Noel,
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"
Sorry for all the questions!
Here are my commands and the full error info:
cmake ../openbabel-2.3.0 -DCMAKE_INSTALL_PREFIX=~/Tools/OBabel
-DCMAKE_BUILD_TYPE=DEBUG -DEIGEN2_INCLUDE_DIR=/opt/local/include/eigen2
-DPYTHON_BINDINGS=ON
Using included inchi library.
GUI will not be built
-- Python bindings will be compiled
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/sindhikara/Downloads/build
13:26:36 [danpc: ~/Downloads/build]$ make && make install
[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
...
[100%] Building CXX object test/CMakeFiles/test_unitcell.dir/unitcell.o
Linking CXX executable ../bin/test_unitcell
[100%] Built target test_unitcell
running build
running build_py
copying openbabel.py -> /Users/sindhikara/Downloads/build/scripts/pybuild
copying pybel.py -> /Users/sindhikara/Downloads/build/scripts/pybuild
running build_ext
building '_openbabel' extension
gcc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -isysroot
/Developer/SDKs/MacOSX10.5.sdk -DNDEBUG -g -O3 -arch x86_64 -isysroot
/Developer/SDKs/MacOSX10.5.sdk
-I/Users/sindhikara/Downloads/openbabel-2.3.0/scripts/python/../../include
-I../include
-I/Library/Frameworks/EPD64.framework/Versions/7.1/include/python2.7 -c
/Users/sindhikara/Downloads/openbabel-2.3.0/scripts/python/openbabel-python.cpp
-o
build/temp.macosx-10.5-x86_64-2.7/Users/sindhikara/Downloads/openbabel-2.3.0/scripts/python/openbabel-python.o
cc1plus: error: unrecognized command line option "-arch"
cc1plus: error: unrecognized command line option "-arch"
error: command 'gcc' failed with exit status 1
make[2]: *** [scripts/CMakeFiles/_openbabel] Error 1
make[1]: *** [scripts/CMakeFiles/_openbabel.dir/all] Error 2
make: *** [all] Error 2
On Tue, Sep 6, 2011 at 9:26 PM, Noel O'Boyle <[email protected]> wrote:
> Well, that's the reason right there. You have several Open Babel
> installations, and there is interference. My advice is to delete all
> of your Open Babel installations, including related Python files. Then
> install the whole thing locally (including the Python bindings), set
> your environment variables appropriately, and then test "obabel -H
> pdb".
>
> - Noel
>
> On 6 September 2011 11:22, Daniel Sindhikara <[email protected]> wrote:
> > Yes it recognizes it, when I check the binary in my unzip directory,
> > however, it does not.
> >
> > 19:21:35 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ obabel -H pdb
> > Protein Data Bank format
> > Read Options e.g. -as
> > s Output single bonds only
> > b Disable bonding entirely
> > c Ignore CONECT records
> >
> >
> > Specification at: http://www.wwpdb.org/docs.html
> > 19:21:39 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ ./obabel -H pdb
> > Format type: was not recognized
> >
> >
> > On Tue, Sep 6, 2011 at 7:07 PM, Noel O'Boyle <[email protected]>
> wrote:
> >>
> >> Does "obabel -H pdb" show the PDB format?
> >>
> >> On 6 September 2011 07:16, Daniel Sindhikara <[email protected]>
> wrote:
> >> > Hello,
> >> > After a long hiatus I got back on this project. After following the
> >> > instructions I successfully installed openbabel/pybel.
> >> > However, when I tried testing the program I got a funny error, "pdb is
> >> > not a
> >> > recognised OpenBabel format".
> >> >
> >> > Enthought Python Distribution -- www.enthought.com
> >> > Version: 7.1-1 (64-bit)
> >> >
> >> > Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul 3 2011, 15:56:02)
> >> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin
> >> > Type "packages", "demo" or "enthought" for more information.
> >> >>>> import pybel as pb
> >> >>>> testmolecule = pb.readfile("pdb","mai.pdb").next()
> >> > Traceback (most recent call last):
> >> > File "<stdin>", line 1, in <module>
> >> > File
> >> >
> >> >
> "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
> >> > line 90, in readfile
> >> > raise ValueError("%s is not a recognised OpenBabel format" %
> format)
> >> > ValueError: pdb is not a recognised OpenBabel format
> >> >
> >> >
> >> > Further, checking the formats variable:
> >> >>>> pb.informats
> >> > {}
> >> >
> >> > It was empty.
> >> > Any clues into why this would happen?
> >> >
> >> > Thanks in advance!
> >> > -Dan
> >> >
> >> >
> >> > --
> >> > Dr. Daniel J. Sindhikara
> >> > Institute for Molecular Science
> >> > E-mail: [email protected]
> >> > Website: http://sites.google.com/site/dansindhikara/
> >> > --
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------------
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> >> > _______________________________________________
> >> > OpenBabel-scripting mailing list
> >> > [email protected]
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >> >
> >> >
> >
> >
> >
> > --
> > 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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