Re: [OpenBabel-scripting] OSX 6.8 Openbabel python bindings

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Hello Pierre,

I've been doing some work on the Python bindings getting them to work
on MacOSX 64-bit. Please try our development code (trunk). You will
need to recreate the bindings using -DRUN_SWIG=TRUE with a recent
version of Swig (>=2.0.1) on the path.

You should also "grep -i python CMakeCache.txt" and check that all of
the Python related variables are pointing to the same desired Python
installation. If not, you can edit CMakeCache.txt directly or else
specify the correct values when calling CMake.

- Noel

On 10 November 2011 20:58, pierrelb <pie...@gm...> wrote:
> 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$
>
>
>
> --
> View this message in context: http://forums.openbabel.org/OSX-6-8-Openbabel-python-bindings-tp4027870p4027870.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
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