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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)

Regards
Afif

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


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