[Biopython] Antwort: Re: Antwort: Re: Antwort: Re: Antwort: Re: installation as non-administrator

[Peter Cock]

On Wed, May 4, 2011 at 1:40 PM,  <Paul.Czodrowski at merck.de> wrote:
>
> Dear Joao & Peter,
>
> this is what I got:
>
> "
> Test error handling when presented with Fasta non-XML data ... ok
> Test error handling when presented with GenBank non-XML data ... ok
> Test parsing XML returned by EFetch, Nucleotide database (first test) ...
> ERROR
> Test parsing XML returned by EFetch, Protein database ... ERROR
> Test parsing XML returned by EFetch, OMIM database ... ERROR
> Test parsing XML returned by EFetch, PubMed database (first test) ...
> Segmentation fault (core dumped)
> "
>
>
> Cheers,
> Paul

Hmm, something amiss with the XML parsing I think, we're
using the Python standard library xml.parsers.expat here.

You said you were using OpenSuse 11.3, and the start of our test
suite reported the following:

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

What version of expat do you have? Try:

$ python
Python 2.6.5 (r265:79063, Apr 16 2010, 13:09:56)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from xml.parsers import expat
>>> print expat.__version__
$Revision: 17640 $

Do you fancy trying gdb to get a stack trace for us?

I've had a quick Google, and the following issue *might* be
related: http://bugs.python.org/issue4877

Peter