Your message dated Mon, 16 Jan 2023 03:35:00 +0000
with message-id <[email protected]>
and subject line Bug#1028774: fixed in macsyfinder 2.0-2
has caused the Debian Bug report #1028774,
regarding macsyfinder: FTBFS: RuntimeError: cannot join current thread
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1028774: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028774
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: macsyfinder
Version: 2.0-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: [email protected]
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;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230113&[email protected]&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.
--- End Message ---
--- Begin Message ---
Source: macsyfinder
Source-Version: 2.0-2
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
macsyfinder, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated macsyfinder package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 16 Jan 2023 08:42:05 +0530
Source: macsyfinder
Architecture: source
Version: 2.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1028774
Changes:
macsyfinder (2.0-2) unstable; urgency=medium
.
[ Andreas Tille ]
* Team upload.
* Create sensible upstream source filename
.
[ Nilesh Patra ]
* Bump Standards-Version to 4.6.2 (no changes needed)
* Add patch to fix random failure on systems with
specific configuration (Closes: #1028774)
Checksums-Sha1:
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65ae392ba74e48116a9d82339d0b160a5737186a 10240 macsyfinder_2.0-2.debian.tar.xz
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macsyfinder_2.0-2_amd64.buildinfo
Checksums-Sha256:
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macsyfinder_2.0-2.dsc
dcec072e6e56eae439a1424f8ee31b87fbb580c5de034d6ac21f4f9d22acdb7c 10240
macsyfinder_2.0-2.debian.tar.xz
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macsyfinder_2.0-2_amd64.buildinfo
Files:
b1de50c61de939666c5a9e8db33dcc8e 1793 science optional macsyfinder_2.0-2.dsc
02f6bb955db1d66af18987b91bb78cd5 10240 science optional
macsyfinder_2.0-2.debian.tar.xz
741ff98e4c1cfa197742a9ecd1ad789a 10326 science optional
macsyfinder_2.0-2_amd64.buildinfo
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2mQfAQCuzJuHcvpwygIzxQmNQZUXUlsOu0JGyXY7QUkEjh93PgD7Bo2PmEUN33/c
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--- End Message ---
