Your message dated Wed, 20 Feb 2019 11:34:54 +0000
with message-id <e1gwq9o-000ebz...@fasolo.debian.org>
and subject line Bug#919928: fixed in python-pysam 0.15.2+ds-2
has caused the Debian Bug report #919928,
regarding htslib breaks python-pysam autopkgtest
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 ow...@bugs.debian.org
immediately.)
--
919928: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919928
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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:
pass fail
htslib from testing 1.9-10
python-pysam from testing 0.15.1+ds-1
all others from testing from 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 = <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
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- 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 919...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <michael.cru...@gmail.com> (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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <michael.cru...@gmail.com>
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-----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=i3nE
-----END PGP SIGNATURE-----
--- End Message ---
