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

[João Rodrigues]

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
do2to3.py   setup.py

The file Peter was talking about should be there.

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



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=$HOME works fine now.
> > >
> > > Should the segmentation fault still be considered?
> >
> > Yes please. I assume it still breaks? Can you try changing to the
> > Tests subdirectory from the Biopython source, and doing:
> >
> > python test_Entrez.py
>
> I cannot find the src directory.
> Here is my Bio/ directory:
> "
> Affy
> Align
> AlignIO
> Alphabet
> Application
> Blast
> CAPS
> Clustalw
> Cluster
> Compass
> cpairwise2.so
> Crystal
> Data
> DocSQL.py
> DocSQL.pyc
> Emboss
> Entrez
> ExPASy
> File.py
> File.pyc
> FSSP
> GA
> GenBank
> Geo
> Graphics
> HMM
> HotRand.py
> HotRand.pyc
> Index.py
> Index.pyc
> __init__.py
> __init__.pyc
> InterPro
> KDTree
> KEGG
> kNN.py
> kNN.pyc
> LogisticRegression.py
> LogisticRegression.pyc
> MarkovModel.py
> MarkovModel.pyc
> MaxEntropy.py
> MaxEntropy.pyc
> Medline
> Motif
> NaiveBayes.py
> NaiveBayes.pyc
> NeuralNetwork
> Nexus
> NMR
> pairwise2.py
> pairwise2.pyc
> Parsers
> ParserSupport.py
> ParserSupport.pyc
> Pathway
> PDB
> Phylo
> PopGen
> _py3k.py
> _py3k.pyc
> Restriction
> SCOP
> Search.py
> Search.pyc
> SeqFeature.py
> SeqFeature.pyc
> SeqIO
> Seq.py
> Seq.pyc
> SeqRecord.py
> SeqRecord.pyc
> Sequencing
> SeqUtils
> Statistics
> SubsMat
> SVDSuperimposer
> SwissProt
> triefind.py
> triefind.pyc
> trie.so
> UniGene
> Wise
> "
>
> BTW, python setup.py install --prefix=$HOME did not break.
>
> Thanks & Ceers,
> Pauö
>
> >
> > 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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