[Debian-med-packaging] Bug#963326: seqmagick: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13
Lucas Nussbaum
lucas at debian.org
Sun Jun 21 21:06:20 BST 2020
Source: seqmagick
Version: 0.8.0-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200620 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules build
> dh build --with python3 --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:217: python3.8 setup.py config
> running config
> /usr/lib/python3/dist-packages/setuptools/dist.py:468: UserWarning: The version specified ('') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details.
> warnings.warn(
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:217: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick
> copying seqmagick/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick
> copying seqmagick/fileformat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick
> copying seqmagick/transform.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/scripts
> copying seqmagick/scripts/cli.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/scripts
> copying seqmagick/scripts/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/scripts
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/primer_trim.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/quality_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/mogrify.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/backtrans_align.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/extract_ids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> copying seqmagick/subcommands/info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/subcommands
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/test_primer_trim.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/test_subcommands_backtrans_align.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/test_transform.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/test_subcommands_common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/test_subcommands_convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> copying seqmagick/test/test_subcommands_quality_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration
> copying seqmagick/test/integration/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration
> copying seqmagick/test/integration/test_convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration
> copying seqmagick/test/integration/test_info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration
> copying seqmagick/test/integration/test_mogrify.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration
> copying seqmagick/test/integration/test_extract_ids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input1.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input5.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input3.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output2_ungap_cut.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output2.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output2.phy -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output5.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input2.fasta.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input4_ambig.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input2.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output2.nex -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output3.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/input2.fasta.bz2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> copying seqmagick/test/integration/data/output4.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/integration/data
> /usr/lib/python3/dist-packages/setuptools/dist.py:468: UserWarning: The version specified ('') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details.
> warnings.warn(
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build; python3.8 -m nose -v
> test_run (seqmagick.test.integration.test_convert.BasicConvertTestCase) ... ok
> test_run (seqmagick.test.integration.test_convert.BzipInputConvertTestCase) ... SKIP: bzip2 not supported
> test_run (seqmagick.test.integration.test_convert.BzipOutputConvertTestCase) ... SKIP: bzip2 not supported
