Please read my analysis I've done at [email protected] (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 <[email protected]> Date: 1/25/2017 06:28 (GMT-08:00) To: > [email protected] 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
