I had some experience in the past with similar issues.
From the g++ command it shows that it tries to compile a bundle
version of the python binding (a library that is both both ppc and
i386) but your version of libopenbabel.dylib seems not to be of the
same architecture.
You can check the architecture and dependences of you openbabel
installation using:
file /Users/guhar/src/openbabel/lib/libopenbabel.dylib
otool -L /Users/guhar/src/openbabel/lib/libopenbabel.dylib
Now, you also need to test your python version and see what
architecture python was compiled for. Those should be identical
otherwise the dylib files will not be compatible.
On May 8, 2011, at 2:43 PM, Noel O'Boyle wrote:
> And I see that it reran SWIG for you, so that should work fine. The
> last line of the compile seem suspicious though:
>
> g++ -Wl,-F. -bundle -undefined dynamic_lookup -arch i386 -arch ppc
> build/temp.macosx-10.5-i386-2.5/Users/guhar/src/openbabel/scripts/
> python/openbabel-python.o
> -L/Users/guhar/src/openbabel/scripts/python/../../lib
> -L/Users/guhar/src/openbabel/scripts/python/../../lib64 -L../lib
> -lopenbabel -o /Users/guhar/src/openbabel/scripts/pybuild/
> _openbabel.so
>
> ld warning: in /Users/guhar/src/openbabel/lib/libopenbabel.dylib, file
> is not of required architecture
>
> Hopefully Geoff knows what's going on...
>
> - Noel
>
> On 8 May 2011 13:31, Rajarshi Guha <[email protected]> wrote:
>> Which is the cmake configure file?
>>
>> I ran the following cmake command
>>
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/openbabel -
>> DPYTHON_BINDINGS=ON
>> ~/src/openbabel
>>
>> and the output of make -j 4 is at https://gist.github.com/961340
>>
>> It looks like the error is due to some issue with the OB dylib
>> generation
>>
>> On Sat, May 7, 2011 at 6:36 AM, Noel O'Boyle <[email protected]>
>> wrote:
>>> Can you show the cmake configure you used? (Did you compile the
>>> Python
>>> bindings? You might be trying to use old bindings against new shared
>>> libraries.)
>>>
>>> - Noel
>>>
>>> On 6 May 2011 23:48, Rajarshi Guha <[email protected]> wrote:
>>>> Hi, I just updated my OB repo to the latest SVN. When I did:
>>>>
>>>> make clean
>>>> make -j 3
>>>> make install
>>>>
>>>> and then tried the openbabel module in Python (OS X 10.6) I get the
>>>> following error:
>>>>
>>>> [GCC 4.0.1 (Apple Inc. build 5465)] on darwin
>>>> Type "help", "copyright", "credits" or "license" for more
>>>> information.
>>>>>>> import openbabel as ob
>>>> Traceback (most recent call last):
>>>> File "<stdin>", line 1, in <module>
>>>> File "/Library/Python/2.5/site-packages/openbabel.py", line 38,
>>>> in <module>
>>>> import _openbabel
>>>> ImportError: dlopen(/Library/Python/2.5/site-packages/
>>>> _openbabel.so,
>>>> 2): Symbol not found: __ZN9OpenBabel10OBUnitCell13GetCellMatrixEv
>>>> Referenced from: /Library/Python/2.5/site-packages/_openbabel.so
>>>> Expected in: /usr/local/openbabel/lib/libopenbabel.4.dylib
>>>>
>>>>
>>>> Has anybody seen this before?
>>>>
>>>> --
>>>> Rajarshi Guha
>>>> NIH Chemical Genomics Center
>>>>
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>>>
>>
>>
>>
>> --
>> Rajarshi Guha
>> NIH Chemical Genomics Center
>>
>
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