[BioPython] Compiling from CVS on OS X

[Michiel De Hoon]

> The problem was that the system wasn't finding the `Numeric/ 
> arrayobject.h` file for inclusion. I "fixed" it by editing the  
> setup.py file and adding '/opt/local/include/python2.4' to the  
> include_dirs param on line 474 so it would pick up the files in my  
> python install (that's just where numeric header was installed from  
> macports).

By default, the directory containing the Python include files is searched for
header files during compilation. If you install Numerical Python from source,
it will put its header files in the same location, and no editing of setup.py
is needed.

If, on the other hand, you use a precompiled package, it may be installed in
a different place. For some reason, the package from macports puts the
Numerical Python header files in a non-standard place, which is why they
could not be found. Apparently macports assumes that Python is installed in
/opt/local/; this may very well be the installation directory used by
macports for Python itself.

In other words, macports uses a non-standard directory, there is no way for
Python to know about it, so the header files cannot be found during
compilation.

--Michiel. 


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032



-----Original Message-----
From: biopython-bounces at lists.open-bio.org on behalf of Steve Lianoglou
Sent: Thu 11/8/2007 2:32 PM
To: BioPython at lists.open-bio.org
Subject: [BioPython] Compiling from CVS on OS X
 
Hi all,

I was having problems compiling biopython from source, specifically  
getting the Bio/Cluster/clustermodule.c file to compile well.

The problem was that the system wasn't finding the `Numeric/ 
arrayobject.h` file for inclusion. I "fixed" it by editing the  
setup.py file and adding '/opt/local/include/python2.4' to the  
include_dirs param on line 474 so it would pick up the files in my  
python install (that's just where numeric header was installed from  
macports).

Is this the expected way to achieve this, or is there some envi-var,  
or site.cfg to tweak to do this correctly (or is my python install  
whacky from the get go?)

FWIW I'm using python 2.4 installed via macports.

Thanks,
-steve
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