Source: macsyfinder Version: 2.0-1 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230113 ftbfs-bookworm
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > debian/rules binary > dh binary --with python3,sphinxdoc --buildsystem=pybuild > dh_update_autotools_config -O--buildsystem=pybuild > dh_autoreconf -O--buildsystem=pybuild > dh_auto_configure -O--buildsystem=pybuild > I: pybuild base:240: python3.11 setup.py config > running config > dh_auto_build -O--buildsystem=pybuild > I: pybuild base:240: /usr/bin/python3 setup.py build > running build > running build_py > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/package.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/solution.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/model.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/definition_parser.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/report.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/model_conf_parser.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/hit.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/profile.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/registries.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/gene.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/system.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/cluster.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/config.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/serialization.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/search_genes.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/database.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/error.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > copying macsypy/utils.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy > creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/__init__.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/macsydata.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/macsyfinder.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/macsyprofile.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/macsy_gembase_split.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/macsy_merge_results.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > copying macsypy/scripts/macsyconfig.py -> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/macsypy/scripts > dh_auto_test -O--buildsystem=pybuild > I: pybuild base:240: python3.11 setup.py test > running test > WARNING: Testing via this command is deprecated and will be removed in a > future version. Users looking for a generic test entry point independent of > test runner are encouraged to use tox. > running egg_info > creating MacSyFinder.egg-info > writing MacSyFinder.egg-info/PKG-INFO > writing dependency_links to MacSyFinder.egg-info/dependency_links.txt > writing entry points to MacSyFinder.egg-info/entry_points.txt > writing requirements to MacSyFinder.egg-info/requires.txt > writing top-level names to MacSyFinder.egg-info/top_level.txt > writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' > reading manifest file 'MacSyFinder.egg-info/SOURCES.txt' > reading manifest template 'MANIFEST.in' > warning: no files found matching '*' under directory 'doc/build/html' > warning: no files found matching 'doc/build/latex/macsyfinder.pdf' > warning: no files found matching 'etc/macsyfinder.conf' > warning: no previously-included files matching '*' found under directory > 'tests/__pycache__/' > warning: no previously-included files found matching 'tests/__init__.pyc' > warning: no previously-included files found matching '.coverage' > warning: no previously-included files found matching 'coverage_html/' > warning: no previously-included files found matching '.gitignore' > warning: no previously-included files found matching '.travis.yml' > warning: no previously-included files found matching '.github/' > warning: no files found matching 'CONTRIBUTORS' > warning: no files found matching 'NEWS' > adding license file 'COPYING' > writing manifest file 'MacSyFinder.egg-info/SOURCES.txt' > running build_ext > test_Config (test_Config.TestConfig.test_Config) ... ok > test_Config_args (test_Config.TestConfig.test_Config_args) ... ok > test_Config_conf_file_virtualenv > (test_Config.TestConfig.test_Config_conf_file_virtualenv) ... ok > test_Config_default_conf_file > (test_Config.TestConfig.test_Config_default_conf_file) ... ok > test_Config_file_bad_values > (test_Config.TestConfig.test_Config_file_bad_values) ... ok > test_Config_file_n_args (test_Config.TestConfig.test_Config_file_n_args) ... > ok > test_bad_db_type (test_Config.TestConfig.test_bad_db_type) ... ok > test_bad_models_dir (test_Config.TestConfig.test_bad_models_dir) ... ok > test_bad_sequence_db (test_Config.TestConfig.test_bad_sequence_db) ... ok > test_bad_topology (test_Config.TestConfig.test_bad_topology) ... ok > test_bad_topology_file (test_Config.TestConfig.test_bad_topology_file) ... ok > test_bad_values (test_Config.TestConfig.test_bad_values) ... ok > test_cmd_config_file (test_Config.TestConfig.test_cmd_config_file) ... ok > test_config_file_2_dict (test_Config.TestConfig.test_config_file_2_dict) ... > ok > test_e_value_search (test_Config.TestConfig.test_e_value_search) ... ok > test_hit_weights (test_Config.TestConfig.test_hit_weights) ... ok > test_model_conf (test_Config.TestConfig.test_model_conf) ... ok > test_models_dir (test_Config.TestConfig.test_models_dir) ... ok > test_no_cut_ga (test_Config.TestConfig.test_no_cut_ga) ... ok > test_out_dir (test_Config.TestConfig.test_out_dir) ... ok > test_previous_n_sequence_db > (test_Config.TestConfig.test_previous_n_sequence_db) ... ignore sequence_db > '/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta' use sequence_db from > previous_run '/<<PKGBUILDDIR>>/tests/data/data_set/results_1'. > ok > test_previous_wo_cfg (test_Config.TestConfig.test_previous_wo_cfg) ... ok > test_project_config_file (test_Config.TestConfig.test_project_config_file) > ... ok > test_save (test_Config.TestConfig.test_save) ... ok > test_set_log_level (test_Config.TestConfig.test_set_log_level) ... ok > test_set_option (test_Config.TestConfig.test_set_option) ... ok > test_str_2_tuple (test_Config.TestConfig.test_str_2_tuple) ... ok > test_working_dir (test_Config.TestConfig.test_working_dir) ... ok > test_NoneConfig (test_Config.TestNoneConfig.test_NoneConfig) ... ok > test_bad_exchangeable_inter_gene_max_space > (test_DefinitionParser.TestModelParser.test_bad_exchangeable_inter_gene_max_space) > ... Models Parsing > Invalid model definition 'foo/bad_exchangeable_inter_gene_max_space': > inter_gene_max_space must be an integer: 1.5 > ok > test_bad_gene_inter_gene_max_space_2 > (test_DefinitionParser.TestModelParser.test_bad_gene_inter_gene_max_space_2) > ... Models Parsing > Invalid model definition 'foo/bad_inter_gene_max_space_2': > inter_gene_max_space must be an integer: 2.5 > ok > test_bad_inter_gene_max_space > (test_DefinitionParser.TestModelParser.test_bad_inter_gene_max_space) ... > Models Parsing > Invalid model definition > (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_inter_gene_max_space.xml): > inter_gene_max_space must be an integer: 12.5 > ok > test_bad_max_nb_genes > (test_DefinitionParser.TestModelParser.test_bad_max_nb_genes) ... Models > Parsing > Invalid model definition > (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_max_nb_genes.xml): > max_nb_genes must be an integer: HOHOHO > ok > test_bad_min_genes_required > (test_DefinitionParser.TestModelParser.test_bad_min_genes_required) ... > Models Parsing > model 'bad_min_genes_required' is not consistent: min_genes_required 16 must > be lesser or equal than the number of "accessory" and "mandatory" components > in the model: 6 > ok > test_bad_min_genes_required_2 > (test_DefinitionParser.TestModelParser.test_bad_min_genes_required_2) ... > Models Parsing > Invalid model definition > (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_min_genes_required_2.xml): > min_genes_required must be an integer: 16.5 > ok > test_bad_min_mandatory_genes_required > (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required) > ... Models Parsing > model 'bad_min_mandatory_genes_required' is not consistent: > min_genes_required 16 must be lesser or equal than the number of "accessory" > and "mandatory" components in the model: 6 > ok > test_bad_min_mandatory_genes_required_2 > (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_2) > ... Models Parsing > ok > test_bad_min_mandatory_genes_required_4 > (test_DefinitionParser.TestModelParser.test_bad_min_mandatory_genes_required_4) > ... Models Parsing > Invalid model definition > (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/bad_min_mandatory_genes_required_4.xml): > min_mandatory_genes_required must be an integer: 12.5 > ok > test_exchangeable_inheritance > (test_DefinitionParser.TestModelParser.test_exchangeable_inheritance) ... > Models Parsing > ok > test_gene_inter_gene_max_space > (test_DefinitionParser.TestModelParser.test_gene_inter_gene_max_space) ... > Models Parsing > ok > test_gene_no_name (test_DefinitionParser.TestModelParser.test_gene_no_name) > ... Models Parsing > Invalid model definition 'foo/gene_no_name': gene without name > ok > test_gene_w_unkown_attr > (test_DefinitionParser.TestModelParser.test_gene_w_unkown_attr) ... Models > Parsing > unable to parse model definition 'foo/gene_w_unknown_attribute' : The model > definition gene_w_unknown_attribute.xml has an unknown attribute > 'multi-system' for a gene. Please fix the definition. > ok > test_inter_gene_max_space_cfg > (test_DefinitionParser.TestModelParser.test_inter_gene_max_space_cfg) ... > Models Parsing > ok > test_invalid_homolog > (test_DefinitionParser.TestModelParser.test_invalid_homolog) ... Models > Parsing > ok > test_invalid_homolog_2 > (test_DefinitionParser.TestModelParser.test_invalid_homolog_2) ... Models > Parsing > Invalid model definition 'foo/invalid_homolog_2': gene without name > ok > test_invalid_presence > (test_DefinitionParser.TestModelParser.test_invalid_presence) ... Models > Parsing > Invalid model 'foo/fail_invalid_presence' definition: presence value must be > either: 'mandatory', 'accessory', 'neutral', 'forbidden' not foo_bar > ok > test_loner (test_DefinitionParser.TestModelParser.test_loner) ... Models > Parsing > Models Parsing > ok > test_max_nb_genes_cfg > (test_DefinitionParser.TestModelParser.test_max_nb_genes_cfg) ... Models > Parsing > Models Parsing > ok > test_min_genes_required_cfg > (test_DefinitionParser.TestModelParser.test_min_genes_required_cfg) ... > Models Parsing > ok > test_min_mandatory_genes_required_cfg > (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_cfg) > ... Models Parsing > ok > test_min_mandatory_genes_required_lesser_than_mandatory_genes > (test_DefinitionParser.TestModelParser.test_min_mandatory_genes_required_lesser_than_mandatory_genes) > ... Models Parsing > model 'bad_min_mandatory_genes_required_3' is not consistent: > 'min_mandatory_genes_required': 6 must be lesser or equal than the number of > 'mandatory' components in the model: 5 > ok > test_model_w_unkown_attr > (test_DefinitionParser.TestModelParser.test_model_w_unkown_attr) ... Models > Parsing > unable to parse model definition 'foo/model_w_unknown_attribute' : The model > definition model_w_unknown_attribute.xml has an unknow attribute > 'multi-loci'. Please fix the definition. > ok > test_multi_loci_cfg > (test_DefinitionParser.TestModelParser.test_multi_loci_cfg) ... Models Parsing > ok > test_multi_model (test_DefinitionParser.TestModelParser.test_multi_model) ... > Models Parsing > ok > test_multi_system (test_DefinitionParser.TestModelParser.test_multi_system) > ... Models Parsing > ok > test_no_inter_gene_max_space > (test_DefinitionParser.TestModelParser.test_no_inter_gene_max_space) ... > Models Parsing > Invalid model definition > (/<<PKGBUILDDIR>>/tests/data/models/foo/definitions/no_inter_gene_max_space.xml): > inter_gene_max_space must be defined > ok > test_only_one_accessory > (test_DefinitionParser.TestModelParser.test_only_one_accessory) ... Models > Parsing > model 'only_one_accessory' is not consistent: there is only one gene in your > model. So its status should be 'mandatory'. > ok > test_parse_model_old_syntax > (test_DefinitionParser.TestModelParser.test_parse_model_old_syntax) ... > skipped 'Just ignore this test which fails' > test_parse_with_exchangeable > (test_DefinitionParser.TestModelParser.test_parse_with_exchangeable) ... > Models Parsing > ok > test_wo_presence (test_DefinitionParser.TestModelParser.test_wo_presence) ... > Models Parsing > Invalid model definition 'foo/fail_wo_presence': gene 'sctN_FLG' without > presence > ok > test_add_exchangeable > (test_Exchangeable.TestExchangeable.test_add_exchangeable) ... ok > test_alternate_of (test_Exchangeable.TestExchangeable.test_alternate_of) ... > ok > test_is_exchangeable > (test_Exchangeable.TestExchangeable.test_is_exchangeable) ... ok > test_loner (test_Exchangeable.TestExchangeable.test_loner) ... ok > test_model (test_Exchangeable.TestExchangeable.test_model) ... ok > test_multi_system (test_Exchangeable.TestExchangeable.test_multi_system) ... > ok > test_add_get_gene (test_GeneBank.Test.test_add_get_gene) ... ok > test_contains (test_GeneBank.Test.test_contains) ... ok > test_genes_fqn (test_GeneBank.Test.test_genes_fqn) ... ok > test_get_uniq_object (test_GeneBank.Test.test_get_uniq_object) ... ok > test_iter (test_GeneBank.Test.test_iter) ... ok > test_build_force (test_Indexes.TestIndex.test_build_force) ... ok > test_build_my_indexes (test_Indexes.TestIndex.test_build_my_indexes) ... > unable to index the sequence dataset: > /tmp/test_macsyfinder_indexes/test_base_with_errors.fa : list index out of > range > Traceback (most recent call last): > File "/<<PKGBUILDDIR>>/macsypy/database.py", line 192, in _build_my_indexes > for seq_id, comment, length in f_iter: > File "/<<PKGBUILDDIR>>/macsypy/database.py", line 53, in fasta_iter > _id = header[0] > ~~~~~~^^^ > IndexError: list index out of range > ok > test_build_no_idx (test_Indexes.TestIndex.test_build_no_idx) ... ok > test_build_not_writable (test_Indexes.TestIndex.test_build_not_writable) ... > The '/tmp/test_macsyfinder_indexes' dir is not writable. > ok > test_build_with_idx (test_Indexes.TestIndex.test_build_with_idx) ... The > '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old format. > Force index building. > The '/tmp/test_macsyfinder_indexes/test_1.fasta.idx' index file is in old > format. Force index building. > ok > test_find_my_indexes (test_Indexes.TestIndex.test_find_my_indexes) ... ok > test_index_dir (test_Indexes.TestIndex.test_index_dir) ... ok > test_iter (test_Indexes.TestIndex.test_iter) ... ok > test_allowed_hits (test_LikelySystem.LikelySystemTest.test_allowed_hits) ... > ok > test_forbidden_hits (test_LikelySystem.LikelySystemTest.test_forbidden_hits) > ... ok > test_hits (test_LikelySystem.LikelySystemTest.test_hits) ... ok > test_init (test_LikelySystem.LikelySystemTest.test_init) ... ok > test_str (test_LikelySystem.LikelySystemTest.test_str) ... ok > test_hits (test_LikelySystem.UnlikelySystemTest.test_hits) ... ok > test_init (test_LikelySystem.UnlikelySystemTest.test_init) ... ok > test_reason (test_LikelySystem.UnlikelySystemTest.test_reason) ... ok > test_str (test_LikelySystem.UnlikelySystemTest.test_str) ... ok > test_MacsyDefaults_no_virtual_env > (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_no_virtual_env) ... > ok > test_MacsyDefaults_virtual_env > (test_MacsyDefaults.TestMacsyDefaults.test_MacsyDefaults_virtual_env) ... ok > test_ordered_match (test_MatchMaker.MatchMakerTest.test_ordered_match) ... ok > test_sort_hits_by_status > (test_MatchMaker.MatchMakerTest.test_sort_hits_by_status) ... Gene 'fliE' not > found in model 'foo/model_B' > ok > test_unordered_match (test_MatchMaker.MatchMakerTest.test_unordered_match) > ... ok > test_accessor_mutator (test_Model.TestModel.test_accessor_mutator) ... ok > test_eq (test_Model.TestModel.test_eq) ... ok > test_filter (test_Model.TestModel.test_filter) ... ok > test_fqn (test_Model.TestModel.test_fqn) ... ok > test_get_gene (test_Model.TestModel.test_get_gene) ... ok > test_gt (test_Model.TestModel.test_gt) ... ok > test_hash (test_Model.TestModel.test_hash) ... ok > test_inter_gene_max_space (test_Model.TestModel.test_inter_gene_max_space) > ... ok > test_lt (test_Model.TestModel.test_lt) ... ok > test_max_nb_genes (test_Model.TestModel.test_max_nb_genes) ... ok > test_min_genes_required (test_Model.TestModel.test_min_genes_required) ... ok > test_min_mandatory_genes_required > (test_Model.TestModel.test_min_mandatory_genes_required) ... ok > test_multi_loci (test_Model.TestModel.test_multi_loci) ... ok > test_str (test_Model.TestModel.test_str) ... ok > test_add_get_model (test_ModelBank.Test.test_add_get_model) ... ok > test_contains (test_ModelBank.Test.test_contains) ... ok > test_get_uniq_object (test_ModelBank.Test.test_get_uniq_object) ... ok > test_iter (test_ModelBank.Test.test_iter) ... ok > test_execute_hmm_protected_path > (test_Profile.TestProfile.test_execute_hmm_protected_path) ... ok > test_execute_hmm_w_GA_n_nocutga > (test_Profile.TestProfile.test_execute_hmm_w_GA_n_nocutga) ... ok > test_execute_hmm_with_GA (test_Profile.TestProfile.test_execute_hmm_with_GA) > ... skipped 'For some reason this fails to find hmmer_results - skipping' > 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-20230113_20-25-26/hmmer_results/abc.search_hmm.out" -E > 0.100000 "/<<PKGBUILDDIR>>/tests/data/models/foo/profiles/abc.hmm" > "/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta" : return code = 127 check > /tmp/macsyfinder-20230113_20-25-26/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-20230113_20-25-26/hmmer_results/abc.search_hmm.out" -E > 0.100000 "/<<PKGBUILDDIR>>/tests/data/models/foo/profiles/abc.hmm" > "/<<PKGBUILDDIR>>/tests/data/base/test_1.fasta" : return code = 127 check > /tmp/macsyfinder-20230113_20-25-26/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'. > 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'. > bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA > 22.00'. > GA score will not used for gene 'bad_GA_2'. > bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA > 22.00'. > GA score will not used for gene 'bad_GA_2'. > ok > test_len (test_Profile.TestProfile.test_len) ... ok > test_str (test_Profile.TestProfile.test_str) ... ok > test_get_profile (test_ProfileFactory.TestProfileFactory.test_get_profile) > ... ok > test_get_uniq_object > (test_ProfileFactory.TestProfileFactory.test_get_uniq_object) ... ok > test_unknow_profile > (test_ProfileFactory.TestProfileFactory.test_unknow_profile) ... ok > test_hits (test_RejectedCandiate.TestRejectedCandidate.test_hits) ... ok > test_init (test_RejectedCandiate.TestRejectedCandidate.test_init) ... ok > test_str (test_RejectedCandiate.TestRejectedCandidate.test_str) ... ok > test_fill_gembase_min_max_default_topology > (test_RepliconDB.Test.test_fill_gembase_min_max_default_topology) ... ok > test_fill_gembase_min_max_with_topology > (test_RepliconDB.Test.test_fill_gembase_min_max_with_topology) ... ok > test_fill_ordered_replicon_min_max > (test_RepliconDB.Test.test_fill_ordered_replicon_min_max) ... ok > test_fill_topology (test_RepliconDB.Test.test_fill_topology) ... ok > test_get (test_RepliconDB.Test.test_get) ... ok > test_getitem (test_RepliconDB.Test.test_getitem) ... ok > test_guess_if_really_gembase > (test_RepliconDB.Test.test_guess_if_really_gembase) ... ok > test_in (test_RepliconDB.Test.test_in) ... ok > test_items (test_RepliconDB.Test.test_items) ... ok > test_iteritems (test_RepliconDB.Test.test_iteritems) ... ok > test_names (test_RepliconDB.Test.test_names) ... ok > test_replicon_infos (test_RepliconDB.Test.test_replicon_infos) ... ok > test_extract (test_Report.TestGembaseHMMReport.test_extract) ... ok > test_extract_concurent > (test_Report.TestGembaseHMMReport.test_extract_concurent) ... > /<<PKGBUILDDIR>>/tests/test_Report.py:369: DeprecationWarning: > currentThread() is deprecated, use current_thread() instead > main_thread = threading.currentThread() > ERROR > test_extract (test_Report.TestGeneralHMMReport.test_extract) ... ok > test_extract_concurent > (test_Report.TestGeneralHMMReport.test_extract_concurent) ... > /<<PKGBUILDDIR>>/tests/test_Report.py:539: DeprecationWarning: > currentThread() is deprecated, use current_thread() instead > main_thread = threading.currentThread() > ok > test_HMMReport (test_Report.TestHMMReport.test_HMMReport) ... ok > test_best_hit (test_Report.TestHMMReport.test_best_hit) ... ok > test_build_my_db (test_Report.TestHMMReport.test_build_my_db) ... ok > test_fill_my_db (test_Report.TestHMMReport.test_fill_my_db) ... ok > test_hit_start (test_Report.TestHMMReport.test_hit_start) ... ok > test_parse_hmm_body (test_Report.TestHMMReport.test_parse_hmm_body) ... ok > test_parse_hmm_header (test_Report.TestHMMReport.test_parse_hmm_header) ... ok > test_save_extract (test_Report.TestHMMReport.test_save_extract) ... ok > test_str (test_Report.TestHMMReport.test_str) ... ok > test_extract (test_Report.TestOrderedHMMReport.test_extract) ... hit