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

[Peter Cock]

On Wed, May 4, 2011 at 9:47 AM,  <Paul.Czodrowski at merck.de> wrote:
> Dear Peter,
>
>>
>> Does NumPy work properly? At the very least, if you run python
>> does "import numpy" work or give an error? What happens if you
>> try and do this:
>>
>> $ python
>> >>> import numpy
>> >>> numpy.get_include()
>> '/usr/local/lib/python2.6/site-packages/numpy/core/include'
>>
>> (That's the output on one of our Linux machines)
>
> We have the same output:
>>>>
>>>>
>>>> numpy.get_include()
> '/usr/lib/python2.6/site-packages/numpy/core/include'
>
>
>>
>> If that doesn't work, perhaps your PYTHONPATH needs setting.
>> How/where did you install NumPy? e.g. python setup.py --prefix=$HOME
>
> The /usr/lib python is installed via the yast OpenSuse.
> But it seems to me that this installation did not work properly,
> since, there are only 2 files in the directory
> " /usr/lib/python2.6/site-packages/numpy/core/include/numpy/":
> - ufunc_api.txt
> - multiarray_api.txt
>
> However, we have another installation of NumPy which is located here:
> "/SW/python/lib/python2.6/site-packages/lib/python2.6/site-packages/numpy"
>
> And yes, there is a mix-up of the directories... :)

I think that explains why the Biopython install didn't work originally,
it found the broken NumPy under /usr/lib rather than your good one
installed under /SW/

You might want to try and remove the broken NumPy, as it may
cause you problems installing other python libraries.

>
> By appropiately setting the PYTHONPATH, it works properly.
>

OK, good.

>> >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

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