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
> >
