Dear Edith,

You have overwritten the python that comes with the system with that from a mgltools install. That particular install is 32 bit, your system is 64 bit.
Look in your shell configuration file (.bashrc most probably) for something like export PYTHON_PATH and comment it temporally.
Rerun the instalation http://www.pymolwiki.org/index.php/Linux_Install#Generic_Linux

Best regards,
Marius

On Mon, Mar 21, 2011 at 5:04 PM, Edith Gincel <edith.gincel@parisdescartes.fr> wrote:
I am working on Linux   2.6.18-8.el5  x86_64 GNU/Linux

I had problem with the 0,99 version of pymol (it was working but with
very strange behaviour thant no one could explain), so I am trying to
install the 1.3r2 version

I download it and then followed the instructions :
I untarred and dezipped and then :
python setup.py build install

I get this error message which I don't understand at all. Could someone
help me please?

running build
running build_py
package init file 'modules/web/javascript/__init__.py' not found (or not
a regular file)
package init file 'modules/web/javascript/__init__.py' not found (or not
a regular file)
running build_ext
building 'pymol._cmd' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
-D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
-Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2
-Imodules/cealign/src -Imodules/cealign/src/tnt
-I/home/edith/logiciels/mgltools_i86Linux2_1.5.4/include/python2.5 -c
modules/cealign/src/ccealignmodule.cpp -o
build/temp.linux-x86_64-2.5/modules/cealign/src/ccealignmodule.o
-ffast-math -funroll-loops -O3
cc1plus: attention : l'option de la ligne de commande
"-Wstrict-prototypes" est valide pour Ada/C/ObjC mais pas pour C++
Dans le fichier inclus à partir
de /home/edith/logiciels/mgltools_i86Linux2_1.5.4/include/python2.5/Python.h:57,
         à partir de layer0/os_python.h:30,
         à partir de modules/cealign/src/ccealignmodule.H:57,
         à partir de modules/cealign/src/ccealignmodule.cpp:32:
/home/edith/logiciels/mgltools_i86Linux2_1.5.4/include/python2.5/pyport.h:734:2: erreur: #error "LONG_BIT definition appears wrong for platform (bad gcc/glibc config?)."
modules/cealign/src/ccealignmodule.cpp: In function ‘PyObject*
findBest(cePoint*, cePoint*, afp**, int, int, int)’:
modules/cealign/src/ccealignmodule.cpp:553: attention : comparaison
entre des expressions entières signée et non signée
modules/cealign/src/ccealignmodule.cpp: In function
‘TNT::Array2D<double> transpose(const TNT::Array2D<double>&)’:
modules/cealign/src/ccealignmodule.cpp:628: attention : comparaison
entre des expressions entières signée et non signée
modules/cealign/src/ccealignmodule.cpp:629: attention : comparaison
entre des expressions entières signée et non signée
error: command 'gcc' failed with exit status 1



------------------------------------------------------------------------------
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-sfd2d
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net