I'm running OSX 10.6.8, and I'm having trouble installing openbabel with
python bindings. Any help would be appreciated
Below are the results of the build.
running build_py
creating build/lib.macosx-10.3-fat-2.6
copying openbabel.py -> build/lib.macosx-10.3-fat-2.6
copying pybel.py -> build/lib.macosx-10.3-fat-2.6
running build_ext
building '_openbabel' extension
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
-O2 -DNDEBUG -g -O3 -I/usr/local/include/eigen2
-I/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../include
-I../include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.cpp
-o
build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
In file included from /usr/include/architecture/i386/math.h:626,
from /usr/include/math.h:28,
from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/pyport.h:235,
from
/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:58,
from
/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.cpp:150:
/usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
Intel with Mac OS X Deployment Target < 10.4 is invalid.
c++ -arch ppc -arch i386 -g -bundle -undefined dynamic_lookup
-I/usr/local/include/eigen2
build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
-L/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib
-L/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64
-L../lib -lopenbabel -o build/lib.macosx-10.3-fat-2.6/_openbabel.so
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib'
following -L not found
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64'
following -L not found
ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
file format which is not the architecture being linked (ppc)
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib'
following -L not found
ld: warning: directory
'/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/../../lib64'
following -L not found
ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
file format which is not the architecture being linked (i386)
running install_lib
copying build/lib.macosx-10.3-fat-2.6/_openbabel.so ->
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
copying build/lib.macosx-10.3-fat-2.6/openbabel.py ->
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
copying build/lib.macosx-10.3-fat-2.6/pybel.py ->
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
byte-compiling
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py
to openbabel.pyc
byte-compiling
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pybel.py
to pybel.pyc
running install_egg_info
Writing
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel-1.7-py2.6.egg-info
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ python
Python 2.6.6 (r266:84374, Aug 31 2010, 11:00:51)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pybel.py",
line 16, in <module>
import openbabel as ob
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py",
line 65, in <module>
_openbabel = swig_import_helper()
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/openbabel.py",
line 61, in swig_import_helper
_mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError:
dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/_openbabel.so,
2): Symbol not found: __ZN9OpenBabel8OBPlugin7DisplayERSsPKcS3_
Referenced from:
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/_openbabel.so
Expected in: dynamic lookup
Here's my attempt to link
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ file
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
Mach-O 64-bit dynamically linked shared library x86_64
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$ otool -L
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
/Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.4.dylib
(compatibility version 4.0.0, current version 4.0.1)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 125.2.11)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
1.2.3)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
version 7.9.0)
Pierre-Bhoorasinghs-MacBook-Pro:build PierreB$
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