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

Wed May 4 13:36:42 UTC 2011

 Dr. Paul Czodrowski                                                       

 Merck KGaA                                                                

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biopython-bounces at lists.open-bio.org wrote on 04.05.2011 15:17:21:

> 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 $

$Revision: 1.1 $

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

How shall I understand your question? Shall I use the gnu debugger in order
to get some debuggable output?

What is the worst case scenario related to biopython, i.e. could it
ultimately lead to any errors/instabilities?

Cheers,
Paul

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