[Debian-med-packaging] Bug#763218: Bug#763218: python-pysam: FTBFS: Tests failures

[Charles Plessy]

Control: tag -1 - jessie

Le Sun, Sep 28, 2014 at 07:15:05PM +0200, David Suárez a écrit :
> Source: python-pysam
> Version: 0.7.7-1
> Severity: serious
> Tags: jessie sid
> User: debian-qa at lists.debian.org
> Usertags: qa-ftbfs-20140926 qa-ftbfs
> Justification: FTBFS on amd64
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
> 
> Relevant part (hopefully):
> > ======================================================================
> > FAIL: testBAM (__main__.TestUnmappedReads)
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "./pysam_test_offline.py", line 998, in testBAM
> >     self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 )
> > AssertionError: 0 != 2
> > 
> > ----------------------------------------------------------------------
> > Ran 158 tests in 9.110s
> > 
> > FAILED (failures=2, errors=31)
> > E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: cd tests && PYTHONPATH=/«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build python2.7 ./pysam_test_offline.py
> > dh_auto_test: pybuild --test -i python{version} -p 2.7 --dir . returned exit code 13
> > make[1]: *** [override_dh_auto_test] Error 13
> > debian/rules:29: recipe for target 'override_dh_auto_test' failed
> 
> The full build log is available from:
>    http://aws-logs.debian.net/ftbfs-logs/2014/09/26/python-pysam_0.7.7-1_unstable.log

Thanks David.

The build logs show that the tests fail because the version of samtools is not
0.1.19.  Here is an example:

	======================================================================
	ERROR: testBam2fq (__main__.BinaryTest)
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "./pysam_test_offline.py", line 303, in setUp
	    samtools_version ))
	ValueError: versions of pysam/samtools and samtools differ: 0.1.19 != 1.1

Given that samtools is still at version 0.1.19 in Jessie and that it is unsure
whether the version in sid (1.1) will migrate before the Freeze, I am removing the
tag 'jessie' from this bug.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan