[Debian-med-packaging] BioPython unit tests: Samtools

[Andreas Tille]

[Bouncing my mails to Peter Cock since spam means rejected my mails,
 sorry Peter, just let me know how to at best report bugs preferably
 via mail]

Hi,

I try to activate all possible tests of BioPython at Debian package
build time but I found some issues.  I will discuss these in separate
mails, continuing with test_samtools_tool and python2.7:

======================================================================
ERROR: test_mpileup_list (test_samtools_tool.SamtoolsTestCase)
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Traceback (most recent call last):
  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_samtools_tool.py", line 220, in test_mpileup_list
    stdout, stderr = cmdline()
  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 515, in __call__
    stdout_str, stderr_str)
ApplicationError: Non-zero return code 255 from 'samtools mpileup /tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/SamBam/bam1.bam /tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/SamBam/bam2.bam', message '[mpileup] 2 samples in 2 input files'

======================================================================
FAIL: test_view (test_samtools_tool.SamtoolsTestCase)
Test for samtools view
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Traceback (most recent call last):
  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_samtools_tool.py", line 123, in test_view
    % (cmdline, stderr_sam))
AssertionError: SAM file  viewing failed:
samtools view -S /tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/SamBam/sam1.sam
Stderr:

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Unfortunately I have no idea how to deal with this.  Any hint?

Kind regards

        Andreas.

-- 
http://fam-tille.de