Re: Bug#798066: Multiarch-renamed python extensions not found during autopkgtest testing
على الجمعـة 11 كانون الأول 2015 03:09، كتب Antonio Terceiro: > I also > don't see other python packages that contain compiled extensions needing > to do this sort of thing. > I have a few other packages that have this problem -- python-cobra is one. For two other packages (python-pbh5tools and kineticstools), I disabled tests that require the compiled extensions because they were failing for this reason. > I tried python-pysam here, and after some trial and error, I can also > reproduce > the same issue outside of autopkgtest. The issue is that Python load path is > being confused by the fact that you are on root of the source package: > [...] Many thanks for that information. I can reproduce that effect as well and things are making much more sense now. Now, I just need to find a proper solution to this python module priority problem. > > So your problem has nothing to do autopkgtest, other than the fact that > autopkgtest always starts the tests from the root of the source package. > Thanks-- I didn't set out to bash autopkgtest with this. I just wanted to know why the tests weren't running properly and how to resolve that problem. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name signature.asc Description: OpenPGP digital signature
Re: Bug#798066: Multiarch-renamed python extensions not found during autopkgtest testing
On Thu, Dec 10, 2015 at 10:52:05PM -0800, Afif Elghraoui wrote:
> Hi,
>
> على الأربعاء 9 كانون الأول 2015 05:25، كتب Antonio Terceiro:
> > autopkgtest does not do anything special wrt dependencies, it will
> > install exactly what you told it to in debian/tests/control
> [...]
> >
> > I am therefore closing this bug.
>
> The problem is not that something is not installed. The problem is that
> the multiarch configuration for python is not right in autopkgtest (or
> schroot). During the package build, dh-python renames the compiled
> extension to contain the multiarch triplet. For some reason, only in
> autopkgtest, python is not properly configured to find the extension
> after it has been renamed, so autopkgtest runs requiring the compiled
> extensions fail.
ci.debian.net does not use schroot anymore, since a few weeks ago. and
autopkgtest does not do anything special to packages, it just installs
them on an otherwise regular testbed, be it a schroot chroot, an lxc
container (what ci.debian.net currently uses), and so on.
> So should we continue to have hacks like this to get autopkgtest to find
> multiarch-renamed extensions?
>
> cd /usr/lib/python2.7/dist-packages/pysam
> gnutype=`dpkg-architecture -qDEB_TARGET_GNU_TYPE`
> for so in *.${gnutype}.so ; do sudo ln -sf $so `basename $so
> .${gnutype}.so`.so ; done
>
> http://anonscm.debian.org/cgit/debian-med/python-pysam.git/tree/debian/tests/run-nose-tests
Again, there is nothing special in the autopkgtest test beds. I also
don't see other python packages that contain compiled extensions needing
to do this sort of thing.
I tried python-pysam here, and after some trial and error, I can also reproduce
the same issue outside of autopkgtest. The issue is that Python load path is
being confused by the fact that you are on root of the source package:
# pwd
/tmp/python-pysam-0.8.4+ds
# ls
AUTHORS INSTALL MANIFEST.in THANKS debian install-CGAT-tools.sh
pysam.py samtools setup.cfg tests
COPYING KNOWN_BUGS README.rst benchmark doc pysam
requirements.txt save setup.py win32
# python
Python 2.7.11 (default, Dec 9 2015, 00:29:25)
[GCC 5.3.1 20151205] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
Traceback (most recent call last):
File "", line 1, in
File "pysam/__init__.py", line 1, in
from pysam.libchtslib import *
ImportError: No module named libchtslib
>>>
# cd /
# python
Python 2.7.11 (default, Dec 9 2015, 00:29:25)
[GCC 5.3.1 20151205] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>>
#
So your problem has nothing to do autopkgtest, other than the fact that
autopkgtest always starts the tests from the root of the source package.
--
Antonio Terceiro
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Description: PGP signature
Re: Bug#798066: Multiarch-renamed python extensions not found during autopkgtest testing
Hi,
على الأربعاء 9 كانون الأول 2015 05:25، كتب Antonio Terceiro:
> autopkgtest does not do anything special wrt dependencies, it will
> install exactly what you told it to in debian/tests/control
[...]
>
> I am therefore closing this bug.
The problem is not that something is not installed. The problem is that
the multiarch configuration for python is not right in autopkgtest (or
schroot). During the package build, dh-python renames the compiled
extension to contain the multiarch triplet. For some reason, only in
autopkgtest, python is not properly configured to find the extension
after it has been renamed, so autopkgtest runs requiring the compiled
extensions fail.
So should we continue to have hacks like this to get autopkgtest to find
multiarch-renamed extensions?
cd /usr/lib/python2.7/dist-packages/pysam
gnutype=`dpkg-architecture -qDEB_TARGET_GNU_TYPE`
for so in *.${gnutype}.so ; do sudo ln -sf $so `basename $so
.${gnutype}.so`.so ; done
http://anonscm.debian.org/cgit/debian-med/python-pysam.git/tree/debian/tests/run-nose-tests
regards
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
Re: Bug#798066: Multiarch-renamed python extensions not found during autopkgtest testing
Control: On Tue, Dec 08, 2015 at 11:25:47PM -0800, Afif Elghraoui wrote: > Hi, debian-python, > > For Debian Med's python packages that have compiled extensions, I > noticed that test suites run via autopkgtest fail because the package > cannot find those extensions, as they've been renamed with the multiarch > triplet. > > It seems to only be a problem with autopkgtest because I have in one > case manually installed such a package and successfully ran its test > suite. I therefore reported #798066 [1] against autopkgtest, but quite > some time has elapsed since then and I'd like to get this resolved. > > Does anyone know why this might be the case? Autopkgtest for these > packages is currently not very helpful because there are many spurious > failures due to this issue. There are more details in my original bug > report [1]. > > Many thanks and regards > Afif > > 1. http://bugs.debian.org/798066 autopkgtest does not do anything special wrt dependencies, it will install exactly what you told it to in debian/tests/control (see the spec¹ for reference), so I doubt this would be a problem with autopkgtest. ¹ http://anonscm.debian.org/cgit/autopkgtest/autopkgtest.git/tree/doc/README.package-tests.rst I am therefore closing this bug. -- Antonio Terceiro signature.asc Description: PGP signature
Multiarch-renamed python extensions not found during autopkgtest testing
Hi, debian-python, For Debian Med's python packages that have compiled extensions, I noticed that test suites run via autopkgtest fail because the package cannot find those extensions, as they've been renamed with the multiarch triplet. It seems to only be a problem with autopkgtest because I have in one case manually installed such a package and successfully ran its test suite. I therefore reported #798066 [1] against autopkgtest, but quite some time has elapsed since then and I'd like to get this resolved. Does anyone know why this might be the case? Autopkgtest for these packages is currently not very helpful because there are many spurious failures due to this issue. There are more details in my original bug report [1]. Many thanks and regards Afif 1. http://bugs.debian.org/798066 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
