Re: Status of python-pysam
... and again,
On Wed, Jan 25, 2017 at 02:44:00PM +0100, Andreas Tille wrote:
> Hi again,
>
> in addition to my mail below: I do not get any rpath issue when droping
> the rpath patch completely. The test failure does not happen as well. I
> commited the current status with adapted lintian overrides leaving it
> with spelling issues only.
>
> I'd welcome if somebody can confirm that an upload of this status is OK.
I've tested some builds with the new pysam:
> > $ apt-cache rdepends python-pysam | grep -v med-bio-dev
> > python-pysam
> > Reverse Depends:
> > pbhoney, python-pbsuite-utils - source is pbsuite
Builds ... but does not Build-Depends python-pysam - so this is
no effective test.
> > python-pbalign
OK.
> > sga
OK
> > python-pbcore
Does NOT build ...
======================================================================
ERROR: Failure: ImportError (libchtslib.so: cannot open shared object file: No such file or directory)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/build/python-pbcore-1.2.10+dfsg/tests/test_pbcore_io_FastaTable.py", line 3, in <module>
from pbcore.io import FastaReader, FastaWriter, IndexedFastaReader
File "/build/python-pbcore-1.2.10+dfsg/pbcore/io/__init__.py", line 38, in <module>
from .align import *
File "/build/python-pbcore-1.2.10+dfsg/pbcore/io/align/__init__.py", line 32, in <module>
from BamIO import *
File "/build/python-pbcore-1.2.10+dfsg/pbcore/io/align/BamIO.py", line 35, in <module>
from pysam import AlignmentFile
File "/usr/lib/python2.7/dist-packages/pysam/__init__.py", line 6, in <module>
from pysam.libcutils import *
ImportError: libchtslib.so: cannot open shared object file: No such file or directory
... this is due to the fact that libchtslib.so is actually not
*installed* inside the resulting python-pysam package. I'll try
to manually copy and report here about success.
> > gasic
OK (does not Build-Depends python-pysam)
> > fitgcp
OK
> > $ apt-cache rdepends python3-pysam | grep -v med-bio-dev
> > python3-pysam
> > Reverse Depends:
> > circlator
OK
> > ariba
OK
> > iva
OK.
I'll try to fix the missing libchtslib.so issue and report here.
Kind regards
Andreas.
--
http://fam-tille.de
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