Re: Status of python-pysam
Many thanks for helping with this. At least for pbcore, there is a new release that hasn't been tagged upstream. Upstream's CI testing passes and I verified that it's using pysam 0.10.0.
I previously looked at pysam 0.10.0's release notes and didn't see anything about API changes. Maybe if would be faster to test the reverse-dependencies with rebuild-all-the-things.
I can see what I can do tonight (currently morning here)
Sent from my T-Mobile 4G LTE Device
... and again,
-------- Original message --------
From: Andreas Tille <email@example.com>
Date: 1/25/2017 06:28 (GMT-08:00)
Subject: Re: Status of python-pysam
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
> > sga
> > 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
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
> > $ apt-cache rdepends python3-pysam | grep -v med-bio-dev
> > python3-pysam
> > Reverse Depends:
> > circlator
> > ariba
> > iva
I'll try to fix the missing libchtslib.so issue and report here.