[Biopython] expat and biopython 1.58 problem on linux x64

[Peter Cock]

On Fri, Oct 28, 2011 at 2:09 PM, Jaime Tovar <jmtc21 at bath.ac.uk> wrote:
> Got the tarball for latest,
>
> but:
>
> ...
> ~/tmp/biop/biopython-biopython-59f9cbd/Tests> python test_Entrez.py
> 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
>
> Can we try to find where exactly is the problem?
>
> Thanks for the help.
> J

OK, so it doesn't look like the problem with closed handles,
http://bugs.python.org/issue4877

Although to be sure please try the example in my last email,

from Bio import Entrez
handle = open("NEWS")
handle.close()
Entrez.read(handle)

(You can use any file that exists).

Beyond that I only have questions rather than answers for now.
My guess is something is broken on your system with conflicting
versions of expat, see for example:

http://www.dscpl.com.au/wiki/ModPython/Articles/ExpatCausingApacheCrash

What does this give you, and does it match expat 2.0.1 which you
said earlier was installed?

import pyexpat
print pyexpat.version_info

Can you try to get a strack trace?

Alternatively, you could disable individual tests which trigger
the segmentation fault one by one and then we can attempt to
spot any commonalities. e.g. The segmentation fault is from:
"Test parsing XML returned by EFetch, PubMed database (first test)"
which is method test_pubmed1, rename it to xtest_test_pubmed1
(or anything that doesn't start test_*) and it will be skipped.

Peter