verbose) ... [Errno 2] No such file or directory: '/tmp/tmpoe01_ruh/models/fake_1/metadata.yml' ok test_no_subcommand (test_macsydata.TestMacsydata.test_no_subcommand) ... ok test_search_in_pack_desc (test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok @@ -1995,30 +2031,30 @@ test_search_in_pack_name_match_case (test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok test_search_reach_limit (test_macsydata.TestMacsydata.test_search_reach_limit) ... bla ok -test_uninstall (test_macsydata.TestMacsydata.test_uninstall) ... models 'fake_1' in /tmp/tmp44pdzycb/models/fake_1 uninstalled. +test_uninstall (test_macsydata.TestMacsydata.test_uninstall) ... models 'fake_1' in /tmp/tmpuepvp4h9/models/fake_1 uninstalled. Models 'foo' not found locally. ok test_verbosity_to_log_level (test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok -test_db_type_set_to_gembase (test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... GA bit thresholds unavailable on profile ComM_comC. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilA. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_fimT. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilO. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilT. Switch to e-value threshold (-E 0.100000) +test_db_type_set_to_gembase (test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... GA bit thresholds unavailable on profile T4P_pilP. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilX. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile MSH_mshM. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilU. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilN. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilV. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilW. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilO. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilQ. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile MSH_mshM. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T2SS_gspO. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilD. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilM. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilU. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_fimT. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilD. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilB. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilY. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilT. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilC. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilN. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T2SS_gspO. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile T4P_pilA. Switch to e-value threshold (-E 0.100000) +GA bit thresholds unavailable on profile ComM_comC. Switch to e-value threshold (-E 0.100000) GA bit thresholds unavailable on profile T4P_pilE. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilP. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilY. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilX. Switch to e-value threshold (-E 0.100000) -GA bit thresholds unavailable on profile T4P_pilW. Switch to e-value threshold (-E 0.100000) Most of replicons contains only ONE sequence are you sure that '/build/reproducible-path/macsyfinder-2.0/tests/data/base/ordered_replicon_base.fasta' is a 'gembase'. ok test_likely_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok @@ -2050,7 +2086,7 @@ test_functional_no_hits (test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok test_functional_no_previous_run (test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... nimportnaoik: No such directory. ok -test_functional_out_exists (test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... The file /tmp/tmpakn2wgjc already exists. Remove it or specify a new output name --out or use --force option +test_functional_out_exists (test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... The file /tmp/tmptcc0ht69 already exists. Remove it or specify a new output name --out or use --force option ok test_functional_pattern (test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok test_getProfile_len (test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok @@ -2063,7 +2099,7 @@ test_pasre_args (test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok test_verbosity_to_log_level (test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok test_init_logger_default (test_macsypy.Test.test_init_logger_default) ... ok -test_init_logger_logfile (test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpgiukdmea' mode='a' encoding='utf-8'> +test_init_logger_logfile (test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.11/unittest/case.py:584: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmprtl9du81' mode='a' encoding='utf-8'> self.tearDown() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok @@ -2174,7 +2210,7 @@ test_threads_available (test_utils.TestUtils.test_threads_available) ... ok ---------------------------------------------------------------------- -Ran 486 tests in 21.217s +Ran 486 tests in 20.690s OK (skipped=2) create-stamp debian/debhelper-build-stamp @@ -4577,7 +4613,7 @@ -Output written on macsyfinder.pdf (183 pages, 2455971 bytes). +Output written on macsyfinder.pdf (183 pages, 2455975 bytes). Transcript written on macsyfinder.log. Latexmk: Missing input file 'macsyfinder.toc' (or dependence on it) from following: No file macsyfinder.toc. @@ -5889,7 +5925,7 @@ -Output written on macsyfinder.pdf (193 pages, 2535870 bytes). +Output written on macsyfinder.pdf (193 pages, 2535875 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' @@ -7171,7 +7207,7 @@ -Output written on macsyfinder.pdf (193 pages, 2536098 bytes). +Output written on macsyfinder.pdf (193 pages, 2536091 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' @@ -7217,12 +7253,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1406593/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1406593/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/2249886 and its subdirectories -I: Current time: Sat Jan 6 22:02:45 -12 2024 -I: pbuilder-time-stamp: 1704621765 +I: removing directory /srv/workspace/pbuilder/1406593 and its subdirectories +I: Current time: Sun Feb 9 06:30:01 +14 2025 +I: pbuilder-time-stamp: 1739032201