Hi Ghis On Mon, Nov 24, 2014 at 4:58 PM, Ghislain Vaillant <ghisv...@gmail.com> wrote:
> At worst, can't you just disable the test suite for the Python 3 builds ? > Pybuild should allow to do that easily. > Trying that now. But I would still need to link pysam to the iva package at some point, no? Regards, Jorge > 2014-11-24 16:36 GMT+00:00 Jorge Sebastião Soares <j.s.soa...@gmail.com>: > >> Hi guys, >> >> So essentially the package build halts when it tries to run the test >> suite: >> >> This is the error I'm getting when the pysam module is being imported: >> >> root@debian:~/iva-0.10.0# python3.4 setup.py test >> running test >> running egg_info >> writing top-level names to iva.egg-info/top_level.txt >> writing iva.egg-info/PKG-INFO >> writing dependency_links to iva.egg-info/dependency_links.txt >> reading manifest file 'iva.egg-info/SOURCES.txt' >> writing manifest file 'iva.egg-info/SOURCES.txt' >> running build_ext >> Failure: ImportError (No module named 'pysam') ... ERROR >> >> ====================================================================== >> ERROR: Failure: ImportError (No module named 'pysam') >> ---------------------------------------------------------------------- >> Traceback (most recent call last): >> File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in >> runTest >> raise self.exc_val.with_traceback(self.tb) >> File "/usr/lib/python3/dist-packages/nose/loader.py", line 414, in >> loadTestsFromName >> addr.filename, addr.module) >> File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in >> importFromPath >> return self.importFromDir(dir_path, fqname) >> File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in >> importFromDir >> mod = load_module(part_fqname, fh, filename, desc) >> File "/usr/lib/python3.4/imp.py", line 245, in load_module >> return load_package(name, filename) >> File "/usr/lib/python3.4/imp.py", line 217, in load_package >> return methods.load() >> File "<frozen importlib._bootstrap>", line 1220, in load >> File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked >> File "<frozen importlib._bootstrap>", line 1129, in _exec >> File "<frozen importlib._bootstrap>", line 1471, in exec_module >> File "<frozen importlib._bootstrap>", line 321, in >> _call_with_frames_removed >> File "/tmp/buildd/iva-0.10.0/iva/__init__.py", line 20, in <module> >> from iva import * >> File "/tmp/buildd/iva-0.10.0/iva/assembly.py", line 2, in <module> >> import pysam >> ImportError: No module named 'pysam' >> >> ---------------------------------------------------------------------- >> Ran 1 test in 0.016s >> >> FAILED (errors=1) >> >> >> If pysam is python 3 compliant, I'm tempted to create the needed symlinks >> in python3.4 pointing to pysam in python2.7, eg. >> >> ln -s /usr/lib/python2.7/dist-packages/pysam >> /usr/lib/python3.4/dist-packages/pysam >> >> I'm sure that this is not the proper way of doing things, so is there any >> other way I can get pysam to be installed under python3.4 rather than >> python2.7? >> >> Regards, >> >> Jorge >> > >
