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
