Bug#919928: htslib breaks python-pysam autopkgtest
Hi Michael, guessing from the timing I think this failure is caused by htslib (1.9-10) unstable; urgency=medium * Bring the libdeflate, GCS, and S3 updates back to unstable. -- Michael R. Crusoe Wed, 16 Jan 2019 05:23:22 -0800 Since I have no idea about your latest changes I'm tempted to simply revert to htslib (1.9-9) unstable; urgency=medium (or if test keps on failing htslib (1.9-8) unstable; urgency=medium I'll do so if I will not hear from you in 24hours since lots of our packages now got a testing removal warning. Kind regards Andreas. On Mon, Feb 18, 2019 at 08:13:40PM +0100, Paul Gevers wrote: > Control: severity -1 serious > > On Sun, 20 Jan 2019 19:49:38 +0100 Paul Gevers wrote: > > With a recent upload of htslib the autopkgtest of python-pysam fails in > > testing when that autopkgtest is run with the binary packages of htslib > > from unstable. It passes when run with only packages from testing. In > > tabular form: > >passfail > > htslib from testing1.9-10 > > python-pysam from testing0.15.1+ds-1 > > all others from testingfrom testing > > > > I copied some of the output at the bottom of this report. > > > > Currently this regression is blocking the migration of htslib to testing > > [1]. Due to the nature of this issue, I filed this bug report against > > both packages. Can you please investigate the situation and reassign the > > bug to the right package? If needed, please change the bug's severity. > > Since February 12, this is now officially blocking htslib from > migrating. This bug should be fixed either direction: or htslib fixes > the regression it causes in python-pysam, or python-pysam fixes its > autopkgtest to adapt to the new situation. Please agree which package > should be fixed and reassign it to that package, keeping the version > information. > > Paul > > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
Bug#919928: htslib breaks python-pysam autopkgtest
Control: severity -1 serious On Sun, 20 Jan 2019 19:49:38 +0100 Paul Gevers wrote: > With a recent upload of htslib the autopkgtest of python-pysam fails in > testing when that autopkgtest is run with the binary packages of htslib > from unstable. It passes when run with only packages from testing. In > tabular form: >passfail > htslib from testing1.9-10 > python-pysam from testing0.15.1+ds-1 > all others from testingfrom testing > > I copied some of the output at the bottom of this report. > > Currently this regression is blocking the migration of htslib to testing > [1]. Due to the nature of this issue, I filed this bug report against > both packages. Can you please investigate the situation and reassign the > bug to the right package? If needed, please change the bug's severity. Since February 12, this is now officially blocking htslib from migrating. This bug should be fixed either direction: or htslib fixes the regression it causes in python-pysam, or python-pysam fixes its autopkgtest to adapt to the new situation. Please agree which package should be fixed and reassign it to that package, keeping the version information. Paul signature.asc Description: OpenPGP digital signature
Bug#919928: htslib breaks python-pysam autopkgtest
Source: htslib, python-pysam Control: found -1 htslib/1.9-10 Control: found -1 python-pysam/0.15.1+ds-1 X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: breaks needs-update Dear maintainers, With a recent upload of htslib the autopkgtest of python-pysam fails in testing when that autopkgtest is run with the binary packages of htslib from unstable. It passes when run with only packages from testing. In tabular form: passfail htslib from testing1.9-10 python-pysam from testing0.15.1+ds-1 all others from testingfrom testing I copied some of the output at the bottom of this report. Currently this regression is blocking the migration of htslib to testing [1]. Due to the nature of this issue, I filed this bug report against both packages. Can you please investigate the situation and reassign the bug to the right package? If needed, please change the bug's severity. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=htslib https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-pysam/1739216/log.gz === FAILURES === _ TestIndexing.test_indexing_to_custom_location_works __ self = 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 = 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 = 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 signature.asc Description: OpenPGP digital signature
