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