[chimera-dev] Numpy multiarray import problem

[Mateusz Dobrychłop]

Hi Tom,

Thank you for your quick reply.

I tried reinstalling Chimera and installing BioPython using Chimera's
Python again, but this doesn't solve the problem. Because of that, I
suppose BioPython compiles using numpy 1.8 installed in my system, not the
one 1.7 version that comes with Chimera. Could you please tell me how I can
make sure that BioPython is compiled using Chimera's numpy?

Thank you for your time,
Mateusz


2013/12/4 Tom Goddard <goddard at sonic.net>

> Hi Mateusz,
>
>   I think your error message means that the BioPython _CKDTree module was
> compiled against numpy 1.8 (API version 8) instead of numpy 1.7 (API
> version 7) that is used in Chimera.  Numpy 1.8 was released Oct 30, 2013.
>  If you installed BioPython from source code using Chimera's Python then it
> should use the Chimera numpy 1.7.   So either you didn't compile BioPython
> using the Chimera numpy (maybe you installed a precompiled version), or you
> compiled it and it found numpy 1.8 somewhere outside of Chimera on your
> computer.  To make things work you will need to make sure BioPython is
> compiled using the Chimera numpy, specifically using its numpy header files
> (in site-packages/numpy/core/include).  It will not work to install numpy
> 1.8 in Chimera because that will break all the Chimera modules that were
> compiled with numpy 1.7.
>
> Tom
>
>
>
> On Dec 4, 2013, at 7:18 AM, Mateusz Dobrychłop  wrote:
>
> Dear Chimera Team,
>
> I am working on my own Chimera Extension. After succesful installation of
> BioPython using Chimera's Python copy, I've encountered another BioPython -
> related problem, that is also related to the numpy library.
>
> I'm trying to import something from the BioPython library, and BioPython
> is trying to import from numpy. I recieve a following error:
>
> RuntimeError: module compiled against API version 8 but this version of
> numpy is 7
>
> ...
>
>   File "/home/mateusz/pyry4.4/Modules/Trans/ComponentRepresentation.py",
> line 6, in <module>
>     from Bio.PDB                            import PDBParser, PDBIO,
> NeighborSearch
>   File
> "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/PDB/NeighborSearch.py",
> line 10, in <module>
>     from Bio.KDTree import KDTree
>   File
> "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/__init__.py",
> line 10, in <module>
>     from KDTree import KDTree
>   File
> "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/KDTree.py",
> line 20, in <module>
>     from Bio.KDTree import _CKDTree
> <type 'exceptions.ImportError'>: numpy.core.multiarray failed to import
>
> I tried to install numpy the same way I installed BioPython (using
> Chimera's Python copy), but this does not solve the problem. I also tried
> to import numpy.core.multiarray directly in Chimera's IDLE and it did
> import.
>
> I'm using Chimera 1.8.1 on Ubuntu 12.10 (64 - bit).
>
> Is there anything I can do to make it work?
>
> Best wishes,
> Mateusz
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20131205/b25deb47/attachment.html>