[BioPython] Re: biopython install problems

[Jakob Fredslund]

Brad Chapman wrote:
> Hi Jacob;
> [Copying to the Biopython list]
> 
> 
>>I'm following the instructions at
>>
>>http://www.biopython.org/docs/install/Installation.html
>>
>>python setup.py install --home=~/usr
>>
>>to install the package under my ~/usr directory, and it works fine (the 
>>package is installed in ~/usr/lib/python).
>>
>>I do the exact same thing with the Numeric package and it does put a 
>>directory called Numeric (along with a Numeric.pth file) where I 
>>expected, but it also puts some other files in ~/usr/include/python.
>>
>>And when I try to import this package, I get
>>
>>Python 2.3.2 (#1, Nov 13 2003, 20:02:35)
>>[GCC 3.3.1] on linux2
>>Type "help", "copyright", "credits" or "license" for more information.
>>
>>>>>import mx
>>>>>from Numeric import *
>>
>>Traceback (most recent call last):
>>  File "<stdin>", line 1, in ?
>>ImportError: No module named Numeric
>>
>>When I look in the ~/usr/lib/python/Numeric directory, I find no 
>>__init__.py file as under ~/usr/lib/python/mx. Does that have anything 
>>to do with the problem, and do you have other suggestions?
> 
> 
> Yes, the problem is that Numeric uses that Numeric.pth file to
> basically change the sys.path to include it's directory for
> importing. The problem is, that *.pth files only work in the
> "official" site-packages directory (/usr/local/lib/python2.3/site-packages 
> type places).
> 
> The fix, as you mention, is just to add an __init__.py to the
> Numeric directory to make it executable ('touch __init__.py' in that
> directory works file). Then if ~/usr/lib/Numeric is in your
> PYTHONPATH, everything should work smoothly:
> 
> 
>>>>import Numeric
>>>>Numeric.__file__
> 
> '/usr/home/chapmanb/usr/lib/python/Numeric/__init__.py'
> 
> 
> Hope this makes sense and sorry about the confusion.
> Brad


Hi Brad,

Yup, that solved the problem. Thanks-a-many!

jakob


-- 

Jakob Fredslund, PhD.
Assistant Professor
Bioinformatics Research Center
University of Aarhus
Denmark