[Debian-med-packaging] Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...)
Andreas Tille
tille at debian.org
Fri Oct 30 09:14:52 GMT 2020
Control: tags -1 help
Control: forwarded -1 Aidan Delaney <a.j.delaney at 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-packaging at alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
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