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Re: Status of python-pysam



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.

Kind regards

      Andreas.

On Wed, Jan 25, 2017 at 02:07:07PM +0100, Andreas Tille wrote:
> Hi Afif,
> 
> On Wed, Jan 25, 2017 at 12:23:20AM -0800, Afif Elghraoui wrote:
> > > I noticed some commits of yours for python-pysam version 0.10.0 which
> > > was released yesterday.  I also noticed that you did not added a new
> > > changelog entry for this.
> > 
> > I actually meant to commit an intermediate changelog this time, but
> > forgot. I did it after seeing your message come through.
> 
> :-)
>  
> > >  Is this because you are sharing my suspicion
> > > that it might be the wrong point in time to upload this new version?
> > 
> > On the contrary-- this release wraps htslibe 1.3.2, which is what we
> > have in unstable now. This version also fixes issues building with the
> > version of cython we have in unstable as well, so I think it's quite
> > important to update it.
> 
> Sounds convincing.  I hope we will be up to fix any issues with rdepends:
> 
> $ apt-cache rdepends python-pysam | grep -v med-bio-dev
> python-pysam
> Reverse Depends:
>   pbhoney
>   python-pysam-data
>   python-pbalign
>   sga
>   python-pysam-tests
>   python-pbcore
>   python-pbsuite-utils
>   python-pbalign
>   gasic
>   fitgcp
>  $ apt-cache rdepends python3-pysam | grep -v med-bio-dev
> python3-pysam
> Reverse Depends:
>   circlator
>   mapping-pipeline
>   circlator
>   ariba
>   iva
>   ariba
> 
> in case such might occure.  Its to much to test these seriously all in
> a couple of hours that are left.
> 
> > I meant to do it tonight, but I did not get a
> > chance. I have just enough time probably to update python-cobra, which
> > also had a new release very recently.
> 
> Upload noted.
> 
> > If anybody would like to beat me to pysam, the current quilt patch
> > (rpath.patch) is causing a build failure. If you drop the patch, the
> > build succeeds, but you get the lintian error for package setting rpath.
> > Perhaps only some parts of the patch are unnecessary.
> 
> I think so but for the test you need to set LD_LIBRARY_PATH properly
> which I did in my last commit.  Unfortunately this leaves one test failure
> which seems unrelated to this issue:
> 
> ======================================================================
> ERROR: Failure: ImportError (Building module _compile_test failed: ["DistutilsFileError: could not create '/nonexistent': Permission denied\n"])
> ----------------------------------------------------------------------
> 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-pysam-0.10.0+ds/tests/compile_test.py", line 19, in <module>
>     import _compile_test
>   File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 445, in load_module
>     language_level=self.language_level)
>   File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 234, in load_module
>     exec("raise exc, None, tb", {'exc': exc, 'tb': tb})
>   File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 216, in load_module
>     inplace=build_inplace, language_level=language_level)
>   File "/usr/lib/python2.7/dist-packages/pyximport/pyximport.py", line 192, in build_module
>     reload_support=pyxargs.reload_support)
>   File "/usr/lib/python2.7/dist-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
>     dist.run_commands()
>   File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
>     self.run_command(cmd)
>   File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
>     cmd_obj.run()
>   File "/usr/lib/python2.7/dist-packages/Cython/Distutils/old_build_ext.py", line 185, in run
>     _build_ext.build_ext.run(self)
>   File "/usr/lib/python2.7/distutils/command/build_ext.py", line 340, in run
>     self.build_extensions()
>   File "/usr/lib/python2.7/dist-packages/Cython/Distutils/old_build_ext.py", line 193, in build_extensions
>     self.build_extension(ext)
>   File "/usr/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension
>     depends=ext.depends)
>   File "/usr/lib/python2.7/distutils/ccompiler.py", line 566, in compile
>     depends, extra_postargs)
>   File "/usr/lib/python2.7/distutils/ccompiler.py", line 362, in _setup_compile
>     self.mkpath(os.path.dirname(obj))
>   File "/usr/lib/python2.7/distutils/ccompiler.py", line 882, in mkpath
>     mkpath(name, mode, dry_run=self.dry_run)
>   File "/usr/lib/python2.7/distutils/dir_util.py", line 76, in mkpath
>     "could not create '%s': %s" % (head, exc.args[-1]))
> ImportError: Building module _compile_test failed: ["DistutilsFileError: could not create '/nonexistent': Permission denied\n"]
> 
> ----------------------------------------------------------------------
> Ran 915 tests in 75.909s
> 
> FAILED (errors=1)
> (0, 0)
> E: pybuild pybuild:276: test: plugin custom failed with: exit code=1: set -x; echo "/build/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam python2.7"; LD_LIBRARY_PATH=/build/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam python2.7 -m nose
> dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 --test --system=custom --test-args=set -x; echo "{build_dir}/pysam {interpreter}"; LD_LIBRARY_PATH={build_dir}/pysam {interpreter} -m nose returned exit code 13
> 
> 
> > Or a lintian override is in order.
> 
> ... at least its not necessary.  Some kind of
> 
>     find debian -name "*.so -exec chrpath --delete \{\} \;
> 
> should do the trick afterwards - but that's not the favourite approach.
> I'm currently testing this whether the build failure does not happen in
> this case.
> 
> > I think the rpath is only needed for the private
> > library module it builds (libchtslib).
> 
> Seems so.
> 
> > Otherwise, I think I can get to this tomorrow.
> 
> IMHO it would be safer today - so anybody who might have a clue is
> welcome to enhance. 
> 
> Kind regards
> 
>       Andreas.
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de


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