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 <[email protected]> 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 > > _______________________________________________ > Debian-med-packaging mailing list > [email protected] > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
