Control: tags -1 help Control: forwarded -1 Aidan Delaney <a.j.dela...@brighton.ac.uk>
Hi, I admit I have no idea what might have caused these pkg_resources related errors and how to fix these. Any help would be welcome Andreas. On Sun, Sep 27, 2020 at 08:45:17PM +0200, Lucas Nussbaum wrote: > Source: gubbins > Version: 2.4.1-2 > Severity: serious > Justification: FTBFS on amd64 > Tags: bullseye sid ftbfs > Usertags: ftbfs-20200926 ftbfs-bullseye > > Hi, > > During a rebuild of all packages in sid, your package failed to build > on amd64. > > Relevant part (hopefully): > > make[3]: Entering directory '/<<PKGBUILDDIR>>' > > make[3]: Leaving directory '/<<PKGBUILDDIR>>' > > make[2]: Leaving directory '/<<PKGBUILDDIR>>' > > cd python && \ > > python3 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 gubbins.egg-info > > writing gubbins.egg-info/PKG-INFO > > writing dependency_links to gubbins.egg-info/dependency_links.txt > > writing entry points to gubbins.egg-info/entry_points.txt > > writing requirements to gubbins.egg-info/requires.txt > > writing top-level names to gubbins.egg-info/top_level.txt > > writing manifest file 'gubbins.egg-info/SOURCES.txt' > > reading manifest file 'gubbins.egg-info/SOURCES.txt' > > writing manifest file 'gubbins.egg-info/SOURCES.txt' > > running build_ext > > /<<PKGBUILDDIR>>/python/gubbins/common.py:538: DeprecationWarning: invalid > > escape sequence \d > > elif re.match('^\d', vcf_line) is not None: > > /<<PKGBUILDDIR>>/python/gubbins/common.py:613: DeprecationWarning: invalid > > escape sequence \d > > search_obj = re.search('misc_feature ([\d]+)..([\d]+)$', line) > > /<<PKGBUILDDIR>>/python/gubbins/common.py:620: DeprecationWarning: invalid > > escape sequence \= > > search_taxa = re.search('taxa\=\"([^"]+)\"', line) > > /usr/lib/python3/dist-packages/dendropy/utility/container.py:357: > > DeprecationWarning: Using or importing the ABCs from 'collections' instead > > of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it > > will stop working > > class CaseInsensitiveDict(collections.MutableMapping): > > test_concatenate_fasta_files > > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok > > test_get_sequence_names_from_alignment > > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok > > test_number_of_sequences_in_alignment > > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok > > test_reconvert_fasta_file > > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok > > test_reinsert_gaps_into_fasta_file > > (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok > > test_get_recombination_files > > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) > > ... ok > > test_multiple_files_have_one_match > > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) > > ... ok > > test_reading_embl_file > > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) > > ... ok > > test_two_files_are_different > > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) > > ... ok > > test_two_files_are_same > > (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) > > ... ok > > test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies) ... > > ERROR > > test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies) > > ... ERROR > > test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies) ... > > ERROR > > test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies) ... > > ERROR > > test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies) ... > > ERROR > > test_rename_final_output > > (gubbins.tests.test_dependencies.TestExternalDependencies) ... ERROR > > test_dont_filter_input_file_with_multiple_duplicate_sequences > > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok > > test_filter_out_alignments_with_too_much_missing_data > > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok > > test_input_file_with_all_duplicate_sequences > > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok > > test_input_file_with_multiple_duplicate_sequences > > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok > > test_input_file_with_no_duplicate_sequences > > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok > > test_input_file_with_one_duplicate_sequences > > (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok > > test_filter_out_removed_taxa_from_tree > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_has_tree_been_seen_before > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_internal_node_taxons_removed_when_used_as_starting_tree > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_remove_internal_node_labels > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_at_midpoint > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_with_outgroup > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_with_outgroups > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_with_outgroups_all_in_different_clade > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_with_outgroups_all_in_one_clade > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_with_outgroups_all_in_one_clade_large > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_reroot_tree_with_outgroups_with_two_mixed_clades > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_robinson_foulds_distance > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_root_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_split_all_non_bi_nodes > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_transfer_internal_node_labels_to_tree > > (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok > > test_fasttree_treebuilding_command > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_iqtree_convert_raw_ancestral_states_to_fasta > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_iqtree_replace_internal_node_label > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_iqtree_sequence_reconstruction_command > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_iqtree_treebuilding_command > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_raxml_convert_raw_ancestral_states_to_fasta > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_raxml_replace_internal_node_label > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_raxml_select_executable_based_on_threads > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_raxml_sequence_reconstruction_command > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_raxml_treebuilding_command > > (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok > > test_check_and_fix_window_size (gubbins.tests.test_utils.TestUtilities) ... > > ok > > test_delete_files (gubbins.tests.test_utils.TestUtilities) ... ok > > test_do_files_exist (gubbins.tests.test_utils.TestUtilities) ... ok > > test_gubbins_command (gubbins.tests.test_utils.TestUtilities) ... ok > > test_is_executable (gubbins.tests.test_utils.TestUtilities) ... ok > > test_rename_files (gubbins.tests.test_utils.TestUtilities) ... ok > > test_replace_executable (gubbins.tests.test_utils.TestUtilities) ... ok > > test_translation_of_filenames_to_final_filenames > > (gubbins.tests.test_utils.TestUtilities) ... ok > > test_verbose_printer (gubbins.tests.test_utils.TestUtilities) ... ok > > test_which (gubbins.tests.test_utils.TestUtilities) ... ok > > test_are_all_sequence_names_unique > > (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok > > test_are_all_sequences_the_same_length > > (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok > > test_are_there_enough_sequences_to_build_a_tree > > (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok > > test_does_each_sequence_have_a_name > > (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok > > test_does_the_sequence_have_sensible_characters > > (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok > > test_valid_fasta_file > > (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok > > test_are_all_names_unique > > (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) > > ... ok > > test_do_the_names_match_the_fasta_file > > (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) > > ... ok > > test_is_it_a_valid_newick_tree > > (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) > > ... ok > > > > ====================================================================== > > ERROR: test_cleanup > > (gubbins.tests.test_dependencies.TestExternalDependencies) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 93, in __init__ > > req = REQUIREMENT.parseString(requirement_string) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1654, in parseString > > raise exc > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1644, in parseString > > loc, tokens = self._parse( instring, 0 ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3417, in parseImpl > > loc, exprtokens = e._parse( instring, loc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3739, in parseImpl > > return self.expr._parse( instring, loc, doActions, callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3400, in parseImpl > > loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, > > callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1406, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 2711, in parseImpl > > raise ParseException(instring, loc, self.errmsg, self) > > pkg_resources._vendor.pyparsing.ParseException: Expected W:(abcd...) (at > > char 0), (line:1, col:1) > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line > > 59, in test_cleanup > > common.parse_and_run(parser.parse_args([os.path.join(data_dir, > > 'multiple_recombinations.aln')])) > > File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 62, in > > parse_and_run > > program_version = > > str(pkg_resources.get_distribution(gubbins_exec).version) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 478, in get_distribution > > dist = Requirement.parse(dist) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3153, in parse > > req, = parse_requirements(s) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3098, in parse_requirements > > yield Requirement(line) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3108, in __init__ > > super(Requirement, self).__init__(requirement_string) > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 95, in __init__ > > raise InvalidRequirement( > > pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error > > at "'/build/g'": Expected W:(abcd...) > > > > ====================================================================== > > ERROR: test_fasttree > > (gubbins.tests.test_dependencies.TestExternalDependencies) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 93, in __init__ > > req = REQUIREMENT.parseString(requirement_string) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1654, in parseString > > raise exc > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1644, in parseString > > loc, tokens = self._parse( instring, 0 ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3417, in parseImpl > > loc, exprtokens = e._parse( instring, loc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3739, in parseImpl > > return self.expr._parse( instring, loc, doActions, callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3400, in parseImpl > > loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, > > callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1406, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 2711, in parseImpl > > raise ParseException(instring, loc, self.errmsg, self) > > pkg_resources._vendor.pyparsing.ParseException: Expected W:(abcd...) (at > > char 0), (line:1, col:1) > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line > > 24, in test_fasttree > > common.parse_and_run(parser.parse_args(["--tree_builder", "fasttree", > > File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 62, in > > parse_and_run > > program_version = > > str(pkg_resources.get_distribution(gubbins_exec).version) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 478, in get_distribution > > dist = Requirement.parse(dist) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3153, in parse > > req, = parse_requirements(s) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3098, in parse_requirements > > yield Requirement(line) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3108, in __init__ > > super(Requirement, self).__init__(requirement_string) > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 95, in __init__ > > raise InvalidRequirement( > > pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error > > at "'/build/g'": Expected W:(abcd...) > > > > ====================================================================== > > ERROR: test_hybrid > > (gubbins.tests.test_dependencies.TestExternalDependencies) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 93, in __init__ > > req = REQUIREMENT.parseString(requirement_string) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1654, in parseString > > raise exc > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1644, in parseString > > loc, tokens = self._parse( instring, 0 ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3417, in parseImpl > > loc, exprtokens = e._parse( instring, loc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3739, in parseImpl > > return self.expr._parse( instring, loc, doActions, callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3400, in parseImpl > > loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, > > callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1406, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 2711, in parseImpl > > raise ParseException(instring, loc, self.errmsg, self) > > pkg_resources._vendor.pyparsing.ParseException: Expected W:(abcd...) (at > > char 0), (line:1, col:1) > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line > > 45, in test_hybrid > > common.parse_and_run(parser.parse_args(["--tree_builder", "hybrid", > > File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 62, in > > parse_and_run > > program_version = > > str(pkg_resources.get_distribution(gubbins_exec).version) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 478, in get_distribution > > dist = Requirement.parse(dist) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3153, in parse > > req, = parse_requirements(s) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3098, in parse_requirements > > yield Requirement(line) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3108, in __init__ > > super(Requirement, self).