[BioPython] biopython installation problem (cont.)

[Karin Lagesen]

On Thu, Sep 18, 2003 at 12:14:33PM +0200, Peter Slickers wrote:

[snipped sys.path stuff]
 
> Please check if directory '/site/python_packages' is in the list.

It is.

> Second:
> 
> Within directory '/site/python_packages' you need a '*.pth' file.
> If this file is missing, python will not search any subdirectories
> of '/site/python_packages'. This file can be easily create
> by the following command:
> 
> 
> cd /site/python_packages
> find . -type d -maxdepth 1 | awk '{ if($0 !~ /CVS/) {print substr($0,3)}}' 
> > packages.pth
> 
> cat packages.pth
> 
> As you can see the path file just contains the names of all
> subdirectories (since I assume that every subdirectory contains
> a python package.) Please recreate 'packages.pth' each time
> you install in new package in '/site/python_packages'.

Hmm... I created this file, however, the result of installing both
Numeric and the mxTextTools package there is this:


uracil:13:08> ls /site/python_packages/*/*/*
/site/python_packages/lib/python/Numeric.pth

/site/python_packages/include/python/Numeric:
arrayobject.h  f2c.h  ranlib.h  ufuncobject.h

/site/python_packages/lib/python/Numeric:
ArrayPrinter.py    MLab.pyc       RNG              lapack_lite.so
ArrayPrinter.pyc   Matrix.py      RandomArray.py   multiarray.so
FFT                Matrix.pyc     RandomArray.pyc  numeric_version.py
LinearAlgebra.py   Numeric.py     UserArray.py     numeric_version.pyc
LinearAlgebra.pyc  Numeric.pyc    UserArray.pyc    ranlib.so
MA                 Precision.py   _numpy.so        umath.so
MLab.py            Precision.pyc  arrayfns.so

/site/python_packages/lib/python/mx:
BeeBase    Doc      Log.pyc  NewBuiltins.py   Proxy  TextTools
__init__.pyc
COPYRIGHT  LICENSE  Log.pyo  NewBuiltins.pyc  Queue  Tools
__init__.pyo
DateTime   Log.py   Misc     NewBuiltins.pyo  Stack  __init__.py
uracil:13:09> 

I.e, in /site/python_packages I don't have either mx nor Numeric.

I tried instead setting PYTHONPATH to
/site/python_packages/lib/python,
and then I could import mx but not Numeric.

Curiouser and curiouser...

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at labmed.uio.no