Diff of the two buildlogs: -- --- b1/build.log 2025-11-25 21:54:17.201785405 +0000 +++ b2/build.log 2025-11-25 22:10:17.450851715 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Nov 25 09:49:45 -12 2025 -I: pbuilder-time-stamp: 1764107385 +I: Current time: Tue Dec 29 18:17:19 +14 2026 +I: pbuilder-time-stamp: 1798517839 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying do_not_test_parse_model_old_syntax.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/384198/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1073476/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Dec 29 04:17 /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/1073476/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1073476/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 nocheck' + 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='3a4b2294378f401b8337d2f09c0cdb9a' - 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='384198' - PS1='# ' - PS2='> ' + INVOCATION_ID=c6f00ee05df04e89a56c0cc8d408b75f + 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=1073476 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.Mbs9By7l/pbuilderrc_omKl --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.Mbs9By7l/b1 --logfile b1/build.log macsyfinder_2.1.4-1.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.Mbs9By7l/pbuilderrc_jyqs --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.Mbs9By7l/b2 --logfile b2/build.log macsyfinder_2.1.4-1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) 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/384198/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1073476/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -367,7 +399,7 @@ Get: 216 http://deb.debian.org/debian forky/main amd64 texlive-pictures all 2025.20250927-4 [23.6 MB] Get: 217 http://deb.debian.org/debian forky/main amd64 texlive-latex-extra all 2025.20250927-3 [27.7 MB] Get: 218 http://deb.debian.org/debian forky/main amd64 texlive-plain-generic all 2025.20250927-3 [29.9 MB] -Fetched 301 MB in 7s (43.3 MB/s) +Fetched 301 MB in 13s (23.1 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19866 files and directories currently installed.) @@ -1076,8 +1108,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Nov 25 21:51:48 UTC 2025. -Universal Time is now: Tue Nov 25 21:51:48 UTC 2025. +Local time is now: Tue Dec 29 04:20:26 UTC 2026. +Universal Time is now: Tue Dec 29 04:20:26 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... @@ -1296,7 +1328,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/macsyfinder-2.1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../macsyfinder_2.1.4-1_source.changes +I: user script /srv/workspace/pbuilder/1073476/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1073476/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/macsyfinder-2.1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../macsyfinder_2.1.4-1_source.changes dpkg-buildpackage: info: source package macsyfinder dpkg-buildpackage: info: source version 2.1.4-1 dpkg-buildpackage: info: source distribution unstable @@ -1336,34 +1372,34 @@ running build running build_py creating build/lib/macsypy +copying macsypy/config.py -> build/lib/macsypy +copying macsypy/error.py -> build/lib/macsypy +copying macsypy/system.py -> build/lib/macsypy +copying macsypy/profile.py -> build/lib/macsypy +copying macsypy/package.py -> build/lib/macsypy +copying macsypy/utils.py -> build/lib/macsypy copying macsypy/definition_parser.py -> build/lib/macsypy -copying macsypy/registries.py -> build/lib/macsypy +copying macsypy/cluster.py -> build/lib/macsypy copying macsypy/model.py -> build/lib/macsypy copying macsypy/solution.py -> build/lib/macsypy -copying macsypy/error.py -> build/lib/macsypy +copying macsypy/__init__.py -> build/lib/macsypy copying macsypy/database.py -> build/lib/macsypy -copying macsypy/package.py -> build/lib/macsypy copying macsypy/model_conf_parser.py -> build/lib/macsypy -copying macsypy/search_genes.py -> build/lib/macsypy -copying macsypy/serialization.py -> build/lib/macsypy -copying macsypy/__init__.py -> build/lib/macsypy -copying macsypy/profile.py -> build/lib/macsypy copying macsypy/gene.py -> build/lib/macsypy +copying macsypy/registries.py -> build/lib/macsypy +copying macsypy/serialization.py -> build/lib/macsypy copying macsypy/report.py -> build/lib/macsypy -copying macsypy/config.py -> build/lib/macsypy +copying macsypy/search_genes.py -> build/lib/macsypy copying macsypy/licenses.py -> build/lib/macsypy -copying macsypy/system.py -> build/lib/macsypy -copying macsypy/utils.py -> build/lib/macsypy copying macsypy/metadata.py -> build/lib/macsypy copying macsypy/hit.py -> build/lib/macsypy -copying macsypy/cluster.py -> build/lib/macsypy creating build/lib/macsypy/scripts -copying macsypy/scripts/macsyfinder.py -> build/lib/macsypy/scripts +copying macsypy/scripts/macsy_gembase_split.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsydata.py -> build/lib/macsypy/scripts +copying macsypy/scripts/macsyfinder.py -> build/lib/macsypy/scripts +copying macsypy/scripts/macsyconfig.py -> build/lib/macsypy/scripts copying macsypy/scripts/__init__.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsy_merge_results.py -> build/lib/macsypy/scripts -copying macsypy/scripts/macsyconfig.py -> build/lib/macsypy/scripts -copying macsypy/scripts/macsy_gembase_split.py -> build/lib/macsypy/scripts copying macsypy/scripts/macsyprofile.py -> build/lib/macsypy/scripts creating build/lib/macsypy/data copying macsypy/data/pre-push -> build/lib/macsypy/data @@ -1372,37 +1408,37 @@ running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/macsypy -copying build/lib/macsypy/definition_parser.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/registries.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/model.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/solution.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/config.py -> build/bdist.linux-x86_64/wheel/./macsypy copying build/lib/macsypy/error.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/database.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/package.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/model_conf_parser.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/search_genes.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/serialization.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/__init__.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/system.py -> build/bdist.linux-x86_64/wheel/./macsypy copying build/lib/macsypy/profile.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/gene.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/report.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/config.py -> build/bdist.linux-x86_64/wheel/./macsypy +creating build/bdist.linux-x86_64/wheel/macsypy/data +copying build/lib/macsypy/data/pre-push -> build/bdist.linux-x86_64/wheel/./macsypy/data +copying build/lib/macsypy/package.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/utils.py -> build/bdist.linux-x86_64/wheel/./macsypy creating build/bdist.linux-x86_64/wheel/macsypy/scripts -copying build/lib/macsypy/scripts/macsyfinder.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts +copying build/lib/macsypy/scripts/macsy_gembase_split.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsydata.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts +copying build/lib/macsypy/scripts/macsyfinder.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts +copying build/lib/macsypy/scripts/macsyconfig.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/__init__.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsy_merge_results.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts -copying build/lib/macsypy/scripts/macsyconfig.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts -copying build/lib/macsypy/scripts/macsy_gembase_split.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts copying build/lib/macsypy/scripts/macsyprofile.py -> build/bdist.linux-x86_64/wheel/./macsypy/scripts +copying build/lib/macsypy/definition_parser.