[Debian-med-packaging] Bug#868927: python-pybedtools FTBFS with more than one supported Python3 version

[Andreas Tille]

On Wed, Jul 19, 2017 at 10:47:09PM +0300, Adrian Bunk wrote:
> On Wed, Jul 19, 2017 at 09:37:35PM +0200, Andreas Tille wrote:
> >...
> > I guess python-pysam is not yet build for Python3 3.6.
> 
> That's #867017/#867018, which seems to require that you update 
> python-pysam to 0.11.2.2

That's done now.  Unfortunately there is one remaining issue in the test
suite: 

...
I: pybuild base:184: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
..................................................................................................                                                                                        E.....................................................................................................................................................................................................................................................................................................................................................................................................S..
======================================================================
ERROR: pybedtools.test.test1.test_issue_178
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/test1.py", line 2108, in test_issue_178
    pybedtools.contrib.bigwig.bam_to_bigwig(fn, genome='dm3', output='tmp.bw')
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/contrib/bigwig.py", line 123, in bam_to_bigwig
    p = subprocess.Popen(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
  File "/usr/lib/python3.6/subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "/usr/lib/python3.6/subprocess.py", line 1344, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'bedGraphToBigWig': 'bedGraphToBigWig'

----------------------------------------------------------------------
Ran 491 tests in 12.192s

FAILED (SKIP=1, errors=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
dh_auto_test: pybuild --test --test-nose -i python{version} -p "3.6 3.5" returned exit code 13
...

Kind regards

       Andreas.

-- 
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