Your message dated Wed, 20 Feb 2019 11:34:54 +0000 with message-id <[email protected]> and subject line Bug#920250: fixed in python-pysam 0.15.2+ds-2 has caused the Debian Bug report #920250, regarding python-pysam ftbfs from source (test failures) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 920250: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=920250 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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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--- Begin Message ---Source: python-pysam Source-Version: 0.15.2+ds-2 We believe that the bug you reported is fixed in the latest version of python-pysam, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <[email protected]> (supplier of updated python-pysam package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 20 Feb 2019 02:45:47 -0800 Source: python-pysam Architecture: source Version: 0.15.2+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Michael R. Crusoe <[email protected]> Closes: 919928 920250 Changes: python-pysam (0.15.2+ds-2) unstable; urgency=medium . * Team upload. * For the Tabix tests: test the index contents, not the compression scheme. Closes: #919928, #920250 Checksums-Sha1: 2c9b0391421c2a5afae2904e96a5e44203df88de 2528 python-pysam_0.15.2+ds-2.dsc 70a342ab629c7b2e3e7521e88b87fc581e97e4bf 11716 python-pysam_0.15.2+ds-2.debian.tar.xz c0ac4847d444b3ae784859cac7f3ba78be6c41c8 7920 python-pysam_0.15.2+ds-2_source.buildinfo Checksums-Sha256: 731b29094fc11d56604d8f11be2f6cc8825cfba3d5d4ef724c61521be088bee1 2528 python-pysam_0.15.2+ds-2.dsc 5bb7c2e5ddd78550b437f4917faf9265d71a81f646bd14249389cd18231964b6 11716 python-pysam_0.15.2+ds-2.debian.tar.xz 54cf2f342645b73903ddf3f80073a3de82b19c8804270b9cfc43b0fca92159d0 7920 python-pysam_0.15.2+ds-2_source.buildinfo Files: 604ce362a647367df0f366cfea5eb014 2528 python optional python-pysam_0.15.2+ds-2.dsc 106e19251b96d332b4f9207123712c44 11716 python optional python-pysam_0.15.2+ds-2.debian.tar.xz 8b04bb9566c320dcf227ef4c0fd482a4 7920 python optional python-pysam_0.15.2+ds-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAlxtMBYACgkQPCZ2P2xn 5uLNoA/+L8npyja5CRb38INX0mqMXtTZ0CN85AhyXKcQjDRFuiI5E/hKCTUdYXgT BkluY/PeFOo5od7hc3mkmknzJ9WhQ9pKhcWchJRQZRE5yT2NmSGf13f5PL6sy6kN 0Cxouk8+rEZszcVOnputCz4OZHOLwFCmXkoND02Cth143BFLcIWhsM1DY141zsio JIH0A1beXFTDeCSwzVyIeqyyCoQALsVqGgrt61UMabO+zk3Yux07GMwaOuZjPkOI 1I6+x5HIDa5059yl5gNHnUGjchLSnasHSNgKDFfO5kfKyVu6ziXVteciDrO01tvb VqnfcuGR5ibzz7Me+lKMKgXkC03YmcmeZyAalbrGcdTcXrMWcXaOLj3rclTbw2Wf sPF+YoTftABAD3VtXdqmj+mob5lzwwlfP9YyZQmeoIalskN+Q9G/yhk0nmHGo4uS LXubdyRLprNSJX1JzAv5KYZezGXyqnKh76QaDRJFJ9rFwZ4MUb6wuNwoU/pYveZ+ rlcTXrQYgLYmpTZ9/M35dsPn09QLaknrLFdQ0TfAQwz/zNv8alHn5dO+lxOfBDgx aRWjEvbHYsOEDenCoohnxiOEbS//ZZzoozG4HvLSWlaFQow9/W1nvPSmNzzFgTxm IeqUSnkHsyAdcLWERNa8akHj8fh94avI7g/9M27RDdlLpK4ePy0= =i3nE -----END PGP SIGNATURE-----
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