[Debian-med-packaging] Bug#711376: [mpitt at debian.org: Bug#711376: autopkgtest failing: missing numpy, trying to create 1nz9.full.pickle in system directory]

[Andreas Tille]

Hi Tomas,

your last update of this package is newer than this bug so I have the
impression that you did not noticed the bug at all.  Could you please
confirm that you either subscribed the package you are maintaining in
the package tracking system to get all important information or even
better subscribe our maintainer mailing list[1].  Usually it is a good
idea to respond to some bug at least with some answer like:

  a) I will track this down / ask upstream for help
  b) Will be fixed with soonish upload
  c) I need help

or something like this.

Kind regards

        Andreas.

[1] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging

----- Forwarded message from Martin Pitt <mpitt at debian.org> -----

Date: Thu, 6 Jun 2013 17:56:22 +0200
From: Martin Pitt <mpitt at debian.org>
To: Debian BTS Submit <submit at bugs.debian.org>
Subject: Bug#711376: autopkgtest failing: missing numpy, trying to create 1nz9.full.pickle in system directory
X-Debian-PR-Message: report 711376
X-Debian-PR-Package: python-csb
X-Debian-PR-Keywords: 
X-Debian-PR-Source: python-csb

Package: python-csb
Version: 1.1.1+dfsg-1

Hello,

python-csb's autopkgtest is currently failing [1]:

Traceback (most recent call last):
  File "test/app.py", line 11, in <module>
    main('csb.test.cases.*')
[...]
  File "/usr/lib/python2.7/dist-packages/csb/bio/structure/__init__.py", line 67, in <module>
    import numpy
ImportError: No module named numpy

That bit is easily rectified by adding "python-numpy" to
debian/tests/control's Depends: line. But when I do this, it now runs
into the next failure:

Traceback (most recent call last):
  File "test/app.py", line 11, in <module>
    main('csb.test.cases.*')
  File "/usr/lib/python2.7/dist-packages/csb/test/__init__.py", line 804, in __init__
    self.run()
  File "/usr/lib/python2.7/dist-packages/csb/test/__init__.py", line 850, in run
    Config().ensureDataConsistency()
  File "/usr/lib/python2.7/dist-packages/csb/test/__init__.py", line 312, in ensureDataConsistency
    self.updateDataFiles()
  File "/usr/lib/python2.7/dist-packages/csb/test/__init__.py", line 330, in updateDataFiles
    Pickle.dump(ensemble, open(os.path.join(self.data, '1nz9.full.pickle'), 'wb'))
IOError: [Errno 13] Permission denied: '/usr/lib/python2.7/dist-packages/csb/test/data/1nz9.full.pickle'

It seems strange that csb wants to write pickle files into the system
python module directory, so this might point out an actual bug? (I
have no idea what this module does, though).

Thank you,

Martin

[1] https://jenkins.qa.ubuntu.com/view/Saucy/view/AutoPkgTest/job/saucy-adt-python-csb/
-- 
Martin Pitt                        | http://www.piware.de
Ubuntu Developer (www.ubuntu.com)  | Debian Developer  (www.debian.org)

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