OK sorry for taking so much time. I did get it to work. Basically I had to
get gcc 4.6 off my system. After that it worked (with gcc 4.5.3)
Thanks all again for the help.
-Dan
On Fri, Sep 9, 2011 at 3:50 PM, Daniel Sindhikara <[email protected]>wrote:
> Geoff,
> That's basically the problem, but reversed. It does find the correct
> Enthought version of python, but for some reason Enthought chose to use gcc
> 4.0.1 to compile. This is getting difficult now. I don't think I can change
> the compiler in Enthought and recompile. Do the two versions of gcc need to
> be compatible? I can't find where this "-arch" option is to change it. I
> can change the specs for cmake to point to gcc4.0.1 but I end up with other
> problems.
> e.g.:
> [ 49%] Building CXX object src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.o
> Linking CXX shared module ../../lib/cdxmlformat.so
> ld: warning: in /opt/local/lib/libxml2.dylib, file was built for
> unsupported file format which is not the architecture being linked (i386)
> Undefined symbols:
> "_xmlResetError", referenced from:
> OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
> OpenBabel::OBBase*)in xml.o
> "_xmlOutputBufferFlush", referenced from:
> ....
>
>
>
>
>
>
> On Wed, Sep 7, 2011 at 5:03 PM, Geoff Hutchison
> <[email protected]>wrote:
>
>> Thanks for the help. I deleted all versions of Openbabel then started
>> from scratch. I now get a new error (after "100%" installing). I believe
>> there is some incompatibility with my version of gcc (4.6). I'm not sure,
>> however which version I should use, and which file to modify to point to a
>> different gcc.
>> The error is: cc1plus: error: unrecognized command line option "-arch"
>>
>>
>> Well, I don't know much about the Enthought version of python, but that's
>> an issue with a non-Apple version of gcc when compiling the Python
>> extension. I'd look at the CMakeCache.txt file in your build directory and
>> see:
>>
>> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2.7
>>
>> My guess is that it's not the python you expect from Enthought, but the
>> rest of Open Babel has been compiled by the GCC provided by either Enthought
>> or MacPorts.
>>
>> That's the confusion.
>>
>> -Geoff
>>
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: [email protected]
> Website: http://sites.google.com/site/dansindhikara/
> --
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: [email protected]
Website: http://sites.google.com/site/dansindhikara/
--
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