__init__(requirement_string) > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 95, in __init__ > > raise InvalidRequirement( > > pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error > > at "'/build/g'": Expected W:(abcd...) > > > > ====================================================================== > > ERROR: test_iqtree > > (gubbins.tests.test_dependencies.TestExternalDependencies) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 93, in __init__ > > req = REQUIREMENT.parseString(requirement_string) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1654, in parseString > > raise exc > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1644, in parseString > > loc, tokens = self._parse( instring, 0 ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3417, in parseImpl > > loc, exprtokens = e._parse( instring, loc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3739, in parseImpl > > return self.expr._parse( instring, loc, doActions, callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3400, in parseImpl > > loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, > > callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1406, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 2711, in parseImpl > > raise ParseException(instring, loc, self.errmsg, self) > > pkg_resources._vendor.pyparsing.ParseException: Expected W:(abcd...) (at > > char 0), (line:1, col:1) > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line > > 31, in test_iqtree > > common.parse_and_run(parser.parse_args(["--tree_builder", "iqtree", > > File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 62, in > > parse_and_run > > program_version = > > str(pkg_resources.get_distribution(gubbins_exec).version) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 478, in get_distribution > > dist = Requirement.parse(dist) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3153, in parse > > req, = parse_requirements(s) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3098, in parse_requirements > > yield Requirement(line) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3108, in __init__ > > super(Requirement, self).__init__(requirement_string) > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 95, in __init__ > > raise InvalidRequirement( > > pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error > > at "'/build/g'": Expected W:(abcd...) > > > > ====================================================================== > > ERROR: test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 93, in __init__ > > req = REQUIREMENT.parseString(requirement_string) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1654, in parseString > > raise exc > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1644, in parseString > > loc, tokens = self._parse( instring, 0 ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3417, in parseImpl > > loc, exprtokens = e._parse( instring, loc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3739, in parseImpl > > return self.expr._parse( instring, loc, doActions, callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3400, in parseImpl > > loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, > > callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1406, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 2711, in parseImpl > > raise ParseException(instring, loc, self.errmsg, self) > > pkg_resources._vendor.pyparsing.ParseException: Expected W:(abcd...) (at > > char 0), (line:1, col:1) > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line > > 38, in test_raxml > > common.parse_and_run(parser.parse_args(["--tree_builder", "raxml", > > File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 62, in > > parse_and_run > > program_version = > > str(pkg_resources.get_distribution(gubbins_exec).version) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 478, in get_distribution > > dist = Requirement.parse(dist) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3153, in parse > > req, = parse_requirements(s) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3098, in parse_requirements > > yield Requirement(line) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3108, in __init__ > > super(Requirement, self).__init__(requirement_string) > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 95, in __init__ > > raise InvalidRequirement( > > pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error > > at "'/build/g'": Expected W:(abcd...) > > > > ====================================================================== > > ERROR: test_rename_final_output > > (gubbins.tests.test_dependencies.TestExternalDependencies) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 93, in __init__ > > req = REQUIREMENT.parseString(requirement_string) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1654, in parseString > > raise exc > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1644, in parseString > > loc, tokens = self._parse( instring, 0 ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3417, in parseImpl > > loc, exprtokens = e._parse( instring, loc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3739, in parseImpl > > return self.expr._parse( instring, loc, doActions, callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1402, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 3400, in parseImpl > > loc, resultlist = self.exprs[0]._parse( instring, loc, doActions, > > callPreParse=False ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 1406, in _parseNoCache > > loc,tokens = self.parseImpl( instring, preloc, doActions ) > > File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", > > line 2711, in parseImpl > > raise ParseException(instring, loc, self.errmsg, self) > > pkg_resources._vendor.pyparsing.ParseException: Expected W:(abcd...) (at > > char 0), (line:1, col:1) > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line > > 52, in test_rename_final_output > > common.parse_and_run(parser.parse_args(["--prefix", "different_prefix", > > File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 62, in > > parse_and_run > > program_version = > > str(pkg_resources.get_distribution(gubbins_exec).version) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 478, in get_distribution > > dist = Requirement.parse(dist) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3153, in parse > > req, = parse_requirements(s) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3098, in parse_requirements > > yield Requirement(line) > > File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line > > 3108, in __init__ > > super(Requirement, self).__init__(requirement_string) > > File > > "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", > > line 95, in __init__ > > raise InvalidRequirement( > > pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error > > at "'/build/g'": Expected W:(abcd...) > > > > ---------------------------------------------------------------------- > > Ran 67 tests in 0.288s > > > > FAILED (errors=6) > > Test failed: <unittest.runner.TextTestResult run=67 errors=6 failures=0> > > error: Test failed: <unittest.runner.TextTestResult run=67 errors=6 > > failures=0> > > make[1]: *** [debian/rules:25: override_dh_auto_test] Error 1 > > The full build log is available from: > http://qa-logs.debian.net/2020/09/26/gubbins_2.4.1-2_unstable.log > > 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! > > About the archive rebuild: The rebuild was done on EC2 VM instances from > Amazon Web Services, using a clean, minimal and up-to-date chroot. Every > failed build was retried once to eliminate random failures. > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de