> test_run (seqmagick.test.integration.test_convert.ConvertToNexusTestCase) ... ok
> test_convert (seqmagick.test.integration.test_convert.ConvertToStdOutTestCase) ... ok
> test_convert_noformat (seqmagick.test.integration.test_convert.ConvertToStdOutTestCase) ... ok
> test_run (seqmagick.test.integration.test_convert.ConvertUngapCutTestCase) ... ok
> test_run (seqmagick.test.integration.test_convert.GzipInputConvertTestCase) ... ok
> test_run (seqmagick.test.integration.test_convert.GzipOutputConvertTestCase) ... ok
> test_run (seqmagick.test.integration.test_convert.TestConvertFromStdin) ... ok
> test_run (seqmagick.test.integration.test_convert.TestCutRelative) ... ok
> test_unknown_seq (seqmagick.test.integration.test_convert.TestCutRelative) ... ok
> test_run (seqmagick.test.integration.test_convert.TestSample) ... ok
> test_run (seqmagick.test.integration.test_convert.TestStdin) ... ok
> test_run (seqmagick.test.integration.test_convert.TestTranslateAmbiguous) ... ok
> test_descriptions (seqmagick.test.integration.test_extract_ids.Bz2ExtractIdsTestCase) ... SKIP: bzip2 not supported
> test_ids (seqmagick.test.integration.test_extract_ids.Bz2ExtractIdsTestCase) ... SKIP: bzip2 not supported
> test_descriptions (seqmagick.test.integration.test_extract_ids.GzipExtractIdsTestCase) ... ok
> test_ids (seqmagick.test.integration.test_extract_ids.GzipExtractIdsTestCase) ... ok
> test_descriptions (seqmagick.test.integration.test_extract_ids.SimpleExtractIdsTestCase) ... ok
> test_ids (seqmagick.test.integration.test_extract_ids.SimpleExtractIdsTestCase) ... ok
> test_info (seqmagick.test.integration.test_info.MultithreadedInfoTestCase) ... ok
> test_info (seqmagick.test.integration.test_info.SimpleBzip2InfoTestCase) ... SKIP: bzip2 not supported
> test_info (seqmagick.test.integration.test_info.SimpleGzipInfoTestCase) ... ok
> test_info (seqmagick.test.integration.test_info.SimpleInfoTestCase) ... ok
> test_run (seqmagick.test.integration.test_mogrify.MogrifyBzipInputTestCase) ... SKIP: bzip2 not supported
> test_run (seqmagick.test.integration.test_mogrify.MogrifyGzipInputTestCase) ... ok
> test_run (seqmagick.test.integration.test_mogrify.MogrifyUngapCutTestCase) ... ok
> test_all_different (seqmagick.test.test_primer_trim.HammingDistanceTestCase) ... ok
> test_ambiguous (seqmagick.test.test_primer_trim.HammingDistanceTestCase) ... ok
> test_basic (seqmagick.test.test_primer_trim.HammingDistanceTestCase) ... ok
> test_no_difference (seqmagick.test.test_primer_trim.HammingDistanceTestCase) ... ok
> test_unequal_length (seqmagick.test.test_primer_trim.HammingDistanceTestCase) ... ok
> Should fail if reverse primer occurs before forward primer ... ok
> test_basic (seqmagick.test.test_primer_trim.LocatePrimersTestCase) ... ok
> test_no_forward (seqmagick.test.test_primer_trim.LocatePrimersTestCase) ... ok
> test_no_reverse (seqmagick.test.test_primer_trim.LocatePrimersTestCase) ... ok
> test_align_exact (seqmagick.test.test_primer_trim.PrimerAlignerTestCase) ... ok
> test_align_gap (seqmagick.test.test_primer_trim.PrimerAlignerTestCase) ... ok
> test_max_score (seqmagick.test.test_primer_trim.PrimerAlignerTestCase) ... ok
> test_map_alignment (seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase) ... ok
> test_map_alignment_excess_codons (seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase) ... ok
> test_map_alignment_insufficient_codons (seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase) ... ok
> test_validate_invalid (seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase) ... ok
> test_validate_valid (seqmagick.test.test_subcommands_backtrans_align.AlignmentMapperTestCase) ... ok
> test_doubles (seqmagick.test.test_subcommands_backtrans_align.BatchTestCase) ... ok
> test_no_input (seqmagick.test.test_subcommands_backtrans_align.BatchTestCase) ... ok
> test_partial (seqmagick.test.test_subcommands_backtrans_align.BatchTestCase) ... ok
> test_singletons (seqmagick.test.test_subcommands_backtrans_align.BatchTestCase) ... ok
> test_provided_umask (seqmagick.test.test_subcommands_common.ApplyUmaskTestCase) ... ok
> test_user_umask (seqmagick.test.test_subcommands_common.ApplyUmaskTestCase) ... ok
