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

[Paul.Czodrowski at merck.de]

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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