OSX 6.8 Openbabel python bindings

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OSX 6.8 Openbabel python bindings

pierrelb
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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Re: OSX 6.8 Openbabel python bindings

Geoffrey Hutchison
> I'm running OSX 10.6.8, and I'm having trouble installing openbabel with
> python bindings. Any help would be appreciated

So there are two problems. First, your python version seems to be trying to build for Mac OS X 10.3:

> build/temp.macosx-10.3-fat-2.6/Users/PierreB/Downloads/openbabel-2.3.1/scripts/python/openbabel-python.o
...
> /usr/include/AvailabilityMacros.h:108:14: warning: #warning Building for
> Intel with Mac OS X Deployment Target < 10.4 is invalid.

Second, it looks like your libopenbabel.dylib is not built "fat":

> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (ppc)
...
> ld: warning: in ../lib/libopenbabel.dylib, file was built for unsupported
> file format which is not the architecture being linked (i386)
...
> /Users/PierreB/Downloads/openbabel-2.3.1/build/lib/libopenbabel.dylib:
> Mach-O 64-bit dynamically linked shared library x86_64

So you should probably find the "native" python, which should be /usr/bin/python-2.6 which should build for 10.6 (and handle x86_64) and consider changing the architectures for CMake / OSX for libopenbabel. (Edit the CMakeCache.txt   for CMAKE_OSX_ARCHITECTURES:STRING=…)

Hope that helps,
-Geoff
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Re: OSX 6.8 Openbabel python bindings

Noel O'Boyle
Administrator
In reply to this post by pierrelb
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 <[hidden email]> 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.
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
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