> test_exception_leaves_unchanged (seqmagick.test.test_subcommands_common.AtomicWriteTestCase) ... ok
> test_write (seqmagick.test.test_subcommands_common.AtomicWriteTestCase) ... ok
> test_negative (seqmagick.test.test_subcommands_common.CutRangeTestCase) ... ok
> test_no_end (seqmagick.test.test_subcommands_common.CutRangeTestCase) ... ok
> test_no_start (seqmagick.test.test_subcommands_common.CutRangeTestCase) ... ok
> test_out_of_order (seqmagick.test.test_subcommands_common.CutRangeTestCase) ... ok
> test_start (seqmagick.test.test_subcommands_common.CutRangeTestCase) ... ok
> test_read (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... ok
> test_read_bz2 (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... SKIP: bzip2 not supported
> test_read_gz (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... ok
> test_read_text (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... ok
> test_stdin (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... ok
> test_stdout (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... ok
> test_write (seqmagick.test.test_subcommands_common.FileTypeTestCase) ... ok
> test_multi_arg (seqmagick.test.test_subcommands_common.PartialAppendTestCase) ... ok
> test_no_arg (seqmagick.test.test_subcommands_common.PartialAppendTestCase) ... ok
> test_single_arg (seqmagick.test.test_subcommands_common.PartialAppendTestCase) ... ok
> test_negative (seqmagick.test.test_subcommands_common.PositiveValueTestCase) ... ok
> test_positive (seqmagick.test.test_subcommands_common.PositiveValueTestCase) ... ok
> test_zero (seqmagick.test.test_subcommands_common.PositiveValueTestCase) ... ok
> test_multiple (seqmagick.test.test_subcommands_common.SequenceSlicesTestCase) ... ok
> test_single (seqmagick.test.test_subcommands_common.SequenceSlicesTestCase) ... ok
> test_argument_type (seqmagick.test.test_subcommands_convert.ArgumentTypeTestCase) ... ok
> test_parse (seqmagick.test.test_subcommands_convert.ArgumentTypeTestCase) ... ok
> test_parse (seqmagick.test.test_subcommands_convert.IdModificationTransformsTestCase) ... ok
> test_parse (seqmagick.test.test_subcommands_convert.OrderRespectedTestCase) ... ok
> test_parse (seqmagick.test.test_subcommands_convert.SeqSelectTransformsTestCase) ... ok
> test_parse (seqmagick.test.test_subcommands_convert.SequenceModTransformsTestCase) ... ok
> Failure: ImportError (cannot import name 'triefind' from 'Bio' (/usr/lib/python3/dist-packages/Bio/__init__.py)) ... ERROR
> test_nowarn (seqmagick.test.test_transform.CodonWarningTableTestCase) ... ok
> test_warn (seqmagick.test.test_transform.CodonWarningTableTestCase) ... ok
> test_cut_sequences (seqmagick.test.test_transform.CutTestCase) ... ok
> test_full_sequence (seqmagick.test.test_transform.CutTestCase) ... ok
> test_no_sequences (seqmagick.test.test_transform.CutTestCase) ... ok
> test_basic (seqmagick.test.test_transform.DashesCleanupTestCase) ... ok
> test_basic (seqmagick.test.test_transform.DropColumnsTestCase) ... ok
> test_multi (seqmagick.test.test_transform.DropColumnsTestCase) ... ok
> test_filter (seqmagick.test.test_transform.ExcludeFromFileTestCase) ... ok
> Try specifying some minus values. ... ok
> Test that -0 returns all sequences ... ok
> Specifying more sequences than are in input records should return ... ok
> Try specifying some values. ... ok
> test_zero (seqmagick.test.test_transform.HeadTestCase) ... ok
> test_filter (seqmagick.test.test_transform.IncludeFromFileTestCase) ... ok
> test_invalid (seqmagick.test.test_transform.IsolateRegionTestCase) ... ok
> test_middle (seqmagick.test.test_transform.IsolateRegionTestCase) ... ok
> test_no_isolation (seqmagick.test.test_transform.IsolateRegionTestCase) ... ok
> test_single_loc (seqmagick.test.test_transform.IsolateRegionTestCase) ... ok
> test_all_pass (seqmagick.test.test_transform.MinUngapLengthTestCase) ... ok
> test_none_pass (seqmagick.test.test_transform.MinUngapLengthTestCase) ... ok
> test_partial (seqmagick.test.test_transform.MinUngapLengthTestCase) ... ok
> test_multicut (seqmagick.test.test_transform.MultiCutTestCase) ... ok
> test_mask (seqmagick.test.test_transform.MultiMaskSequences) ... ok
> test_mask_whole (seqmagick.test.test_transform.MultiMaskSequences) ... ok
