The error
Symbol not found:
__ZTVN9OpenBabel20OBRMSDConformerScoreE
means that you did not compile OB with Eigen2 as required to use the
language bindings. See the install information. Several people seem to
run into this problem - I'm not sure how we can make it clearer in the
docs.
- Noel
On 27 July 2011 07:58, Amelie Stein <amelie.st...@ucsf.edu> wrote:
> Hi,
>
> I have compiled openbabel with support for python on Mac OS X, and
> while the compilation is successful (and the command line version,
> obabel, works) the module is not functional because of a missing symbol:
>
> import openbabel
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/home/amelie/software/local_disk/openbabel_2.3/ob_build/
> scripts/pybuild/openbabel.py", line 175, in <module>
> _openbabel = swig_import_helper()
> File "/home/amelie/software/local_disk/openbabel_2.3/ob_build/
> scripts/pybuild/openbabel.py", line 171, in swig_import_helper
> _mod = imp.load_module('_openbabel', fp, pathname, description)
> ImportError: dlopen(/home/amelie/software/local_disk/openbabel_2.3/
> ob_build/scripts/pybuild/_openbabel.so, 2): Symbol not found:
> __ZTVN9OpenBabel20OBRMSDConformerScoreE
> Referenced from: /home/amelie/software/local_disk/openbabel_2.3/
> ob_build/scripts/pybuild/_openbabel.so
> Expected in: flat namespace
> in /home/amelie/software/local_disk/openbabel_2.3/ob_build/scripts/
> pybuild/_openbabel.so
>
>
> I did get the following warning when compiling the module, not sure if
> this has anything to do with the issue:
>
>
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -
> fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -
> pipe -I/home/amelie/software/local_disk/openbabel_2.3/ob_src/scripts/
> python/../../include -I../include -I/System/Library/Frameworks/
> Python.framework/Versions/2.6/include/python2.6 -c /home/amelie/
> software/local_disk/openbabel_2.3/ob_src/scripts/python/openbabel-
> python.cpp -o build/temp.macosx-10.6-universal-2.6/home/amelie/
> software/local_disk/openbabel_2.3/ob_src/scripts/python/openbabel-
> python.o
> cc1plus: warning: command line option "-Wstrict-prototypes" is valid
> for C/ObjC but not for C++
> /home/amelie/software/local_disk/openbabel_2.3/ob_src/scripts/python/
> openbabel-python.cpp: In static member function ‘static Type
> swig::traits_as<Type, swig::value_category>::as(PyObject*, bool) [with
> Type = unsigned int]’:
> /home/amelie/software/local_disk/openbabel_2.3/ob_src/scripts/python/
> openbabel-python.cpp:3596: warning: ‘v’ may be used uninitialized in
> this function
> /home/amelie/software/local_disk/openbabel_2.3/ob_src/scripts/python/
> openbabel-python.cpp: In static member function ‘static Type
> swig::traits_as<Type, swig::value_category>::as(PyObject*, bool) [with
> Type = int]’:
> /home/amelie/software/local_disk/openbabel_2.3/ob_src/scripts/python/
> openbabel-python.cpp:3596: warning: ‘v’ may be used uninitialized in
> this function
>
>
> Also, I had to re-run compilation of _openbabel [the python module] by
> hand as the setting CMAKE_OSX_ARCHITECTURES:STRING=x86_64 seems to be
> ignored in the compilation of the module.
>
> If you have any advice on how to get the module to work I'd appreciate
> it!
> Amelie
>
>
>
>
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