[BioPython] Re: <Numeric/arrayobject.h>

[Brad Chapman]

Hi Yosep;

> I just downloaded your biopython package and now am trying to install it.
> However, I get the following message.
> 
> Bio/KDTree/_KDTree.swig.C:544: Numeric/arrayobject.h: No such
> file or directory
> 
> I have searched through my machine to look for the arrayobject.h file.  I
> was wondering if the file belongs to some other packages, or dependecies.
> Any would be great.  Thank you very much!

This file belongs to the Numeric package. You have two choices:

1. Install Numeric -- Installation instructions for this are available
in section 3.2 of the Biopython installation docs:

http://www.biopython.org/docs/install/Installation.html

If you are on an RPM-type system, you'll need to make sure you
install the "devel" RPMs, which include the header files.

2. Comment out KDTree in the setup.py file (which will not install
it, but everything else should be fine):

    #Extension('Bio.KDTree._KDTreecmodule',
    #          ["Bio/KDTree/_KDTree.C", 
    #           "Bio/KDTree/_KDTree.swig.C"],
    #          libraries=["stdc++"]
    #          ),

Hope this helps.
Brad