> test_filter_description (seqmagick.test.test_transform.NameExcludeTestCase) ... ok
> test_filter_id (seqmagick.test.test_transform.NameExcludeTestCase) ... ok
> test_filter_description (seqmagick.test.test_transform.NameIncludeTestCase) ... ok
> test_filter_id (seqmagick.test.test_transform.NameIncludeTestCase) ... ok
> test_modify (seqmagick.test.test_transform.NamePrefixTestCase) ... ok
> test_modify (seqmagick.test.test_transform.NameSuffixTestCase) ... ok
> test_pattern_replace_anchored_add_to_description (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_pattern_replace_anchored_id_from_description (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_pattern_replace_anchored_match (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_pattern_replace_anchored_nomatch (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_pattern_replace_anchored_remove_from_description (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_pattern_replace_anchored_transform_id (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> Substitutions are case insensitive ... ok
> Make sure capturing groups work ... ok
> test_pattern_replace_none (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_pattern_replace_static (seqmagick.test.test_transform.PatternReplaceTestCase) ... ok
> test_multi_pass (seqmagick.test.test_transform.RecordBufferTestCase) ... ok
> test_single_pass (seqmagick.test.test_transform.RecordBufferTestCase) ... ok
> test_exclude (seqmagick.test.test_transform.SeqPatternTestCase) ... ok
> test_include (seqmagick.test.test_transform.SeqPatternTestCase) ... ok
> test_basic_squeeze (seqmagick.test.test_transform.SqueezeTestCase) ... ok
> test_gap_proportion (seqmagick.test.test_transform.SqueezeTestCase) ... ok
> Threshold of 0.001 - nothing should be squeezed. ... ok
> Try specifying some plus values. ... ok
> Test that +0 returns all sequences ... ok
> test_tail_1 (seqmagick.test.test_transform.TailTestCase) ... ok
> test_tail_2 (seqmagick.test.test_transform.TailTestCase) ... ok
> test_tail_3 (seqmagick.test.test_transform.TailTestCase) ... ok
> test_dna_protein_gap (seqmagick.test.test_transform.TranslateTestCase) ... ok
> test_dna_protein_gap_stop (seqmagick.test.test_transform.TranslateTestCase) ... ok
> test_dna_protein_nogap (seqmagick.test.test_transform.TranslateTestCase) ... ok
> test_dna_protein_nogap_stop (seqmagick.test.test_transform.TranslateTestCase) ... ok
> test_dash_gap (seqmagick.test.test_transform.UngapSequencesTestCase) ... ok
> test_dot_gap (seqmagick.test.test_transform.UngapSequencesTestCase) ... ok
>
> ======================================================================
> ERROR: Failure: ImportError (cannot import name 'triefind' from 'Bio' (/usr/lib/python3/dist-packages/Bio/__init__.py))
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
> raise self.exc_val.with_traceback(self.tb)
> File "/usr/lib/python3/dist-packages/nose/loader.py", line 416, in loadTestsFromName
> module = self.importer.importFromPath(
> File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
> return self.importFromDir(dir_path, fqname)
> File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
> mod = load_module(part_fqname, fh, filename, desc)
> File "/usr/lib/python3.8/imp.py", line 234, in load_module
> return load_source(name, filename, file)
> File "/usr/lib/python3.8/imp.py", line 171, in load_source
> module = _load(spec)
> File "<frozen importlib._bootstrap>", line 702, in _load
> File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 783, in exec_module
> File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/seqmagick/test/test_subcommands_quality_filter.py", line 10, in <module>
> from Bio import triefind
> ImportError: cannot import name 'triefind' from 'Bio' (/usr/lib/python3/dist-packages/Bio/__init__.py)
>
> ----------------------------------------------------------------------
> Ran 139 tests in 0.424s
>
> FAILED (SKIP=7, errors=1)
> E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build; python3.8 -m nose -v
> dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2020/06/20/seqmagick_0.8.0-1_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.
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