Path: csiph.com!news.uzoreto.com!fu-berlin.de!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.bugs.dist,linux.debian.maint.python Subject: Bug#971111: gubbins: FTBFS: pkg_resources.extern.packaging.requirements.InvalidRequirement: Parse error at "'/build/g'": Expected W:(abcd...) Date: Fri, 30 Oct 2020 11:50:01 +0100 Message-ID: References: X-Original-To: 971111@bugs.debian.org, Aidan Delaney X-Mailbox-Line: From debian-bugs-dist-request@lists.debian.org Fri Oct 30 10:45:15 2020 Old-Return-Path: X-Spam-Flag: NO X-Spam-Score: -4.2 Reply-To: Andreas Tille , 971111@bugs.debian.org Resent-To: debian-bugs-dist@lists.debian.org Resent-Cc: Debian Med Packaging Team X-Debian-Pr-Message: followup 971111 X-Debian-Pr-Package: src:gubbins X-Debian-Pr-Keywords: bullseye ftbfs sid X-Debian-Pr-Source: gubbins X-Spam-Bayes: score:0.0000 Tokens: new, 18; hammy, 150; neutral, 448; spammy, 0. spammytokens: hammytokens:0.000-+--python3, 0.000-+--H*UA:1.10.1, 0.000-+--H*u:1.10.1, 0.000-+--H*UA:2018-07-13, 0.000-+--H*u:2018-07-13 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.10.1 (2018-07-13) X-Debian-Message: from BTS X-Mailing-List: archive/latest/1629959 List-ID: List-URL: Approved: robomod@news.nic.it Lines: 428 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Debian Python X-Original-Date: Fri, 30 Oct 2020 10:14:52 +0100 X-Original-Message-ID: <20201030091452.GB17235@an3as.eu> X-Original-References: <20200927184517.GA19619@xanadu.blop.info> <20200927184517.GA19619@xanadu.blop.info> Xref: csiph.com linux.debian.bugs.dist:1030635 linux.debian.maint.python:12981 Control: tags -1 help Control: forwarded -1 Aidan Delaney 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 '/<>' > > make[3]: Leaving directory '/<>' > > make[2]: Leaving directory '/<>' > > 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 > > /<>/python/gubbins/common.py:538: DeprecationWarning: invalid escape sequence \d > > elif re.match('^\d', vcf_line) is not None: > > /<>/python/gubbins/common.py:613: DeprecationWarning: invalid escape sequence \d > > search_obj = re.search('misc_feature ([\d]+)..([\d]+)$', line) > > /<>/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 "/<>/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 "/<>/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 "/<>/python/gubbins/tests/test_dependencies.py", line 24, in test_fasttree > > common.parse_and_run(parser.parse_args(["--tree_builder", "fasttree", > > File "/<>/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 "/<>/python/gubbins/tests/test_dependencies.py", line 45, in test_hybrid > > common.parse_and_run(parser.parse_args(["--tree_builder", "hybrid", > > File "/<>/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 "/<>/python/gubbins/tests/test_dependencies.py", line 31, in test_iqtree > > common.parse_and_run(parser.parse_args(["--tree_builder", "iqtree", > > File "/<>/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 "/<>/python/gubbins/tests/test_dependencies.py", line 38, in test_raxml > > common.parse_and_run(parser.parse_args(["--tree_builder", "raxml", > > File "/<>/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 "/<>/python/gubbins/tests/test_dependencies.py", line 52, in test_rename_final_output > > common.parse_and_run(parser.parse_args(["--prefix", "different_prefix", > > File "/<>/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: > > error: Test failed: > > 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@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de