Your message dated Sun, 02 Dec 2018 07:19:07 +0000
with message-id <e1gtm1z-000h7x...@fasolo.debian.org>
and subject line Bug#911492: fixed in htslib 1.9-4
has caused the Debian Bug report #911492,
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.
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--
911492: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=911492
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: htslib, python-pysam
Control: found -1 htslib/1.9-3
Control: found -1 python-pysam/0.14+ds-2
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 1.9-3
python-pysam from testing 0.14+ds-2
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is contributing to the delay of 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/1182495/log.gz
=================================== FAILURES
===================================
___________________ TestLargeCigar.test_reading_writing_cram
___________________
self = <AlignmentFile_test.TestLargeCigar
testMethod=test_reading_writing_cram>
def test_reading_writing_cram(self):
read = self.build_read()
> self.check_read(read, mode="cram")
tests/AlignmentFile_test.py:2265:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
tests/AlignmentFile_test.py:2244: in check_read
ref_read = next(inf)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
> raise IOError('truncated file')
E OSError: truncated file
pysam/libcalignmentfile.pyx:1804: OSError
=============================== warnings summary
===============================
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2
/tmp/autopkgtest-lxc.uirvm7sh/downtmp/build.e1l/src/tests/AlignmentFile_test.py:1395:
UserWarning: no BGZF EOF marker; file may be truncated
ignore_truncation=True)
-- Docs: http://doc.pytest.org/en/latest/warnings.html
======== 1 failed, 902 passed, 9 skipped, 1 warnings in 146.53 seconds
=========
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: htslib
Source-Version: 1.9-4
We believe that the bug you reported is fixed in the latest version of
htslib, 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 911...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated htslib 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: SHA256
Format: 1.8
Date: Sun, 02 Dec 2018 07:54:46 +0100
Source: htslib
Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix
Architecture: source
Version: 1.9-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
htslib-test - Test data for HTSlib
libhts-dev - development files for the HTSlib
libhts-private-dev - private development files for the HTSlib (use with care)
libhts2 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Closes: 911492
Changes:
htslib (1.9-4) unstable; urgency=medium
.
* Add Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
(Thanks to Graham Inggs <gin...@debian.org>)
Closes: #911492
Checksums-Sha1:
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b942b957e00e688308f81ab815270e338879786c 13768 htslib_1.9-4.debian.tar.xz
Checksums-Sha256:
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htslib_1.9-4.dsc
0f118678a98dd37cbb046cffe0e62e7e4c8dcb8c5e96eb6864c8be63f36bec09 13768
htslib_1.9-4.debian.tar.xz
Files:
ed50d2321f31f95330ebcfd6aff82471 2896 science optional htslib_1.9-4.dsc
bda423d3f74add547c35f5f21adb1d50 13768 science optional
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