[Debian-med-packaging] Bug#920250: python-pysam ftbfs from source (test failures)

[Andreas Tille]

Hi Michael,

are you aware that it seems that your latest change


htslib (1.9-10) unstable; urgency=medium

  * Bring the libdeflate, GCS, and S3 updates back to unstable.

 -- Michael R. Crusoe <michael.crusoe at gmail.com>  Wed, 16 Jan 2019 05:23:22 -0800


seems to have broken python-pysam?  I have reported this to upstream[1]
but I have no idea whether your change might be responsible for the
break or not.

Kind regards

      Andreas.


[1] https://github.com/pysam-developers/pysam/issues/761

On Wed, Jan 23, 2019 at 10:44:51AM +0100, Matthias Klose wrote:
> Package: src:python-pysam
> Version: 0.15.2+ds-1
> Severity: serious
> Tags: sid buster
> 
> =================================== FAILURES ===================================
> _____________ TestIndexing.test_indexing_to_custom_location_works ______________
> 
> self = <tabix_test.TestIndexing testMethod=test_indexing_to_custom_location_works>
> 
>     def test_indexing_to_custom_location_works(self):
>         '''test indexing a file with a non-default location.'''
> 
>         index_path = get_temp_filename(suffix='custom.tbi')
>         pysam.tabix_index(self.tmpfilename, preset="gff",
>                           index=index_path, force=True)
> >       self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))
> E       AssertionError: False is not true
> 
> tests/tabix_test.py:89: AssertionError
> ____________ TestIndexing.test_indexing_with_explict_columns_works _____________
> 
> self = <tabix_test.TestIndexing testMethod=test_indexing_with_explict_columns_works>
> 
>     def test_indexing_with_explict_columns_works(self):
>         '''test indexing via preset.'''
> 
>         pysam.tabix_index(self.tmpfilename,
>                           seq_col=0,
>                           start_col=3,
>                           end_col=4,
>                           line_skip=0,
>                           zerobased=False)
>         self.assertTrue(checkBinaryEqual(
> >           self.tmpfilename + ".tbi", self.filename_idx))
> E       AssertionError: False is not true
> 
> tests/tabix_test.py:102: AssertionError
> _________________ TestIndexing.test_indexing_with_preset_works _________________
> 
> self = <tabix_test.TestIndexing testMethod=test_indexing_with_preset_works>
> 
>     def test_indexing_with_preset_works(self):
>         '''test indexing via preset.'''
> 
>         pysam.tabix_index(self.tmpfilename, preset="gff")
>         self.assertTrue(checkBinaryEqual(
> >           self.tmpfilename + ".tbi", self.filename_idx))
> E       AssertionError: False is not true
> 
> tests/tabix_test.py:81: AssertionError
> =============================== warnings summary ===============================
> /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367
>   /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning:
> Cython directive 'language_level' not set, using 2 for now (Py2). This will
> change in a later release! File:
> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx
>     tree = Parsing.p_module(s, pxd, full_module_name)
> 
> .pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
> 
> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459:
> UserWarning: no BGZF EOF marker; file may be truncated
>     ignore_truncation=True)
> 
> -- Docs: https://docs.pytest.org/en/latest/warnings.html
> ======== 3 failed, 906 passed, 17 skipped, 2 warnings in 60.36 seconds =========
> E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd
> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build;
> python2.7 -m pytest tests
> dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned
> exit code 13
> make[1]: *** [debian/rules:32: override_dh_auto_test] Error 25
> make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds'
> make: *** [debian/rules:24: build-arch] Error 2
> dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
> 
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