[Biopython] Antwort: Re: Antwort: Re: Antwort: Re: installation as non-administrator
anaryin at gmail.com
Wed May 4 11:41:07 UTC 2011
On the same level of Bio/ you have another directory called Tests/.
If I list my biopython directory:
joaor at home: ls biopython-git/
*Bio* BioSQL CONTRIB DEPRECATED Doc LICENSE
MANIFEST.in NEWS README Scripts *Tests* build
The file Peter was talking about should be there.
João [...] Rodrigues
On Wed, May 4, 2011 at 1:30 PM, <Paul.Czodrowski at merck.de> wrote:
> Dear Peter,
> > >> >From the test results,
> > >>
> > >> > python setup.py test
> > >> > running test
> > >> > Python version: 2.6.5 (r265:79063, Oct 28 2010, 20:56:56)
> > >> > [GCC 4.5.0 20100604 [gcc-4_5-branch revision 160292]]
> > >> > Operating system: posix linux2
> > >> > test_Ace ... ok
> > >> > ...
> > >> > test_Entrez ... Segmentation fault (core dumped)
> > >>
> > >> Oh, nasty! That should *not* happen, and is probably a separate
> > >> issue to the NumPy header install issue.
> > >
> > > python setup.py install --prefix=$HOME works fine now.
> > >
> > > Should the segmentation fault still be considered?
> > Yes please. I assume it still breaks? Can you try changing to the
> > Tests subdirectory from the Biopython source, and doing:
> > python test_Entrez.py
> I cannot find the src directory.
> Here is my Bio/ directory:
> BTW, python setup.py install --prefix=$HOME did not break.
> Thanks & Ceers,
> > That should run just the Entrez tests, and hopefully give a bit
> > more information about what/when the segmentation fault
> > occurs. I suspect a problem in one of the Python C libraries
> > that Biopython is using (since as far as I can recall, all the
> > Bio.Entrez code is pure python).
> > Peter
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