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.