id > 'NC_xxxxx_xx_056141' was not indexed, rebuild sequence 'test_base.fa' index > ok > test_extract_concurent > (test_Report.TestOrderedHMMReport.test_extract_concurent) ... > /<<PKGBUILDDIR>>/tests/test_Report.py:460: DeprecationWarning: > currentThread() is deprecated, use current_thread() instead > main_thread = threading.currentThread() > ok > test_HitSystemTracker (test_System.SystemTest.test_HitSystemTracker) ... ok > test_count (test_System.SystemTest.test_count) ... ok > test_fulfilled_function (test_System.SystemTest.test_fulfilled_function) ... > ok > test_get_hits_encoding_multisystem > (test_System.SystemTest.test_get_hits_encoding_multisystem) ... ok > test_get_loners (test_System.SystemTest.test_get_loners) ... ok > test_get_multisystems (test_System.SystemTest.test_get_multisystems) ... ok > test_hits (test_System.SystemTest.test_hits) ... ok > test_init (test_System.SystemTest.test_init) ... ok > test_is_compatible (test_System.SystemTest.test_is_compatible) ... ok > test_loci_nb (test_System.SystemTest.test_loci_nb) ... ok > test_loci_num (test_System.SystemTest.test_loci_num) ... ok > test_multi_loci (test_System.SystemTest.test_multi_loci) ... ok > test_occurrence (test_System.SystemTest.test_occurrence) ... ok > test_position (test_System.SystemTest.test_position) ... ok > test_score (test_System.SystemTest.test_score) ... ok > test_wholeness (test_System.SystemTest.test_wholeness) ... ok > test_build_clusters (test_cluster.TestBuildCluster.test_build_clusters) ... ok > test_clusterize (test_cluster.TestBuildCluster.test_clusterize) ... ok > test_colocates (test_cluster.TestBuildCluster.test_colocates) ... ok > test_get_true_loners (test_cluster.TestBuildCluster.test_get_true_loners) ... > ok > test_contains (test_cluster.TestCluster.test_contains) ... ok > test_fulfilled_function (test_cluster.TestCluster.test_fulfilled_function) > ... ok > test_init (test_cluster.TestCluster.test_init) ... Cannot build a cluster > from hits coming from different replicons > ok > test_len (test_cluster.TestCluster.test_len) ... ok > test_loner (test_cluster.TestCluster.test_loner) ... ok > test_merge (test_cluster.TestCluster.test_merge) ... ok > test_multi_system (test_cluster.TestCluster.test_multi_system) ... ok > test_replace (test_cluster.TestCluster.test_replace) ... ok > test_replicon_name (test_cluster.TestCluster.test_replicon_name) ... ok > test_score (test_cluster.TestCluster.test_score) ... ok > test_str (test_cluster.TestCluster.test_str) ... ok > test_2_systems_not_compatible > (test_functional_test.Test.test_2_systems_not_compatible) ... ok > test_cfg_n_previous_run (test_functional_test.Test.test_cfg_n_previous_run) > ... ok > test_degenerated_systems (test_functional_test.Test.test_degenerated_systems) > ... ok > test_gembase (test_functional_test.Test.test_gembase) ... ok > test_index_dir (test_functional_test.Test.test_index_dir) ... ok > test_model_unknown (test_functional_test.Test.test_model_unknown) ... ok > test_no_db_type (test_functional_test.Test.test_no_db_type) ... ok > test_no_models (test_functional_test.Test.test_no_models) ... ok > test_no_seq_db (test_functional_test.Test.test_no_seq_db) ... ok > test_only_loners (test_functional_test.Test.test_only_loners) ... ok > test_ordered_1_cluster_3_loners > (test_functional_test.Test.test_ordered_1_cluster_3_loners) ... ok > test_ordered_1_clusters_3_loners_w_exchangeable > (test_functional_test.Test.test_ordered_1_clusters_3_loners_w_exchangeable) > ... ok > test_ordered_1_loner_exch_in_clust > (test_functional_test.Test.test_ordered_1_loner_exch_in_clust) ... ok > test_ordered_1_loner_in_clust > (test_functional_test.Test.test_ordered_1_loner_in_clust) ... ok > test_ordered_2_clusters_1_loner > (test_functional_test.Test.test_ordered_2_clusters_1_loner) ... ok > test_ordered_2_clusters_3_loners > (test_functional_test.Test.test_ordered_2_clusters_3_loners) ... ok > test_ordered_circular (test_functional_test.Test.test_ordered_circular) ... ok > test_ordered_linear (test_functional_test.Test.test_ordered_linear) ... ok > test_ordered_multi_loci (test_functional_test.Test.test_ordered_multi_loci) > ... ok > test_ordered_multi_model (test_functional_test.Test.test_ordered_multi_model) > ... ok > test_ordered_multi_system > (test_functional_test.Test.test_ordered_multi_system) ... ok > test_ordered_multi_system_out_system > (test_functional_test.Test.test_ordered_multi_system_out_system) ... ok > test_ordered_only_one_multi_model > (test_functional_test.Test.test_ordered_only_one_multi_model) ... ok > test_ordered_single_loci (test_functional_test.Test.test_ordered_single_loci) > ... ok > test_uncomplete_degenerated_systems > (test_functional_test.Test.test_uncomplete_degenerated_systems) ... ok > test_unordered (test_functional_test.Test.test_unordered) ... ok > test_unordered_no_hits (test_functional_test.Test.test_unordered_no_hits) ... > ok > test_unordered_only_forbidden > (test_functional_test.Test.test_unordered_only_forbidden) ... ok > test_working_dir_exists (test_functional_test.Test.test_working_dir_exists) > ... ok > test_working_dir_exists_and_not_dir > (test_functional_test.Test.test_working_dir_exists_and_not_dir) ... ok > test_core_gene (test_gene.TestCoreGene.test_core_gene) ... ok > test_str (test_gene.TestGeneStatus.test_str) ... ok > test_add_exchangeable (test_gene.TestModelGene.test_add_exchangeable) ... ok > test_alternate_of (test_gene.TestModelGene.test_alternate_of) ... ok > test_core_gene (test_gene.TestModelGene.test_core_gene) > test getter/setter for core_gene property ... ok > test_exhangeables (test_gene.TestModelGene.test_exhangeables) ... ok > test_hash (test_gene.TestModelGene.test_hash) ... ok > test_init (test_gene.TestModelGene.test_init) ... ok > test_inter_gene_max_space (test_gene.TestModelGene.test_inter_gene_max_space) > test getter for inter_gene_max_space property ... ok > test_is_Forbidden (test_gene.TestModelGene.test_is_Forbidden) > test if gene belong to model mandatory genes ... ok > test_is_accessory (test_gene.TestModelGene.test_is_accessory) > test if gene belong to model mandatory genes ... ok > test_is_exchangeable (test_gene.TestModelGene.test_is_exchangeable) ... ok > test_is_mandatory (test_gene.TestModelGene.test_is_mandatory) > test if gene belong to model mandatory genes ... ok > test_loner (test_gene.TestModelGene.test_loner) > test getter for loner property ... ok > test_model (test_gene.TestModelGene.test_model) > test getter/setter for model property ... ok > test_multi_model (test_gene.TestModelGene.test_multi_model) > test getter for multi_modelproperty ... ok > test_multi_system (test_gene.TestModelGene.test_multi_system) > test getter for multi_system property ... ok > test_str (test_gene.TestModelGene.test_str) ... ok > test_unknown_attribute (test_gene.TestModelGene.test_unknown_attribute) ... ok > test_cmp (test_hit.CoreHitTest.test_cmp) ... ok > test_eq (test_hit.CoreHitTest.test_eq) ... ok > test_get_position (test_hit.CoreHitTest.test_get_position) ... ok > test_hash (test_hit.CoreHitTest.test_hash) ... ok > test_str (test_hit.CoreHitTest.test_str) ... ok > test_compute_best_MSHit (test_hit.GetBestHitTest.test_compute_best_MSHit) ... > ok > test_get_best_hits (test_hit.GetBestHitTest.test_get_best_hits) ... ok > test_get_best_hits_4_func (test_hit.GetBestHitTest.test_get_best_hits_4_func) > ... ok > test_sort_multisystem_hits > (test_hit.GetBestHitTest.test_sort_multisystem_hits) ... ok > test_hit_weight_default (test_hit.HitWeightTest.test_hit_weight_default) ... > ok > test_hit_weight_not_default > (test_hit.HitWeightTest.test_hit_weight_not_default) ... ok > test_counterpart (test_hit.LonerMultiSystemTest.test_counterpart) ... Try to > set counterpart for hit 'gspD' with non compatible hits: ['gspD', 'sctJ'] > ok > test_init (test_hit.LonerMultiSystemTest.test_init) ... hit_2 cannot be a > multi systems, gene_ref 'sctJ' not tag as multi_system > ok > test_loner (test_hit.LonerMultiSystemTest.test_loner) ... ok > test_multi_system (test_hit.LonerMultiSystemTest.test_multi_system) ... ok > test_str (test_hit.LonerMultiSystemTest.test_str) ... ok > test_counterpart (test_hit.LonerTest.test_counterpart) ... ok > test_init (test_hit.LonerTest.test_init) ... hit_2 cannot be a loner gene_ref > 'sctJ' not tag as loner > ok > test_len (test_hit.LonerTest.test_len) ... ok > test_loner (test_hit.LonerTest.test_loner) ... ok > test_multi_system (test_hit.LonerTest.test_multi_system) ... ok > test_str (test_hit.LonerTest.test_str) ... ok > test_delegation (test_hit.ModelHitTest.test_delegation) ... ok > test_eq (test_hit.ModelHitTest.test_eq) ... ok > test_hash (test_hit.ModelHitTest.test_hash) ... ok > test_init (test_hit.ModelHitTest.test_init) ... ok > test_loner (test_hit.ModelHitTest.test_loner) ... ok > test_multi_model (test_hit.ModelHitTest.test_multi_model) ... ok > test_multi_system (test_hit.ModelHitTest.test_multi_system) ... ok > test_counterpart (test_hit.MultiSystemTest.test_counterpart) ... ok > test_init (test_hit.MultiSystemTest.test_init) ... hit_2 cannot be a multi > systems, gene_ref 'sctJ' not tag as multi_system > ok > test_len (test_hit.MultiSystemTest.test_len) ... ok > test_loner (test_hit.MultiSystemTest.test_loner) ... ok > test_multi_system (test_hit.MultiSystemTest.test_multi_system) ... ok > test_str (test_hit.MultiSystemTest.test_str) ... ok > test_functional_split > (test_macsy_gembase_split.TestSplit.test_functional_split) ... > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_unordered_only_forbidden/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_unordered_no_hits/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_unordered/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_uncomplete_degenerated_systems/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_single_loci/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_only_one_multi_model/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_multi_system_out_system/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_multi_system/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_multi_model/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_multi_loci/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_linear/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_circular/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_2_clusters_3_loners/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_2_clusters_1_loner/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_1_loner_in_clust/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_1_loner_exch_in_clust/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_1_clusters_3_loners_w_exchangeable/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_ordered_1_cluster_3_loners/macsyfinder.log' > mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_only_loners/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_no_seq_db/macsyfinder.log' mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_no_models/macsyfinder.log' mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_no_db_type/macsyfinder.log' mode='a' encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_model_unkwon/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_index_dir/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_gembase/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/tests/test_macsy_gembase_split.py:59: ResourceWarning: > unclosed file <_io.TextIOWrapper > name='/tmp/macsyfinder_test_degenerated_systems/macsyfinder.log' mode='a' > encoding='UTF-8'> > for h in logger.handlers[:]: > ResourceWarning: Enable tracemalloc to get the object allocation traceback > /<<PKGBUILDDIR>>/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/tmpzxbvlb40/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/tmpzxebm_9j/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/tmpgvamesko/macsyfinder_test_split/base is not writable > Cannot create /tmp/tmpgvamesko/macsyfinder_test_split/base : [Errno 13] > Permission denied: '/tmp/tmpgvamesko/macsyfinder_test_split/base' > ok > test_functional_merge > (test_macsy_merge_results.TestMerge.test_functional_merge) ... Merging > 'all_best_solutions.tsv' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_all_best_solutions.tsv' > Merging 'best_solution.tsv' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_best_solution.tsv' > Merging 'all_systems.tsv' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_all_systems.tsv' > Merging 'best_solution_multisystems.tsv' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_best_solution_multisystems.tsv' > Merging 'best_solution_loners.tsv' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_best_solution_loners.tsv' > Merging 'rejected_candidates.tsv' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_rejected_candidates.tsv' > Merging 'all_systems.txt' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_all_systems.txt' > Merging 'rejected_candidates.txt' in to > '/tmp/tmp8zkqlr4k/macsyfinder_test_merge/merged_results/merged_rejected_candidates.txt' > Merging 'best_solution_summary' in to > '/tmp/tmp8zkqlr4k/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/tmp8zkqlr4k/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/tmpvny_7btj/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/tmpw40thfyj/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/tmpf_ng36ni/macsyfinder_test_merge/merged_results is not writable > Cannot create /tmp/tmpf_ng36ni/macsyfinder_test_merge/merged_results : [Errno > 13] Permission denied: > '/tmp/tmpf_ng36ni/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/tmpe_pnb0az/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_merge_and_reindex_invalid_solid > (test_macsy_merge_results.TestMerge.test_merge_and_reindex_invalid_solid) ... > Cannot reindex int(GCF_000006845) + 1: invalid literal for int() with base > 10: 'GCF_000006845' > ok > test_add_comment > (test_macsyconfig.TestConfigParserWithComment.test_add_comment) ... ok > test_write (test_macsyconfig.TestConfigParserWithComment.test_write) ... ok > test_ask (test_macsyconfig.TestMacsyconfig.test_ask) ... ok > test_ask_bad_value (test_macsyconfig.TestMacsyconfig.test_ask_bad_value) ... > ok > test_ask_default_is_sequence > (test_macsyconfig.TestMacsyconfig.test_ask_default_is_sequence) ... ok > test_ask_use_default (test_macsyconfig.TestMacsyconfig.test_ask_use_default) > ... ok > test_ask_value_is_sequence > (test_macsyconfig.TestMacsyconfig.test_ask_value_is_sequence) ... ok > test_check_bool (test_macsyconfig.TestMacsyconfig.test_check_bool) ... ok > test_check_choice (test_macsyconfig.TestMacsyconfig.test_check_choice) ... ok > test_check_dir (test_macsyconfig.TestMacsyconfig.test_check_dir) ... ok > test_check_exe (test_macsyconfig.TestMacsyconfig.test_check_exe) ... ok > test_check_file (test_macsyconfig.TestMacsyconfig.test_check_file) ... ok > test_check_float (test_macsyconfig.TestMacsyconfig.test_check_float) ... ok > test_check_positive_int > (test_macsyconfig.TestMacsyconfig.test_check_positive_int) ... ok > test_check_str (test_macsyconfig.TestMacsyconfig.test_check_str) ... ok > test_functional_dark_theme > (test_macsyconfig.TestMacsyconfig.test_functional_dark_theme) ... ok > test_functional_file_already_exists > (test_macsyconfig.TestMacsyconfig.test_functional_file_already_exists) ... ok > test_parse_args (test_macsyconfig.TestMacsyconfig.test_parse_args) ... ok > test_set_base_options > (test_macsyconfig.TestMacsyconfig.test_set_base_options) ... ok > test_set_general_options > (test_macsyconfig.TestMacsyconfig.test_set_general_options) ... ok > test_set_hmmer_options > (test_macsyconfig.TestMacsyconfig.test_set_hmmer_options) ... ok > test_set_path_options > (test_macsyconfig.TestMacsyconfig.test_set_path_options) ... ok > test_set_path_options_with_system_models_dir > (test_macsyconfig.TestMacsyconfig.test_set_path_options_with_system_models_dir) > ... ok > test_set_score_options > (test_macsyconfig.TestMacsyconfig.test_set_score_options) ... ok > test_set_section (test_macsyconfig.TestMacsyconfig.test_set_section) ... ok > test_set_section_use_defaults > (test_macsyconfig.TestMacsyconfig.test_set_section_use_defaults) ... ok > test_available (test_macsydata.TestMacsydata.test_available) ... ok > 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/tmputacv03z/fake_1 > Transform the models into a git repository > git init . > git add . > git commit -m 'initial commit' > add a remote repository to host the models > for instance if you want to add the models to 'macsy-models' > git remote add origin https://github.com/macsy-models/ > git tag 0.0b2 > git push origin 0.0b2 > ok > test_check_with_errors (test_macsydata.TestMacsydata.test_check_with_errors) > ... The package 'fake_1' have no 'definitions' directory. > The package 'fake_1' have no 'profiles' directory. > Please fix issues above, before publishing these models. > ok > test_check_with_warnings > (test_macsydata.TestMacsydata.test_check_with_warnings) ... The package > 'fake_1' have not any LICENSE file. May be you have not right to use it. > The package 'fake_1' have not any README file. > > macsydata says: You're only giving me a partial QA payment? > I'll take it this time, but I'm not happy. > I'll be really happy, if you fix warnings above, before to publish these > models. > ok > 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) ... > /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed > file <_io.TextIOWrapper > name='/tmp/tmp19ot__bb/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 > /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed > file <_io.TextIOWrapper > name='/tmp/tmp19ot__bb/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 > (test_macsydata.TestMacsydata.test_definition_bad_def) ... Model > 'fake_1/niportnaoik' not found. > ok > test_definition_bad_pack > (test_macsydata.TestMacsydata.test_definition_bad_pack) ... Package > 'nimportnaoik' not found. > 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) ... > /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed > file <_io.TextIOWrapper > name='/tmp/tmp4_83v8cv/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 > /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed > file <_io.TextIOWrapper > name='/tmp/tmp4_83v8cv/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) ... > /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed > file <_io.TextIOWrapper > name='/tmp/tmp0hvvp48h/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 > /<<PKGBUILDDIR>>/macsypy/scripts/macsydata.py:609: ResourceWarning: unclosed > file <_io.TextIOWrapper > name='/tmp/tmp0hvvp48h/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/tmpwmz1rms7/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 > github limit error > ok > test_freeze (test_macsydata.TestMacsydata.test_freeze) ... ok > test_help (test_macsydata.TestMacsydata.test_help) ... Models 'nimportnaoik' > not found locally. > ok > test_info (test_macsydata.TestMacsydata.test_info) ... Models 'nimportnaoik' > not found locally. > 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/tmpvcptz5q8/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/tmpvcptz5q8/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/tmp0ucvfmbn/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/tmptvpuhwz8/models > Cleaning. > The models fake_pack (0.0b2) have been installed successfully. > Requirement already satisfied: fake_pack==0.0b2 in > /tmp/tmptvpuhwz8/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/tmpi6ny6aqy/models > Cleaning. > The models fake_pack (0.0b2) have been installed successfully. > Extracting fake_pack (0.0b2). > Installing fake_pack (0.0b2) in /tmp/tmpi6ny6aqy/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/tmpkoqfiwyd/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/tmpotwcicrz/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/tmppwa8rety/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/tmpzrta4d2b/models is not readable: [Errno 13] Permission denied: > '/tmp/tmpzrta4d2b/models' : skip it. > Downloading fake_pack (0.0b2). > Extracting fake_pack (0.0b2). > Installing fake_pack (0.0b2) in /tmp/tmpzrta4d2b/models > /tmp/tmpzrta4d2b/models is not writable: [Errno 13] Permission denied: > '/tmp/tmpzrta4d2b/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' > ok > test_install_remote_upper_in_local > (test_macsydata.TestMacsydata.test_install_remote_upper_in_local) ... > fake_pack (0.0b2) is already installed. > 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/tmpjslt62b5/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/tmp28zz4ksd/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 > test_search_in_pack_desc_match_case > (test_macsydata.TestMacsydata.test_search_in_pack_desc_match_case) ... ok > test_search_in_pack_name > (test_macsydata.TestMacsydata.test_search_in_pack_name) ... ok > 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/tmp1hsfknlp/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 T4P_pilA. 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_pilT. 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_fimT. 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_pilX. 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_pilM. 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 T4P_pilW. 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_pilU. 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_pilY. 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 MSH_mshM. 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_pilN. Switch to e-value > threshold (-E 0.100000) > GA bit thresholds unavailable on profile ComM_comC. Switch to e-value > threshold (-E 0.100000) > Most of replicons contains only ONE sequence are you sure that > '/<<PKGBUILDDIR>>/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 > test_likely_systems_to_txt > (test_macsyfinder.TestMacsyfinder.test_likely_systems_to_txt) ... ok > test_list_models (test_macsyfinder.TestMacsyfinder.test_list_models) ... ok > test_loners_to_tsv (test_macsyfinder.TestMacsyfinder.test_loners_to_tsv) ... > ok > test_multisystem_to_tsv > (test_macsyfinder.TestMacsyfinder.test_multisystem_to_tsv) ... ok > test_parse_args (test_macsyfinder.TestMacsyfinder.test_parse_args) ... ok > test_rejected_candidates_to_tsv > (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_tsv) ... ok > test_rejected_candidates_to_txt > (test_macsyfinder.TestMacsyfinder.test_rejected_candidates_to_txt) ... ok > test_search_systems (test_macsyfinder.TestMacsyfinder.test_search_systems) > ... ok > test_search_systems_unordered > (test_macsyfinder.TestMacsyfinder.test_search_systems_unordered) ... ok > test_solutions_to_tsv > (test_macsyfinder.TestMacsyfinder.test_solutions_to_tsv) ... ok > test_summary_best_solution > (test_macsyfinder.TestMacsyfinder.test_summary_best_solution) ... ok > test_summary_best_solution_empty > (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_empty) ... ok > test_summary_best_solution_lack_models > (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models) ... > ok > test_summary_best_solution_lack_models_replicons > (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_models_replicons) > ... ok > test_summary_best_solution_lack_replicon > (test_macsyfinder.TestMacsyfinder.test_summary_best_solution_lack_replicon) > ... ok > test_systems_to_tsv (test_macsyfinder.TestMacsyfinder.test_systems_to_tsv) > ... ok > test_systems_to_txt (test_macsyfinder.TestMacsyfinder.test_systems_to_txt) > ... ok > test_unnlikely_systems_to_txt > (test_macsyfinder.TestMacsyfinder.test_unnlikely_systems_to_txt) ... ok > test_LightHit (test_macsyprofile.TestMacsyprofile.test_LightHit) ... ok > test_build_my_db (test_macsyprofile.TestMacsyprofile.test_build_my_db) ... ok > test_fill_my_db (test_macsyprofile.TestMacsyprofile.test_fill_my_db) ... ok > test_functional (test_macsyprofile.TestMacsyprofile.test_functional) ... ok > test_functional_best_score > (test_macsyprofile.TestMacsyprofile.test_functional_best_score) ... ok > test_functional_coverage > (test_macsyprofile.TestMacsyprofile.test_functional_coverage) ... ok > test_functional_evalue > (test_macsyprofile.TestMacsyprofile.test_functional_evalue) ... ok > 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/tmp544kb7n2 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 > test_get_gene_name (test_macsyprofile.TestMacsyprofile.test_get_gene_name) > ... ok > test_header (test_macsyprofile.TestMacsyprofile.test_header) ... ok > test_hit_start (test_macsyprofile.TestMacsyprofile.test_hit_start) ... ok > test_parse (test_macsyprofile.TestMacsyprofile.test_parse) ... ok > test_parse_hmm_body (test_macsyprofile.TestMacsyprofile.test_parse_hmm_body) > ... ok > test_parse_hmm_header > (test_macsyprofile.TestMacsyprofile.test_parse_hmm_header) ... ok > 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/tmpwuyaxxtq' mode='a' encoding='UTF-8'> > self.tearDown() > ResourceWarning: Enable tracemalloc to get the object allocation traceback > ok > test_init_logger_no_out (test_macsypy.Test.test_init_logger_no_out) ... ok > test_logger_set_level_bad_level > (test_macsypy.Test.test_logger_set_level_bad_level) ... ok > test_logger_set_level_default > (test_macsypy.Test.test_logger_set_level_default) ... ok > test_logger_set_level_error (test_macsypy.Test.test_logger_set_level_error) > ... ok > test_logger_set_level_handlers > (test_macsypy.Test.test_logger_set_level_handlers) ... ok > test_parse (test_model_conf_parser.TestModelConfParser.test_parse) ... ok > test_parse_bad_file > (test_model_conf_parser.TestModelConfParser.test_parse_bad_file) ... unable > to parse model configuration > '/<<PKGBUILDDIR>>/tests/data/conf_files/project.conf' : syntax error: line 2, > column 0 > ok > test_parse_filtering > (test_model_conf_parser.TestModelConfParser.test_parse_filtering) ... cannot > parse 'cut_ga' element in > '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' expect True, 1, > False, 0 got : 'FOO' > ok > test_parse_w_bad_value > (test_model_conf_parser.TestModelConfParser.test_parse_w_bad_value) ... The > model configuration file > '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' cannot be parsed: > could not convert string to float: 'FOO' > ok > test_parse_w_unkown_tag > (test_model_conf_parser.TestModelConfParser.test_parse_w_unkown_tag) ... > unknown element 'nimportnaoik' in > '/<<PKGBUILDDIR>>/tests/data/conf_files/model_conf.xml' ignore it. > ok > test_parse_weights > (test_model_conf_parser.TestModelConfParser.test_parse_weights) ... ok > test_parse_wo_filtering > (test_model_conf_parser.TestModelConfParser.test_parse_wo_filtering) ... ok > test_parse_wo_weights > (test_model_conf_parser.TestModelConfParser.test_parse_wo_weights) ... ok > test_init (test_package.TestLocalModelIndex.test_init) ... ok > test_init (test_package.TestModelIndex.test_init) ... ok > test_check (test_package.TestPackage.test_check) ... ok > test_check_metadata (test_package.TestPackage.test_check_metadata) ... ok > test_check_model_conf (test_package.TestPackage.test_check_model_conf) ... ok > test_check_model_conf_bad_conf > (test_package.TestPackage.test_check_model_conf_bad_conf) ... The model > configuration file '/tmp/macsy_test_package/fake_model/model_conf.xml' cannot > be parsed: could not convert string to float: 'FOO' > ok > test_check_model_conf_no_conf > (test_package.TestPackage.test_check_model_conf_no_conf) ... ok > test_check_model_consistency > (test_package.TestPackage.test_check_model_consistency) ... ok > test_check_model_consistency_bad_definitions > (test_package.TestPackage.test_check_model_consistency_bad_definitions) ... ok > test_check_model_consistency_extra_profile > (test_package.TestPackage.test_check_model_consistency_extra_profile) ... ok > test_check_model_consistency_lack_one_profile > (test_package.TestPackage.test_check_model_consistency_lack_one_profile) ... > ok > test_check_no_readme_n_no_license > (test_package.TestPackage.test_check_no_readme_n_no_license) ... ok > test_check_structure (test_package.TestPackage.test_check_structure) ... ok > test_check_structure_bad_path > (test_package.TestPackage.test_check_structure_bad_path) ... ok > test_check_structure_no_def > (test_package.TestPackage.test_check_structure_no_def) ... ok > test_check_structure_no_license > (test_package.TestPackage.test_check_structure_no_license) ... ok > test_check_structure_no_metadata > (test_package.TestPackage.test_check_structure_no_metadata) ... ok > test_check_structure_no_profiles > (test_package.TestPackage.test_check_structure_no_profiles) ... ok > test_check_structure_no_readme > (test_package.TestPackage.test_check_structure_no_readme) ... ok > test_find_readme (test_package.TestPackage.test_find_readme) ... ok > test_help (test_package.TestPackage.test_help) ... ok > test_info (test_package.TestPackage.test_info) ... ok > test_init (test_package.TestPackage.test_init) ... ok > test_metadata (test_package.TestPackage.test_metadata) ... ok > test_parse_arch_path (test_package.TestPackageFunc.test_parse_arch_path) ... > ok > test_download (test_package.TestRemoteModelIndex.test_download) ... ok > test_get_metadata (test_package.TestRemoteModelIndex.test_get_metadata) ... ok > test_init (test_package.TestRemoteModelIndex.test_init) ... ok > test_list_package_vers > (test_package.TestRemoteModelIndex.test_list_package_vers) ... ok > test_list_packages (test_package.TestRemoteModelIndex.test_list_packages) ... > ok > test_remote_exists (test_package.TestRemoteModelIndex.test_remote_exists) ... > ok > test_unarchive (test_package.TestRemoteModelIndex.test_unarchive) ... ok > test_url_json (test_package.TestRemoteModelIndex.test_url_json) ... ok > test_url_json_reach_limit > (test_package.TestRemoteModelIndex.test_url_json_reach_limit) ... ok > test_DefinitionLocationn > (test_registries.DefinitionLocationTest.test_DefinitionLocationn) ... ok > test_add_submodel (test_registries.DefinitionLocationTest.test_add_submodel) > ... ok > test_all (test_registries.DefinitionLocationTest.test_all) ... ok > test_eq (test_registries.DefinitionLocationTest.test_eq) ... ok > test_family_name (test_registries.DefinitionLocationTest.test_family_name) > ... ok > test_greater (test_registries.DefinitionLocationTest.test_greater) ... ok > test_hash (test_registries.DefinitionLocationTest.test_hash) ... ok > test_lesser (test_registries.DefinitionLocationTest.test_lesser) ... ok > test_root_name (test_registries.DefinitionLocationTest.test_root_name) ... ok > test_separator (test_registries.DefinitionLocationTest.test_separator) ... ok > test_split_fqn (test_registries.DefinitionLocationTest.test_split_fqn) ... ok > test_str (test_registries.DefinitionLocationTest.test_str) ... ok > test_ModelLocation (test_registries.ModelLocationTest.test_ModelLocation) ... > ok > test_get_all_definitions > (test_registries.ModelLocationTest.test_get_all_definitions) ... ok > test_get_definition (test_registries.ModelLocationTest.test_get_definition) > ... ok > test_get_definitions (test_registries.ModelLocationTest.test_get_definitions) > ... ok > test_get_profile (test_registries.ModelLocationTest.test_get_profile) ... ok > test_get_profiles_names > (test_registries.ModelLocationTest.test_get_profiles_names) ... ok > test_str (test_registries.ModelLocationTest.test_str) ... ok > test_version (test_registries.ModelLocationTest.test_version) ... ok > test_version_no_metadata > (test_registries.ModelLocationTest.test_version_no_metadata) ... The models > package 'simple' is not versioned contact the package manager to fix it. > ok > test_add_get (test_registries.ModelRegistryTest.test_add_get) ... ok > test_models (test_registries.ModelRegistryTest.test_models) ... ok > test_scan_models_dir (test_registries.ModelRegistryTest.test_scan_models_dir) > ... ok > test_str (test_registries.ModelRegistryTest.test_str) ... ok > test_join_def_path (test_registries.RegitriesUtilsTest.test_join_def_path) > ... ok > test_split_def_name (test_registries.RegitriesUtilsTest.test_split_def_name) > ... ok > test_search (test_search_genes.TestSearchGenes.test_search) ... ok > test_search_fail (test_search_genes.TestSearchGenes.test_search_fail) ... ok > test_search_recover (test_search_genes.TestSearchGenes.test_search_recover) > ... ok > test_LikelySystemSerializer_txt > (test_serialization.SerializationTest.test_LikelySystemSerializer_txt) ... ok > test_RejectedClusters_tsv > (test_serialization.SerializationTest.test_RejectedClusters_tsv) ... ok > test_SolutionSerializer_tsv > (test_serialization.SerializationTest.test_SolutionSerializer_tsv) ... ok > test_SpecialHitSerializer_tsv > (test_serialization.SerializationTest.test_SpecialHitSerializer_tsv) ... ok > test_SystemSerializer_str > (test_serialization.SerializationTest.test_SystemSerializer_str) ... ok > test_SystemSerializer_tsv > (test_serialization.SerializationTest.test_SystemSerializer_tsv) ... ok > test_UnlikelySystemSerializer_txt > (test_serialization.SerializationTest.test_UnlikelySystemSerializer_txt) ... > ok > test_combine_clusters > (test_solution.SolutionExplorerTest.test_combine_clusters) ... ok > test_combine_multisystems > (test_solution.SolutionExplorerTest.test_combine_multisystems) ... ok > test_find_best_solution > (test_solution.SolutionExplorerTest.test_find_best_solution) ... ok > test_average_wholeness (test_solution.SolutionTest.test_average_wholeness) > ... ok > test_gt (test_solution.SolutionTest.test_gt) ... ok > test_hits_number (test_solution.SolutionTest.test_hits_number) ... ok > test_hits_positions (test_solution.SolutionTest.test_hits_positions) ... ok > test_iteration (test_solution.SolutionTest.test_iteration) ... ok > test_lt (test_solution.SolutionTest.test_lt) ... ok > test_score (test_solution.SolutionTest.test_score) ... ok > test_sorting (test_solution.SolutionTest.test_sorting) ... ok > test_systems (test_solution.SolutionTest.test_systems) ... ok > test_get_def_to_detect (test_utils.TestUtils.test_get_def_to_detect) ... ok > test_get_replicon_names (test_utils.TestUtils.test_get_replicon_names) ... ok > test_threads_available (test_utils.TestUtils.test_threads_available) ... ok > > ====================================================================== > ERROR: test_extract_concurent > (test_Report.TestGembaseHMMReport.test_extract_concurent) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/<<PKGBUILDDIR>>/tests/test_Report.py", line 373, in > test_extract_concurent > t.join() > File "/usr/lib/python3.11/threading.py", line 1109, in join > raise RuntimeError("cannot join current thread") > RuntimeError: cannot join current thread > > ---------------------------------------------------------------------- > Ran 486 tests in 11.325s > > FAILED (errors=1, skipped=2) > Test failed: <unittest.runner.TextTestResult run=486 errors=1 failures=0> > error: Test failed: <unittest.runner.TextTestResult run=486 errors=1 > failures=0> > E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: > python3.11 setup.py test > dh_auto_test: error: pybuild --test -i python{version} -p 3.11 returned exit > code 13 The full build log is available from: http://qa-logs.debian.net/2023/01/13/macsyfinder_2.0-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230113;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230113&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
