Re: Status of python-pysam
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
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