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/cluster.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/model.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/solution.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/__init__.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/database.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/model_conf_parser.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/gene.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/registries.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/serialization.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/report.py -> build/bdist.linux-x86_64/wheel/./macsypy +copying build/lib/macsypy/search_genes.py -> build/bdist.linux-x86_64/wheel/./macsypy copying build/lib/macsypy/licenses.py -> build/bdist.linux-x86_64/wheel/./macsypy -creating build/bdist.linux-x86_64/wheel/macsypy/data -copying build/lib/macsypy/data/pre-push -> build/bdist.linux-x86_64/wheel/./macsypy/data -copying build/lib/macsypy/system.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/utils.py -> build/bdist.linux-x86_64/wheel/./macsypy copying build/lib/macsypy/metadata.py -> build/bdist.linux-x86_64/wheel/./macsypy copying build/lib/macsypy/hit.py -> build/bdist.linux-x86_64/wheel/./macsypy -copying build/lib/macsypy/cluster.py -> build/bdist.linux-x86_64/wheel/./macsypy running install_data creating build/bdist.linux-x86_64/wheel/macsyfinder-2.1.4.data/data creating build/bdist.linux-x86_64/wheel/macsyfinder-2.1.4.data/data/share/macsyfinder/models @@ -1435,7 +1471,7 @@ Copying MacSyFinder.egg-info to build/bdist.linux-x86_64/wheel/./MacSyFinder-2.1.4.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/macsyfinder-2.1.4.dist-info/WHEEL -creating '/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/.tmp-skd6caju/macsyfinder-2.1.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/.tmp-2lg25h7z/macsyfinder-2.1.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'macsyfinder-2.1.4.data/data/share/macsyfinder/models/README' adding 'macsyfinder-2.1.4.dist-info/licenses/COPYING' adding 'macsypy/__init__.py' @@ -1475,713 +1511,7 @@ removing build/bdist.linux-x86_64/wheel Successfully built macsyfinder-2.1.4-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module - dh_auto_test -O--buildsystem=pybuild -I: pybuild base:311: cd /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v -/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:56: UserWarning: GitPython is not installed, `macsydata init` is disabled () -To turn this feature ON: - - install git - - then run `python -m pip install macsyfinder[model]` in your activated environment. - warnings.warn("GitPython is not installed, `macsydata init` is disabled ()\n" -test_Config (tests.test_Config.TestConfig.test_Config) ... ok -test_Config_args (tests.test_Config.TestConfig.test_Config_args) ... ok -test_Config_conf_file_virtualenv (tests.test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok -test_Config_default_conf_file (tests.test_Config.TestConfig.test_Config_default_conf_file) ... ok -test_Config_file_bad_values (tests.test_Config.TestConfig.test_Config_file_bad_values) ... ok -test_Config_file_n_args (tests.test_Config.TestConfig.test_Config_file_n_args) ... ok -test_bad_db_type (tests.test_Config.TestConfig.test_bad_db_type) ... ok -test_bad_models_dir (tests.test_Config.TestConfig.test_bad_models_dir) ... ok -test_bad_sequence_db (tests.test_Config.TestConfig.test_bad_sequence_db) ... ok -test_bad_topology (tests.test_Config.TestConfig.test_bad_topology) ... ok -test_bad_topology_file (tests.test_Config.TestConfig.test_bad_topology_file) ... ok -test_bad_values (tests.test_Config.TestConfig.test_bad_values) ... ok -test_cmd_config_file (tests.test_Config.TestConfig.test_cmd_config_file) ... ok -test_config_file_2_dict (tests.test_Config.TestConfig.test_config_file_2_dict) ... ok -test_cut_ga (tests.test_Config.TestConfig.test_cut_ga) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. - if filtering_node: -ok -test_e_value_search (tests.test_Config.TestConfig.test_e_value_search) ... ok -test_hit_weights (tests.test_Config.TestConfig.test_hit_weights) ... ok -test_hmmsearch (tests.test_Config.TestConfig.test_hmmsearch) ... ok -test_hmmsearch_set_by_user (tests.test_Config.TestConfig.test_hmmsearch_set_by_user) ... ok -test_model_conf (tests.test_Config.TestConfig.test_model_conf) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/model_conf_parser.py:59: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. - if weights_node: -ok -test_models_dir (tests.test_Config.TestConfig.test_models_dir) ... ok -test_no_hmmsearch (tests.test_Config.TestConfig.test_no_hmmsearch) ... ok -test_out_dir (tests.test_Config.TestConfig.test_out_dir) ... ok -test_previous_n_sequence_db (tests.test_Config.TestConfig.test_previous_n_sequence_db) ... ok -test_previous_wo_cfg (tests.test_Config.TestConfig.test_previous_wo_cfg) ... ok -test_project_config_file (tests.test_Config.TestConfig.test_project_config_file) ... ok -test_save (tests.test_Config.TestConfig.test_save) ... ok -test_set_log_level (tests.test_Config.TestConfig.test_set_log_level) ... ok -test_set_option (tests.test_Config.TestConfig.test_set_option) ... ok -test_str_2_tuple (tests.test_Config.TestConfig.test_str_2_tuple) ... ok -test_working_dir (tests.test_Config.TestConfig.test_working_dir) ... ok -test_NoneConfig (tests.test_Config.TestNoneConfig.test_NoneConfig) ... ok -test_bad_exchangeable_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) ... ok -test_bad_gene_inter_gene_max_space_2 (tests.test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) ... ok -test_bad_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... ok -test_bad_max_nb_genes (tests.test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... ok -test_bad_min_genes_required (tests.test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... ok -test_bad_min_genes_required_2 (tests.test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... ok -test_bad_min_mandatory_genes_required (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) ... ok -test_bad_min_mandatory_genes_required_2 (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) ... ok -test_bad_min_mandatory_genes_required_4 (tests.test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) ... ok -test_exchangeable_inheritance (tests.test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... ok -test_gene_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... ok -test_gene_no_name (tests.test_DefinitionParser.TestModelParser.test_gene_no_name) ... ok -test_gene_w_unkown_attr (tests.test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... ok -test_inter_gene_max_space_cfg (tests.test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... ok -test_invalid_homolog (tests.test_DefinitionParser.TestModelParser.test_invalid_homolog) ... ok -test_invalid_homolog_2 (tests.test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... ok -test_invalid_presence (tests.test_DefinitionParser.TestModelParser.test_invalid_presence) ... ok -test_loner (tests.test_DefinitionParser.TestModelParser.test_loner) ... ok -test_max_nb_genes_cfg (tests.test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... ok -test_min_genes_required_cfg (tests.test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... ok -test_min_mandatory_genes_required_cfg (tests.test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) ... ok -test_min_mandatory_genes_required_lesser_than_mandatory_genes (tests.test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) ... ok -test_model_w_unkown_attr (tests.test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... ok -test_multi_loci_cfg (tests.test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... ok -test_multi_model (tests.test_DefinitionParser.TestModelParser.test_multi_model) ... ok -test_multi_system (tests.test_DefinitionParser.TestModelParser.test_multi_system) ... ok -test_no_inter_gene_max_space (tests.test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... ok -test_only_one_accessory (tests.test_DefinitionParser.TestModelParser.test_only_one_accessory) ... ok -test_parse_model_old_syntax (tests.test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... skipped 'Just ignore this test which fails' -test_parse_with_exchangeable (tests.test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... ok -test_wo_presence (tests.test_DefinitionParser.TestModelParser.test_wo_presence) ... ok -test_add_exchangeable (tests.test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok -test_alternate_of (tests.test_Exchangeable.TestExchangeable.test_alternate_of) ... ok -test_is_exchangeable (tests.test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok -test_loner (tests.test_Exchangeable.TestExchangeable.test_loner) ... ok -test_model (tests.test_Exchangeable.TestExchangeable.test_model) ... ok -test_multi_system (tests.test_Exchangeable.TestExchangeable.test_multi_system) ... ok -test_add_get_gene (tests.test_GeneBank.Test.test_add_get_gene) ... ok -test_contains (tests.test_GeneBank.Test.test_contains) ... ok -test_genes_fqn (tests.test_GeneBank.Test.test_genes_fqn) ... ok -test_get_uniq_object (tests.test_GeneBank.Test.test_get_uniq_object) ... ok -test_iter (tests.test_GeneBank.Test.test_iter) ... ok -test_fasta_iter (tests.test_Indexes.TestFastaIter.test_fasta_iter) ... ok -test_fasta_iter_bad_fasta (tests.test_Indexes.TestFastaIter.test_fasta_iter_bad_fasta) ... ok -test_build_force (tests.test_Indexes.TestIndex.test_build_force) ... ok -test_build_idx_gzip_seq (tests.test_Indexes.TestIndex.test_build_idx_gzip_seq) ... ok -test_build_idx_older_than_fasta (tests.test_Indexes.TestIndex.test_build_idx_older_than_fasta) ... ok -test_build_idx_point_wrong_fasta (tests.test_Indexes.TestIndex.test_build_idx_point_wrong_fasta) ... ok -test_build_my_indexes (tests.test_Indexes.TestIndex.test_build_my_indexes) ... ok -test_build_no_idx (tests.test_Indexes.TestIndex.test_build_no_idx) ... ok -test_build_not_writable (tests.test_Indexes.TestIndex.test_build_not_writable) ... ok -test_build_with_idx (tests.test_Indexes.TestIndex.test_build_with_idx) ... ok -test_empty_fasta (tests.test_Indexes.TestIndex.test_empty_fasta) ... ok -test_find_my_indexes (tests.test_Indexes.TestIndex.test_find_my_indexes) ... ok -test_index_dir (tests.test_Indexes.TestIndex.test_index_dir) ... ok -test_iter (tests.test_Indexes.TestIndex.test_iter) ... ok -test_allowed_hits (tests.test_LikelySystem.LikelySystemTest.test_allowed_hits) ... ok -test_forbidden_hits (tests.test_LikelySystem.LikelySystemTest.test_forbidden_hits) ... ok -test_hits (tests.test_LikelySystem.LikelySystemTest.test_hits) ... ok -test_init (tests.test_LikelySystem.LikelySystemTest.test_init) ... ok -test_str (tests.test_LikelySystem.LikelySystemTest.test_str) ... ok -test_hits (tests.test_LikelySystem.UnlikelySystemTest.test_hits) ... ok -test_init (tests.test_LikelySystem.UnlikelySystemTest.test_init) ... ok -test_reason (tests.test_LikelySystem.UnlikelySystemTest.test_reason) ... ok -test_str (tests.test_LikelySystem.UnlikelySystemTest.test_str) ... ok -test_MacsyDefaults_no_virtual_env (tests.test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... ok -test_MacsyDefaults_virtual_env (tests.test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok -test_ordered_match (tests.test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok -test_sort_hits_by_status (tests.test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... ok -test_unordered_match (tests.test_MatchMaker.MatchMakerTest.test_unordered_match) ... ok -test_accessor_mutator (tests.test_Model.TestModel.test_accessor_mutator) ... ok -test_eq (tests.test_Model.TestModel.test_eq) ... ok -test_filter (tests.test_Model.TestModel.test_filter) ... ok -test_fqn (tests.test_Model.TestModel.test_fqn) ... ok -test_get_gene (tests.test_Model.TestModel.test_get_gene) ... ok -test_gt (tests.test_Model.TestModel.test_gt) ... ok -test_hash (tests.test_Model.TestModel.test_hash) ... ok -test_inter_gene_max_space (tests.test_Model.TestModel.test_inter_gene_max_space) ... ok -test_lt (tests.test_Model.TestModel.test_lt) ... ok -test_max_nb_genes (tests.test_Model.TestModel.test_max_nb_genes) ... ok -test_min_genes_required (tests.test_Model.TestModel.test_min_genes_required) ... ok -test_min_mandatory_genes_required (tests.test_Model.TestModel.test_min_mandatory_genes_required) ... ok -test_multi_loci (tests.test_Model.TestModel.test_multi_loci) ... ok -test_str (tests.test_Model.TestModel.test_str) ... ok -test_add_get_model (tests.test_ModelBank.Test.test_add_get_model) ... ok -test_contains (tests.test_ModelBank.Test.test_contains) ... ok -test_get_uniq_object (tests.test_ModelBank.Test.test_get_uniq_object) ... ok -test_iter (tests.test_ModelBank.Test.test_iter) ... ok -test_execute_hmm_protected_path (tests.test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok -test_execute_hmm_w_GA_n_nocutga (tests.test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok -test_execute_hmm_with_GA (tests.test_Profile.TestProfile.test_execute_hmm_with_GA) ... skipped 'For some reason this fails to find hmmer_results - skipping' -test_execute_hmm_wo_GA (tests.test_Profile.TestProfile.test_execute_hmm_wo_GA) ... ok -test_execute_hmmer_failed (tests.test_Profile.TestProfile.test_execute_hmmer_failed) ... ok -test_execute_unknown_binary (tests.test_Profile.TestProfile.test_execute_unknown_binary) ... ok -test_ga_threshold (tests.test_Profile.TestProfile.test_ga_threshold) ... ok -test_len (tests.test_Profile.TestProfile.test_len) ... ok -test_str (tests.test_Profile.TestProfile.test_str) ... ok -test_get_profile (tests.test_ProfileFactory.TestProfileFactory.test_get_profile) ... ok -test_get_uniq_object (tests.test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok -test_unknow_profile (tests.test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok -test_hits (tests.test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok -test_init (tests.test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok -test_str (tests.test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok -test_fill_gembase_min_max_default_topology (tests.test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok -test_fill_gembase_min_max_with_topology (tests.test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok -test_fill_ordered_replicon_min_max (tests.test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok -test_fill_topology (tests.test_RepliconDB.Test.test_fill_topology) ... ok -test_get (tests.test_RepliconDB.Test.test_get) ... ok -test_getitem (tests.test_RepliconDB.Test.test_getitem) ... ok -test_guess_if_really_gembase (tests.test_RepliconDB.Test.test_guess_if_really_gembase) ... ok -test_in (tests.test_RepliconDB.Test.test_in) ... ok -test_items (tests.test_RepliconDB.Test.test_items) ... ok -test_iteritems (tests.test_RepliconDB.Test.test_iteritems) ... ok -test_names (tests.test_RepliconDB.Test.test_names) ... ok -test_replicon_infos (tests.test_RepliconDB.Test.test_replicon_infos) ... ok -test_extract (tests.test_Report.TestGembaseHMMReport.test_extract) ... ok -test_extract_concurent (tests.test_Report.TestGembaseHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/tests/test_Report.py:369: DeprecationWarning: currentThread() is deprecated, use current_thread() instead - main_thread = threading.currentThread() -ok -test_extract (tests.test_Report.TestGeneralHMMReport.test_extract) ... ok -test_extract_concurent (tests.test_Report.TestGeneralHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/tests/test_Report.py:541: DeprecationWarning: currentThread() is deprecated, use current_thread() instead - main_thread = threading.currentThread() -ok -test_HMMReport (tests.test_Report.TestHMMReport.test_HMMReport) ... ok -test_best_hit (tests.test_Report.TestHMMReport.test_best_hit) ... ok -test_build_my_db (tests.test_Report.TestHMMReport.test_build_my_db) ... ok -test_fill_my_db (tests.test_Report.TestHMMReport.test_fill_my_db) ... ok -test_hit_start (tests.test_Report.TestHMMReport.test_hit_start) ... ok -test_parse_hmm_body (tests.test_Report.TestHMMReport.test_parse_hmm_body) ... ok -test_parse_hmm_header (tests.test_Report.TestHMMReport.test_parse_hmm_header) ... ok -test_save_extract (tests.test_Report.TestHMMReport.test_save_extract) ... ok -test_str (tests.test_Report.TestHMMReport.test_str) ... ok -test_extract (tests.test_Report.TestOrderedHMMReport.test_extract) ... ok -test_extract_concurent (tests.test_Report.TestOrderedHMMReport.test_extract_concurent) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/tests/test_Report.py:461: DeprecationWarning: currentThread() is deprecated, use current_thread() instead - main_thread = threading.currentThread() -ok -test_HitSystemTracker (tests.test_System.SystemTest.test_HitSystemTracker) ... ok -test_count (tests.test_System.SystemTest.test_count) ... ok -test_fulfilled_function (tests.test_System.SystemTest.test_fulfilled_function) ... ok -test_get_hits_encoding_multisystem (tests.test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok -test_get_loners (tests.test_System.SystemTest.test_get_loners) ... ok -test_get_multisystems (tests.test_System.SystemTest.test_get_multisystems) ... ok -test_hits (tests.test_System.SystemTest.test_hits) ... ok -test_init (tests.test_System.SystemTest.test_init) ... ok -test_is_compatible (tests.test_System.SystemTest.test_is_compatible) ... ok -test_loci_nb (tests.test_System.SystemTest.test_loci_nb) ... ok -test_loci_num (tests.test_System.SystemTest.test_loci_num) ... ok -test_multi_loci (tests.test_System.SystemTest.test_multi_loci) ... ok -test_occurrence (tests.test_System.SystemTest.test_occurrence) ... ok -test_position (tests.test_System.SystemTest.test_position) ... ok -test_score (tests.test_System.SystemTest.test_score) ... ok -test_wholeness (tests.test_System.SystemTest.test_wholeness) ... ok -test_build_clusters (tests.test_cluster.TestBuildCluster.test_build_clusters) ... ok -test_clusterize (tests.test_cluster.TestBuildCluster.test_clusterize) ... ok -test_colocates (tests.test_cluster.TestBuildCluster.test_colocates) ... ok -test_get_true_loners (tests.test_cluster.TestBuildCluster.test_get_true_loners) ... ok -test_contains (tests.test_cluster.TestCluster.test_contains) ... ok -test_fulfilled_function (tests.test_cluster.TestCluster.test_fulfilled_function) ... ok -test_init (tests.test_cluster.TestCluster.test_init) ... ok -test_len (tests.test_cluster.TestCluster.test_len) ... ok -test_loner (tests.test_cluster.TestCluster.test_loner) ... ok -test_merge (tests.test_cluster.TestCluster.test_merge) ... ok -test_multi_system (tests.test_cluster.TestCluster.test_multi_system) ... ok -test_replace (tests.test_cluster.TestCluster.test_replace) ... ok -test_replicon_name (tests.test_cluster.TestCluster.test_replicon_name) ... ok -test_score (tests.test_cluster.TestCluster.test_score) ... ok -test_str (tests.test_cluster.TestCluster.test_str) ... ok -test_2_systems_not_compatible (tests.test_functional_test.Test.test_2_systems_not_compatible) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_2_systems_not_compatible/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_cfg_n_previous_run (tests.test_functional_test.Test.test_cfg_n_previous_run) ... ok -test_degenerated_systems (tests.test_functional_test.Test.test_degenerated_systems) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_force (tests.test_functional_test.Test.test_force) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_functional_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_gembase (tests.test_functional_test.Test.test_gembase) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. - if filtering_node: -/usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_gzip (tests.test_functional_test.Test.test_gzip) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_gzip/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_index_dir (tests.test_functional_test.Test.test_index_dir) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_model_unknown (tests.test_functional_test.Test.test_model_unknown) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_no_db_type (tests.test_functional_test.Test.test_no_db_type) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_no_models (tests.test_functional_test.Test.test_no_models) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_no_seq_db (tests.test_functional_test.Test.test_no_seq_db) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_no_sequence (tests.test_functional_test.Test.test_no_sequence) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_no_sequence/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_only_loners (tests.test_functional_test.Test.test_only_loners) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_1_cluster_3_loners (tests.test_functional_test.Test.test_ordered_1_cluster_3_loners) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_1_cluster_and_clusters_of_loners (tests.test_functional_test.Test.test_ordered_1_cluster_and_clusters_of_loners) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_cluster_and_clusters_of_loners/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_1_clusters_3_loners_w_exchangeable (tests.test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_1_loner_exch_in_clust (tests.test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_1_loner_in_clust (tests.test_functional_test.Test.test_ordered_1_loner_in_clust) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_2_clusters_1_loner (tests.test_functional_test.Test.test_ordered_2_clusters_1_loner) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_2_clusters_3_loners (tests.test_functional_test.Test.test_ordered_2_clusters_3_loners) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_circular (tests.test_functional_test.Test.test_ordered_circular) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_linear (tests.test_functional_test.Test.test_ordered_linear) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_multi_loci (tests.test_functional_test.Test.test_ordered_multi_loci) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_multi_model (tests.test_functional_test.Test.test_ordered_multi_model) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_multi_system (tests.test_functional_test.Test.test_ordered_multi_system) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_multi_system_out_system (tests.test_functional_test.Test.test_ordered_multi_system_out_system) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_only_one_multi_model (tests.test_functional_test.Test.test_ordered_only_one_multi_model) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_ordered_single_loci (tests.test_functional_test.Test.test_ordered_single_loci) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_timeout (tests.test_functional_test.Test.test_timeout) ... ok -test_uncomplete_degenerated_systems (tests.test_functional_test.Test.test_uncomplete_degenerated_systems) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_unordered (tests.test_functional_test.Test.test_unordered) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_unordered_no_hits (tests.test_functional_test.Test.test_unordered_no_hits) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_unordered_only_forbidden (tests.test_functional_test.Test.test_unordered_only_forbidden) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_working_dir_exists (tests.test_functional_test.Test.test_working_dir_exists) ... ok -test_working_dir_exists_and_not_dir (tests.test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok -test_core_gene (tests.test_gene.TestCoreGene.test_core_gene) ... ok -test_str (tests.test_gene.TestGeneStatus.test_str) ... ok -test_add_exchangeable (tests.test_gene.TestModelGene.test_add_exchangeable) ... ok -test_alternate_of (tests.test_gene.TestModelGene.test_alternate_of) ... ok -test_core_gene (tests.test_gene.TestModelGene.test_core_gene) -test