ftbfs with python2.7

[Matthias Klose]

http://launchpadlibrarian.net/60076636/buildlog_ubuntu-natty-i386.pymvpa_0.4.5~dev23-2build1_FAILEDTOBUILD.txt.gz

the tests don't succeed with 2.7

[Barry Warsaw (barry)]

Progress on this is blocked by bug 688721. pymvpa requires shogun-python-modular from the shogun package.

[Barry Warsaw (barry)]

I suspect this is really a numpy/python2.7 problem. Tracing through TuebingenMEG.__init__() from the test, you'll see that the call to N.fromstring() on line 90 is what's segfaulting. That's really numpy.fromstring(). It does not segfault in Python 2.6.

The crash is happening inside Python at Python/_warnings.c:449 where it tries to do:

    PyFrameObject *f = PyThreadState_GET()->frame

but the thread state is bogus. Investigations continue.

[Barry Warsaw (barry)]

I've verified that this is really a numpy bug. When pymvpa is built against patched numpy in pushed branch, it does not crash.

[Pauli Virtanen (pauli-virtanen)]

Probably this one:

http://projects.scipy.org/numpy/ticket/1345

And the fix (included in Numpy >= 1.5.0):

http://projects.scipy.org/numpy/changeset/8394

[Barry Warsaw (barry)]

@Pauli, yes that's it. IIUC we can't upgrade to numpy 1.5 yet, so my branch (linked above) is a backport of the patch to the version we have in Ubuntu. The patch works for me and fixes the pymvpa crash, but I need a sponsor to upload it.

[Barry Warsaw (barry)]

debdiff for doko

[Launchpad Janitor (janitor)]

This bug was fixed in the package python-numpy - 1:1.4.1-5ubuntu4

---------------
python-numpy (1:1.4.1-5ubuntu4) natty; urgency=low

  * Fix pymvpa crash caused by numpy incompatibility with Python 2.7.
    This is a back port of the numpy upstream changeset:
    http://projects.scipy.org/numpy/changeset/8394
    (LP: #685469)
 -- Barry Warsaw <email address hidden> Thu, 16 Dec 2010 15:57:29 -0500