Hi all, I am thinking to go about this in one of two ways:
1 - State python3-pip as a dependency and use pip3 to install pysam the python3 lib folder; 2 - Package python3-pysam. I really don't want to have to package another piece of software right now though. Do you see any other way to do this? Jorge On Mon, Nov 24, 2014 at 5:28 PM, Jorge Sebastião Soares < j.s.soa...@gmail.com> wrote: > Hi Ghis, > > Disabling the tests worked. > > The package builds at least, but not lintian clean > . > > I'll cary on tomorrow. > > Regards, > > Jorge > > On Mon, Nov 24, 2014 at 5:02 PM, Jorge Sebastião Soares < > j.s.soa...@gmail.com> wrote: > >> 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 >>>> >>> >>> >> >