getter/setter for core_gene property ... ok -test_exhangeables (tests.test_gene.TestModelGene.test_exhangeables) ... ok -test_hash (tests.test_gene.TestModelGene.test_hash) ... ok -test_init (tests.test_gene.TestModelGene.test_init) ... ok -test_inter_gene_max_space (tests.test_gene.TestModelGene.test_inter_gene_max_space) -test getter for inter_gene_max_space property ... ok -test_is_Forbidden (tests.test_gene.TestModelGene.test_is_Forbidden) -test if gene belong to model mandatory genes ... ok -test_is_accessory (tests.test_gene.TestModelGene.test_is_accessory) -test if gene belong to model mandatory genes ... ok -test_is_exchangeable (tests.test_gene.TestModelGene.test_is_exchangeable) ... ok -test_is_mandatory (tests.test_gene.TestModelGene.test_is_mandatory) -test if gene belong to model mandatory genes ... ok -test_loner (tests.test_gene.TestModelGene.test_loner) -test getter for loner property ... ok -test_model (tests.test_gene.TestModelGene.test_model) -test getter/setter for model property ... ok -test_multi_model (tests.test_gene.TestModelGene.test_multi_model) -test getter for multi_modelproperty ... ok -test_multi_system (tests.test_gene.TestModelGene.test_multi_system) -test getter for multi_system property ... ok -test_str (tests.test_gene.TestModelGene.test_str) ... ok -test_unknown_attribute (tests.test_gene.TestModelGene.test_unknown_attribute) ... ok -test_cmp (tests.test_hit.CoreHitTest.test_cmp) ... ok -test_eq (tests.test_hit.CoreHitTest.test_eq) ... ok -test_get_position (tests.test_hit.CoreHitTest.test_get_position) ... ok -test_hash (tests.test_hit.CoreHitTest.test_hash) ... ok -test_str (tests.test_hit.CoreHitTest.test_str) ... ok -test_compute_best_MSHit (tests.test_hit.GetBestHitTest.test_compute_best_MSHit) ... ok -test_get_best_hits (tests.test_hit.GetBestHitTest.test_get_best_hits) ... ok -test_get_best_hits_4_func (tests.test_hit.GetBestHitTest.test_get_best_hits_4_func) ... ok -test_sort_multisystem_hits (tests.test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok -test_hit_weight_default (tests.test_hit.HitWeightTest.test_hit_weight_default) ... ok -test_hit_weight_not_default (tests.test_hit.HitWeightTest.test_hit_weight_not_default) ... ok -test_counterpart (tests.test_hit.LonerMultiSystemTest.test_counterpart) ... ok -test_init (tests.test_hit.LonerMultiSystemTest.test_init) ... ok -test_loner (tests.test_hit.LonerMultiSystemTest.test_loner) ... ok -test_multi_system (tests.test_hit.LonerMultiSystemTest.test_multi_system) ... ok -test_str (tests.test_hit.LonerMultiSystemTest.test_str) ... ok -test_counterpart (tests.test_hit.LonerTest.test_counterpart) ... ok -test_init (tests.test_hit.LonerTest.test_init) ... ok -test_len (tests.test_hit.LonerTest.test_len) ... ok -test_loner (tests.test_hit.LonerTest.test_loner) ... ok -test_multi_system (tests.test_hit.LonerTest.test_multi_system) ... ok -test_str (tests.test_hit.LonerTest.test_str) ... ok -test_delegation (tests.test_hit.ModelHitTest.test_delegation) ... ok -test_eq (tests.test_hit.ModelHitTest.test_eq) ... ok -test_hash (tests.test_hit.ModelHitTest.test_hash) ... ok -test_init (tests.test_hit.ModelHitTest.test_init) ... ok -test_loner (tests.test_hit.ModelHitTest.test_loner) ... ok -test_multi_model (tests.test_hit.ModelHitTest.test_multi_model) ... ok -test_multi_system (tests.test_hit.ModelHitTest.test_multi_system) ... ok -test_counterpart (tests.test_hit.MultiSystemTest.test_counterpart) ... ok -test_init (tests.test_hit.MultiSystemTest.test_init) ... ok -test_len (tests.test_hit.MultiSystemTest.test_len) ... ok -test_loner (tests.test_hit.MultiSystemTest.test_loner) ... ok -test_multi_system (tests.test_hit.MultiSystemTest.test_multi_system) ... ok -test_str (tests.test_hit.MultiSystemTest.test_str) ... ok -test_functional_split (tests.test_macsy_gembase_split.TestSplit.test_functional_split) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpoph1x9pm/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 (tests.test_macsy_gembase_split.TestSplit.test_functional_split_out_error) ... ok -test_functional_split_out_not_writable (tests.test_macsy_gembase_split.TestSplit.test_functional_split_out_not_writable) ... ok -test_functional_merge (tests.test_macsy_merge_results.TestMerge.test_functional_merge) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmplcl3jop7/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 (tests.test_macsy_merge_results.TestMerge.test_functional_merge_one_results_empty) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp9ya0c_fw/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 (tests.test_macsy_merge_results.TestMerge.test_functional_merge_out_error) ... ok -test_functional_merge_out_not_writable (tests.test_macsy_merge_results.TestMerge.test_functional_merge_out_not_writable) ... ok -test_functional_merge_results_empty (tests.test_macsy_merge_results.TestMerge.test_functional_merge_results_empty) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp1za3v0ek/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_get_warning (tests.test_macsy_merge_results.TestMerge.test_get_warning) ... ok -test_merge_and_reindex_invalid_solid (tests.test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... ok -test_add_comment (tests.test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok -test_write (tests.test_macsyconfig.TestConfigParserWithComment.test_write) ... ok -test_ask (tests.test_macsyconfig.TestMacsyconfig.test_ask) ... ok -test_ask_bad_value (tests.test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... ok -test_ask_default_is_sequence (tests.test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok -test_ask_use_default (tests.test_macsyconfig.TestMacsyconfig.test_ask_use_default) ... ok -test_ask_value_is_sequence (tests.test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok -test_check_bool (tests.test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok -test_check_choice (tests.test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok -test_check_dir (tests.test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok -test_check_exe (tests.test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok -test_check_file (tests.test_macsyconfig.TestMacsyconfig.test_check_file) ... ok -test_check_float (tests.test_macsyconfig.TestMacsyconfig.test_check_float) ... ok -test_check_positive_int (tests.test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok -test_check_str (tests.test_macsyconfig.TestMacsyconfig.test_check_str) ... ok -test_functional_dark_theme (tests.test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok -test_functional_file_already_exists (tests.test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok -test_parse_args (tests.test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok -test_set_base_options (tests.test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok -test_set_general_options (tests.test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok -test_set_hmmer_options (tests.test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok -test_set_path_options (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok -test_set_path_options_with_system_models_dir (tests.test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) ... ok -test_set_score_options (tests.test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok -test_set_section (tests.test_macsyconfig.TestMacsyconfig.test_set_section) ... ok -test_set_section_use_defaults (tests.test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok -test_available (tests.test_macsydata.TestMacsydata.test_available) ... ok -test_build_argparser (tests.test_macsydata.TestMacsydata.test_build_argparser) ... ok -test_check (tests.test_macsydata.TestMacsydata.test_check) ... ok -test_check_with_errors (tests.test_macsydata.TestMacsydata.test_check_with_errors) ... ok -test_check_with_warnings (tests.test_macsydata.TestMacsydata.test_check_with_warnings) ... ok -test_cite (tests.test_macsydata.TestMacsydata.test_cite) ... ok -test_cmd_name (tests.test_macsydata.TestMacsydata.test_cmd_name) ... ok -test_definition_all_def (tests.test_macsydata.TestMacsydata.test_definition_all_def) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpclbiz86x/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-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpclbiz86x/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_bad_def (tests.test_macsydata.TestMacsydata.test_definition_bad_def) ... ok -test_definition_bad_pack (tests.test_macsydata.TestMacsydata.test_definition_bad_pack) ... ok -test_definition_bad_subfamily (tests.test_macsydata.TestMacsydata.test_definition_bad_subfamily) ... ok -test_definition_models_dir (tests.test_macsydata.TestMacsydata.test_definition_models_dir) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp0ypdcdhn/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-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp0ypdcdhn/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 (tests.test_macsydata.TestMacsydata.test_definition_one_def) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp6fymq05z/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-2.1.4/.pybuild/cpython3_3.13/build/macsypy/scripts/macsydata.py:652: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp6fymq05z/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 (tests.test_macsydata.TestMacsydata.test_download) ... ok -test_freeze (tests.test_macsydata.TestMacsydata.test_freeze) ... ok -test_help (tests.test_macsydata.TestMacsydata.test_help) ... ok -test_info (tests.test_macsydata.TestMacsydata.test_info) ... ok -test_init_dir_exists_look_pack (tests.test_macsydata.TestMacsydata.test_init_dir_exists_look_pack) ... skipped 'GitPython is not installed' -test_init_dir_exists_not_pack (tests.test_macsydata.TestMacsydata.test_init_dir_exists_not_pack) ... skipped 'GitPython is not installed' -test_init_empty_dir_exists (tests.test_macsydata.TestMacsydata.test_init_empty_dir_exists) ... skipped 'GitPython is not installed' -test_init_existing_file (tests.test_macsydata.TestMacsydata.test_init_existing_file) ... ok -test_init_existing_pack (tests.test_macsydata.TestMacsydata.test_init_existing_pack) ... skipped 'GitPython is not installed' -test_init_package_complete (tests.test_macsydata.TestMacsydata.test_init_package_complete) ... skipped 'GitPython is not installed' -test_init_package_minimal (tests.test_macsydata.TestMacsydata.test_init_package_minimal) ... skipped 'GitPython is not installed' -test_install_bad_target (tests.test_macsydata.TestMacsydata.test_install_bad_target) ... ok -test_install_installed_package_corrupted (tests.test_macsydata.TestMacsydata.test_install_installed_package_corrupted) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/package.py:110: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. - tar.extractall(path, members, numeric_owner=numeric_owner) -ok -test_install_local (tests.test_macsydata.TestMacsydata.test_install_local) ... ok -test_install_local_already_installed (tests.test_macsydata.TestMacsydata.test_install_local_already_installed) ... ok -test_install_local_already_installed_force (tests.test_macsydata.TestMacsydata.test_install_local_already_installed_force) ... ok -test_install_remote (tests.test_macsydata.TestMacsydata.test_install_remote) ... ok -test_install_remote_already_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_already_in_local) ... ok -test_install_remote_already_in_local_force (tests.test_macsydata.TestMacsydata.test_install_remote_already_in_local_force) ... ok -test_install_remote_lower_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_lower_in_local) ... ok -test_install_remote_permision_error (tests.test_macsydata.TestMacsydata.test_install_remote_permision_error) ... ok -test_install_remote_spec_not_found (tests.test_macsydata.TestMacsydata.test_install_remote_spec_not_found) ... ok -test_install_remote_upper_in_local (tests.test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... ok -test_install_target (tests.test_macsydata.TestMacsydata.test_install_target) ... ok -test_list (tests.test_macsydata.TestMacsydata.test_list) ... ok -test_list_long (tests.test_macsydata.TestMacsydata.test_list_long) ... ok -test_list_outdated (tests.test_macsydata.TestMacsydata.test_list_outdated) ... ok -test_list_uptodate (tests.test_macsydata.TestMacsydata.test_list_uptodate) ... ok -test_list_verbose (tests.test_macsydata.TestMacsydata.test_list_verbose) ... ok -test_no_subcommand (tests.test_macsydata.TestMacsydata.test_no_subcommand) ... ok -test_search_in_pack_desc (tests.test_macsydata.TestMacsydata.test_search_in_pack_desc) ... ok -test_search_in_pack_desc_match_case (tests.test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok -test_search_in_pack_name (tests.test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok -test_search_in_pack_name_match_case (tests.test_macsydata.TestMacsydata.test_search_in_pack_name_match_case) ... ok -test_search_reach_limit (tests.test_macsydata.TestMacsydata.test_search_reach_limit) ... ok -test_uninstall (tests.test_macsydata.TestMacsydata.test_uninstall) ... ok -test_verbosity_to_log_level (tests.test_macsydata.TestMacsydata.test_verbosity_to_log_level) ... ok -test_db_type_set_to_gembase (tests.test_macsyfinder.TestMacsyfinder.test_db_type_set_to_gembase) ... ok -test_likely_systems_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_likely_systems_to_tsv) ... ok -test_likely_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok -test_list_models (tests.test_macsyfinder.TestMacsyfinder.test_list_models) ... ok -test_loners_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... ok -test_multisystem_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok -test_parse_args (tests.test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok -test_rejected_candidates_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok -test_rejected_candidates_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok -test_search_systems (tests.test_macsyfinder.TestMacsyfinder.test_search_systems) ... ok -test_search_systems_unordered (tests.test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok -test_solutions_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok -test_summary_best_solution (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok -test_summary_best_solution_empty (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok -test_summary_best_solution_lack_models (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... ok -test_summary_best_solution_lack_models_replicons (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) ... ok -test_summary_best_solution_lack_replicon (tests.test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) ... ok -test_systems_to_tsv (tests.test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) ... ok -test_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_systems_to_txt) ... ok -test_unnlikely_systems_to_txt (tests.test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok -test_LightHit (tests.test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok -test_build_my_db (tests.test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok -test_fill_my_db (tests.test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok -test_functional (tests.test_macsyprofile.TestMacsyprofile.test_functional) ... ok -test_functional_best_score (tests.test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok -test_functional_coverage (tests.test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok -test_functional_evalue (tests.test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok -test_functional_no_hits (tests.test_macsyprofile.TestMacsyprofile.test_functional_no_hits) ... ok -test_functional_no_previous_run (tests.test_macsyprofile.TestMacsyprofile.test_functional_no_previous_run) ... ok -test_functional_old_conf (tests.test_macsyprofile.TestMacsyprofile.test_functional_old_conf) ... ok -test_functional_out_exists (tests.test_macsyprofile.TestMacsyprofile.test_functional_out_exists) ... ok -test_functional_pattern (tests.test_macsyprofile.TestMacsyprofile.test_functional_pattern) ... ok -test_getProfile_len (tests.test_macsyprofile.TestMacsyprofile.test_getProfile_len) ... ok -test_get_gene_name (tests.test_macsyprofile.TestMacsyprofile.test_get_gene_name) ... ok -test_header (tests.test_macsyprofile.TestMacsyprofile.test_header) ... ok -test_hit_start (tests.test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok -test_parse (tests.test_macsyprofile.TestMacsyprofile.test_parse) ... ok -test_parse_hmm_body (tests.test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) ... ok -test_parse_hmm_header (tests.test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok -test_pasre_args (tests.test_macsyprofile.TestMacsyprofile.test_pasre_args) ... ok -test_verbosity_to_log_level (tests.test_macsyprofile.TestMacsyprofile.test_verbosity_to_log_level) ... ok -test_init_logger_default (tests.test_macsypy.Test.test_init_logger_default) ... ok -test_init_logger_logfile (tests.test_macsypy.Test.test_init_logger_logfile) ... /usr/lib/python3.13/unittest/case.py:611: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp3uj965ki' mode='a' encoding='utf-8'> - self.tearDown() -ResourceWarning: Enable tracemalloc to get the object allocation traceback -ok -test_init_logger_no_out (tests.test_macsypy.Test.test_init_logger_no_out) ... ok -test_logger_set_level_bad_level (tests.test_macsypy.Test.test_logger_set_level_bad_level) ... ok -test_logger_set_level_default (tests.test_macsypy.Test.test_logger_set_level_default) ... ok -test_logger_set_level_error (tests.test_macsypy.Test.test_logger_set_level_error) ... ok -test_logger_set_level_handlers (tests.test_macsypy.Test.test_logger_set_level_handlers) ... ok -test_cite (tests.test_metadata.TestMetadata.test_cite) ... ok -test_copyright (tests.test_metadata.TestMetadata.test_copyright) ... ok -test_doc (tests.test_metadata.TestMetadata.test_doc) ... ok -test_init (tests.test_metadata.TestMetadata.test_init) ... ok -test_license (tests.test_metadata.TestMetadata.test_license) ... ok -test_load (tests.test_metadata.TestMetadata.test_load) ... ok -test_maintainer (tests.test_metadata.TestMetadata.test_maintainer) ... ok -test_save (tests.test_metadata.TestMetadata.test_save) ... ok -test_short_desc (tests.test_metadata.TestMetadata.test_short_desc) ... ok -test_vers (tests.test_metadata.TestMetadata.test_vers) ... ok -test_parse (tests.test_model_conf_parser.TestModelConfParser.test_parse) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/model_conf_parser.py:59: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. - if weights_node: -/build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/model_conf_parser.py:63: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. - if filtering_node: -ok -test_parse_bad_file (tests.test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... ok -test_parse_filtering (tests.test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... ok -test_parse_w_bad_value (tests.test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... ok -test_parse_w_unkown_tag (tests.test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... ok -test_parse_weights (tests.test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok -test_parse_wo_filtering (tests.test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok -test_parse_wo_weights (tests.test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok -test_init (tests.test_package.TestLocalModelIndex.test_init) ... ok -test_repos_url (tests.test_package.TestLocalModelIndex.test_repos_url) ... ok -test_init (tests.test_package.TestModelIndex.test_init) ... ok -test_check (tests.test_package.TestPackage.test_check) ... ok -test_check_bad_metadata (tests.test_package.TestPackage.test_check_bad_metadata) ... ok -test_check_metadata (tests.test_package.TestPackage.test_check_metadata) ... ok -test_check_metadata_no_cite (tests.test_package.TestPackage.test_check_metadata_no_cite) ... ok -test_check_metadata_no_copyright (tests.test_package.TestPackage.test_check_metadata_no_copyright) ... ok -test_check_metadata_no_desc (tests.test_package.TestPackage.test_check_metadata_no_desc) ... ok -test_check_metadata_no_doc (tests.test_package.TestPackage.test_check_metadata_no_doc) ... ok -test_check_metadata_no_email (tests.test_package.TestPackage.test_check_metadata_no_email) ... ok -test_check_metadata_no_license (tests.test_package.TestPackage.test_check_metadata_no_license) ... ok -test_check_metadata_no_maintainer (tests.test_package.TestPackage.test_check_metadata_no_maintainer) ... ok -test_check_metadata_no_name (tests.test_package.TestPackage.test_check_metadata_no_name) ... ok -test_check_metadata_no_vers (tests.test_package.TestPackage.test_check_metadata_no_vers) ... ok -test_check_metadata_with_vers (tests.test_package.TestPackage.test_check_metadata_with_vers) ... ok -test_check_model_conf (tests.test_package.TestPackage.test_check_model_conf) ... ok -test_check_model_conf_bad_conf (tests.test_package.TestPackage.test_check_model_conf_bad_conf) ... ok -test_check_model_conf_no_conf (tests.test_package.TestPackage.test_check_model_conf_no_conf) ... ok -test_check_model_consistency (tests.test_package.TestPackage.test_check_model_consistency) ... ok -test_check_model_consistency_bad_definitions (tests.test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok -test_check_model_consistency_extra_profile (tests.test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok -test_check_model_consistency_lack_one_profile (tests.test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... ok -test_check_no_readme_n_no_license (tests.test_package.TestPackage.test_check_no_readme_n_no_license) ... ok -test_check_poor_quality_metadata (tests.test_package.TestPackage.test_check_poor_quality_metadata) ... ok -test_check_structure (tests.test_package.TestPackage.test_check_structure) ... ok -test_check_structure_bad_path (tests.test_package.TestPackage.test_check_structure_bad_path) ... ok -test_check_structure_no_def (tests.test_package.TestPackage.test_check_structure_no_def) ... ok -test_check_structure_no_license (tests.test_package.TestPackage.test_check_structure_no_license) ... ok -test_check_structure_no_metadata (tests.test_package.TestPackage.test_check_structure_no_metadata) ... ok -test_check_structure_no_profiles (tests.test_package.TestPackage.test_check_structure_no_profiles) ... ok -test_check_structure_no_readme (tests.test_package.TestPackage.test_check_structure_no_readme) ... ok -test_find_readme (tests.test_package.TestPackage.test_find_readme) ... ok -test_help (tests.test_package.TestPackage.test_help) ... ok -test_info (tests.test_package.TestPackage.test_info) ... ok -test_info_no_citation (tests.test_package.TestPackage.test_info_no_citation) ... ok -test_info_no_doc (tests.test_package.TestPackage.test_info_no_doc) ... ok -test_info_no_license (tests.test_package.TestPackage.test_info_no_license) ... ok -test_init (tests.test_package.TestPackage.test_init) ... ok -test_metadata (tests.test_package.TestPackage.test_metadata) ... ok -test_parse_arch_path (tests.test_package.TestPackageFunc.test_parse_arch_path) ... ok -test_download (tests.test_package.TestRemoteModelIndex.test_download) ... ok -test_get_metadata (tests.test_package.TestRemoteModelIndex.test_get_metadata) ... ok -test_init (tests.test_package.TestRemoteModelIndex.test_init) ... ok -test_list_package_vers (tests.test_package.TestRemoteModelIndex.test_list_package_vers) ... ok -test_list_packages (tests.test_package.TestRemoteModelIndex.test_list_packages) ... ok -test_remote_exists (tests.test_package.TestRemoteModelIndex.test_remote_exists) ... ok -test_repos_url (tests.test_package.TestRemoteModelIndex.test_repos_url) ... ok -test_unarchive (tests.test_package.TestRemoteModelIndex.test_unarchive) ... /build/reproducible-path/macsyfinder-2.1.4/.pybuild/cpython3_3.13/build/macsypy/package.py:110: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. - tar.extractall(path, members, numeric_owner=numeric_owner) -ok -test_url_json (tests.test_package.TestRemoteModelIndex.test_url_json) ... ok -test_url_json_reach_limit (tests.test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok -test_DefinitionLocationn (tests.test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok -test_add_submodel (tests.test_registries.DefinitionLocationTest.test_add_submodel) ... ok -test_all (tests.test_registries.DefinitionLocationTest.test_all) ... ok -test_eq (tests.test_registries.DefinitionLocationTest.test_eq) ... ok -test_family_name (tests.test_registries.DefinitionLocationTest.test_family_name) ... ok -test_greater (tests.test_registries.DefinitionLocationTest.test_greater) ... ok -test_hash (tests.test_registries.DefinitionLocationTest.test_hash) ... ok -test_lesser (tests.test_registries.DefinitionLocationTest.test_lesser) ... ok -test_root_name (tests.test_registries.DefinitionLocationTest.test_root_name) ... ok -test_separator (tests.test_registries.DefinitionLocationTest.test_separator) ... ok -test_split_fqn (tests.test_registries.DefinitionLocationTest.test_split_fqn) ... ok -test_str (tests.test_registries.DefinitionLocationTest.test_str) ... ok -test_ModelLocation (tests.test_registries.ModelLocationTest.test_ModelLocation) ... ok -test_get_all_definitions (tests.test_registries.ModelLocationTest.test_get_all_definitions) ... ok -test_get_definition (tests.test_registries.ModelLocationTest.test_get_definition) ... ok -test_get_definitions (tests.test_registries.ModelLocationTest.test_get_definitions) ... ok -test_get_profile (tests.test_registries.ModelLocationTest.test_get_profile) ... ok -test_get_profiles_names (tests.test_registries.ModelLocationTest.test_get_profiles_names) ... ok -test_str (tests.test_registries.ModelLocationTest.test_str) ... ok -test_version (tests.test_registries.ModelLocationTest.test_version) ... ok -test_version_no_metadata (tests.test_registries.ModelLocationTest.test_version_no_metadata) ... ok -test_add_get (tests.test_registries.ModelRegistryTest.test_add_get) ... ok -test_models (tests.test_registries.ModelRegistryTest.test_models) ... ok -test_scan_models_dir (tests.test_registries.ModelRegistryTest.test_scan_models_dir) ... ok -test_str (tests.test_registries.ModelRegistryTest.test_str) ... ok -test_search (tests.test_search_genes.TestSearchGenes.test_search) ... ok -test_search_fail (tests.test_search_genes.TestSearchGenes.test_search_fail) ... ok -test_search_recover (tests.test_search_genes.TestSearchGenes.test_search_recover) ... ok -test_worker_cpu (tests.test_search_genes.TestSearchGenes.test_worker_cpu) ... ok -test_LikelySystemSerializer_txt (tests.test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok -test_RejectedClusters_tsv (tests.test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok -test_SolutionSerializer_tsv (tests.test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok -test_SpecialHitSerializer_tsv (tests.test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok -test_SystemSerializer_str (tests.test_serialization.SerializationTest.test_SystemSerializer_str) ... ok -test_SystemSerializer_tsv (tests.test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok -test_UnlikelySystemSerializer_txt (tests.test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... ok -test_combine_clusters (tests.test_solution.SolutionExplorerTest.test_combine_clusters) ... ok -test_combine_multisystems (tests.test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok -test_find_best_solution (tests.test_solution.SolutionExplorerTest.test_find_best_solution) ... ok -test_average_wholeness (tests.test_solution.SolutionTest.test_average_wholeness) ... ok -test_gt (tests.test_solution.SolutionTest.test_gt) ... ok -test_hits_number (tests.test_solution.SolutionTest.test_hits_number) ... ok -test_hits_positions (tests.test_solution.SolutionTest.test_hits_positions) ... ok -test_iteration (tests.test_solution.SolutionTest.test_iteration) ... ok -test_lt (tests.test_solution.SolutionTest.test_lt) ... ok -test_score (tests.test_solution.SolutionTest.test_score) ... ok -test_sorting (tests.test_solution.SolutionTest.test_sorting) ... ok -test_systems (tests.test_solution.SolutionTest.test_systems) ... ok -test_get_def_to_detect (tests.test_utils.TestUtils.test_get_def_to_detect) ... ok -test_get_replicon_names_bad_type (tests.test_utils.TestUtils.test_get_replicon_names_bad_type) ... ok -test_get_replicon_names_gembase (tests.test_utils.TestUtils.test_get_replicon_names_gembase) ... ok -test_get_replicon_names_ordered (tests.test_utils.TestUtils.test_get_replicon_names_ordered) ... ok -test_get_replicon_names_unordered (tests.test_utils.TestUtils.test_get_replicon_names_unordered) ... ok -test_parse_time (tests.test_utils.TestUtils.test_parse_time) ... ok -test_threads_available (tests.test_utils.TestUtils.test_threads_available) ... ok - ----------------------------------------------------------------------- -Ran 540 tests in 12.110s - -OK (skipped=8) +dh: command-omitted: The call to "dh_auto_test -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2263,9 +1593,9 @@ copying downloadable files... [100%] _static/msf_summary.py copying static files... +Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/basic.css -Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/html/_static/js/versions.js copying static files: done copying extra files... @@ -2376,10 +1706,10 @@ looking for now-outdated files... none found preparing documents... done copying assets... -copying TeX support files... Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/make.bat -Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/Makefile -Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/latexmkrc +copying TeX support files... Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/Makefile Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/latexmkjarc +Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/latexmkrc +Writing evaluated template result to /build/reproducible-path/macsyfinder-2.1.4/doc/build/latex/make.bat done copying assets: done processing macsyfinder.tex... @@ -5530,7 +4860,7 @@ ve/texmf-dist/fonts/type1/public/txfonts/tcxbtt.pfb> -Output written on macsyfinder.pdf (187 pages, 2517913 bytes). +Output written on macsyfinder.pdf (187 pages, 2517920 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' @@ -7070,7 +6400,7 @@ ve/texmf-dist/fonts/type1/public/txfonts/tcxbtt.pfb> -Output written on macsyfinder.pdf (198 pages, 2603019 bytes). +Output written on macsyfinder.pdf (198 pages, 2603015 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' @@ -8579,7 +7909,7 @@ ve/texmf-dist/fonts/type1/public/txfonts/tcxbtt.pfb> -Output written on macsyfinder.pdf (198 pages, 2603273 bytes). +Output written on macsyfinder.pdf (198 pages, 2603195 bytes). Transcript written on macsyfinder.log. Latexmk: Getting log file 'macsyfinder.log' Latexmk: Examining 'macsyfinder.fls' @@ -8597,12 +7927,12 @@ dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild +I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsymerge I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsyconfig -I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsyprofile I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsyfinder I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsysplit I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsydata -I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsymerge +I: dh_python3 tools:114: replacing shebang in debian/macsyfinder/usr/bin/macsyprofile dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild @@ -8632,12 +7962,14 @@ 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/1073476/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1073476/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/384198 and its subdirectories -I: Current time: Tue Nov 25 09:54:16 -12 2025 -I: pbuilder-time-stamp: 1764107656 +I: removing directory /srv/workspace/pbuilder/1073476 and its subdirectories +I: Current time: Tue Dec 29 18:33:16 +14 2026 +I: pbuilder-time-stamp: 1798518796