Re: Status of python-pysam
Please read my analysis I've done at debian-mentors@l.d.o (our
maintainers list in CC). Something is really wrong with our
python-pysam build independently from pbcore.
On Wed, Jan 25, 2017 at 07:02:15AM -0800, Afif Elghraoui wrote:
> 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)
> RegardsAfif
> Sent from my T-Mobile 4G LTE Device-------- Original message --------From: Andreas Tille <andreas@an3as.eu> Date: 1/25/2017 06:28 (GMT-08:00) To: debian-med@lists.debian.org Subject: 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
>
--
http://fam-tille.de
Reply to: