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.
--
http://fam-tille.de
