[BioPython] non root having problem to install biopython 1.40

[WONG Hua]

I am trying to install the new version of biopython 1.40

I am surprised to see that the "Numeric" tweaks I did on the setup.py doesn't seems to work :(

Here is the line:

NUMPY_EXTENSIONS = [
    Extension('Bio.Cluster.cluster',
              ['Bio/Cluster/clustermodule.c',
               'Bio/Cluster/cluster.c',
               'Bio/Cluster/ranlib.c',
               'Bio/Cluster/com.c',
               'Bio/Cluster/linpack.c'],
              include_dirs=["Bio/Cluster","users/invites/wong/module/include/python2.3/Numeric"]
              ),

And the error:

running build_ext
building 'Bio.Cluster.cluster' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -D_GNU_SOURCE -fPIC -fPIC -IBio/Cluster -Iusers/invites/wong/module/include/python2.3 -I/usr/include/python2.3 -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-2.3/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:2:33: Numeric/arrayobject.h: No such file or directory

...followed by various Bio/Cluster/clustermodule.c: errors...


Although I modified this line, it still can't find Numeric.
Worst is that in fact I don't even need or use the cluster and trees feature...
I am mostly interested in the Bio.PDB part.
Numeric is properly installed (not in root directories, but it is installed). "Import Numeric" works fine when running Python.

Is there a way I can shortcircuit this?

Else, what have I forgot to do in order to point where Numeric is?

Thanks

Wong Hua

#####################################################################
6  Notes for installing with non-administrator permissions
# That's exactly me

Building some C modules, such as Bio.Cluster require that the Numeric include files (normally installed in your_dir/include/python/Numeric) be available. If the compiler can't find these directories you'll normally get an error like:

Bio/Cluster/clustermodule.c:2: Numeric/arrayobject.h: No such file or directory
    

Followed by a long messy list of syntax errors. ##Exact

To fix this, you'll have to edit the setup.py file to let it know where the include directories are located. Look for the line in setup.py that looks like:

    include_dirs=["Bio/Cluster"]
    

and adjust it so that it includes the include directory where the numeric libraries were installed:

    include_dirs=["Bio/Cluster", "your_dir/include/python"]
    

Then you should be able to install everything happily.
# No happy endings :(