[Debian-med-packaging] Bug#911492: htslib breaks python-pysam autopkgtest

[Paul Gevers]

Source: htslib, python-pysam
Control: found -1 htslib/1.9-3
Control: found -1 python-pysam/0.14+ds-2
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at 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
=========

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 488 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20181020/1a2f61e4/attachment.sig>