On 25 January 2011 13:31, Ken Smith <k.w.sm...@qub.ac.uk> wrote: > Hi Noel > > I didn't have this problem on 7 December on my Linux system. However, I did > the necessary installations (SWIG 2 and PCRE to install SWIG) and it > installed OK with the following caveats: > > * Everything compiled OK, but at the installation stage I had to setup a > symbolic link in one of the specified include directories to my Eigen > Include directory (which was installed in /usr/local/include/eigen2, but not > picked up) to get the _openbabel extension to compile.
The location of the Eigen include was not being passed to the Python compile. This has already been fixed in the development version...so I think you are using the release, right? In which case, you shouldn't have needed to run SWIG in the first place....hmmm.... > * As before on my Mac, I have to explicitly setup my PYTHONPATH to use the > openbabel bindings. A minor detail, but I can live with that... > E.g. > > export > PYTHONPATH=$PYTHONPATH:/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages > Cheers, > > Ken > > P.S. For reference, below is the failed make install output before my > symlink setup. > > > sudo make install > [ 21%] Built target openbabel > [ 23%] Built target plugin_charges > [ 25%] Built target plugin_descriptors > [ 25%] Built target plugin_fingerprints > [ 27%] Built target plugin_forcefields > [ 31%] Built target plugin_ops > [ 44%] Built target inchi > [ 44%] Built target APIInterface > [ 44%] Built target CSRformat > [ 44%] Built target MCDLformat > [ 45%] Built target MNAformat > [ 45%] Built target PQSformat > [ 46%] Built target acrformat > [ 46%] Built target adfformat > [ 46%] Built target alchemyformat > [ 47%] Built target amberformat > [ 47%] Built target balstformat > [ 48%] Built target bgfformat > [ 48%] Built target boxformat > [ 48%] Built target cacaoformat > [ 49%] Built target cacheformat > [ 49%] Built target carformat > [ 49%] Built target castepformat > [ 50%] Built target cccformat > [ 50%] Built target cdxmlformat > [ 51%] Built target chem3dformat > [ 51%] Built target chemdrawcdx > [ 51%] Built target chemdrawct > [ 52%] Built target chemkinformat > [ 52%] Built target chemtoolformat > [ 52%] Built target cifformat > [ 53%] Built target cmlformat > [ 54%] Built target cmlreactformat > [ 54%] Built target copyformat > [ 54%] Built target crkformat > [ 55%] Built target cssrformat > [ 55%] Built target dlpolyformat > [ 55%] Built target dmolformat > [ 56%] Built target fastaformat > [ 56%] Built target fastsearchformat > [ 56%] Built target fchkformat > [ 57%] Built target featformat > [ 57%] Built target fhformat > [ 57%] Built target fhiaimsformat > [ 58%] Built target fingerprintformat > [ 58%] Built target freefracformat > [ 58%] Built target gamessformat > [ 58%] Built target gamessukformat > [ 59%] Built target gausscubeformat > [ 59%] Built target gaussformat > [ 59%] Built target gausszmatformat > [ 60%] Built target ghemicalformat > [ 60%] Built target gromos96format > [ 60%] Built target gulpformat > [ 61%] Built target hinformat > [ 62%] Built target inchiformat > [ 62%] Built target jaguarformat > [ 62%] Built target mdlformat > [ 63%] Built target mmcifformat > [ 63%] Built target mmodformat > [ 63%] Built target mol2format > [ 64%] Built target moldenformat > [ 64%] Built target molproformat > [ 64%] Built target molreport > [ 65%] Built target mopacformat > [ 65%] Built target mpdformat > [ 65%] Built target mpqcformat > [ 66%] Built target msiformat > [ 66%] Built target msmsformat > [ 66%] Built target nulformat > [ 67%] Built target nwchemformat > [ 67%] Built target opendxformat > [ 68%] Built target outformat > [ 68%] Built target pcmodelformat > [ 68%] Built target pdbformat > [ 69%] Built target pdbqtformat > [ 70%] Built target pngformat > [ 70%] Built target povrayformat > [ 70%] Built target pqrformat > [ 71%] Built target pubchem > [ 71%] Built target pwscfformat > [ 72%] Built target qchemformat > [ 72%] Built target reportformat > [ 73%] Built target rsmiformat > [ 73%] Built target rxnformat > [ 73%] Built target shelxformat > [ 74%] Built target smilesformat > [ 74%] Built target svgformat > [ 74%] Built target textformat > [ 75%] Built target thermoformat > [ 75%] Built target tinkerformat > [ 75%] Built target titleformat > [ 76%] Built target turbomoleformat > [ 76%] Built target unichemformat > [ 76%] Built target vaspformat > [ 77%] Built target viewmolformat > [ 77%] Built target xedformat > [ 78%] Built target xmlformat > [ 78%] Built target xyzformat > [ 78%] Built target yasaraformat > [ 79%] Built target zindoformat > [ 79%] Built target babel > [ 79%] Built target obabel > [ 79%] Built target obchiral > [ 80%] Built target obconformer > [ 80%] Built target obenergy > [ 80%] Built target obfit > [ 81%] Built target obgen > [ 81%] Built target obgrep > [ 81%] Built target obminimize > [ 82%] Built target obprobe > [ 82%] Built target obprop > [ 82%] Built target obrotamer > [ 83%] Built target obrotate > [ 83%] Built target obspectrophore > [ 83%] Built target roundtrip > [ 83%] Built target test_align > [ 84%] Built target test_aromatest > [ 84%] Built target test_atom > [ 84%] Built target test_automorphism > [ 85%] Built target test_bond > [ 85%] Built target test_builder > [ 85%] Built target test_canonconsistent > [ 86%] Built target test_canonstable > [ 86%] Built target test_cansmi > [ 86%] Built target test_charge-gasteiger > [ 87%] Built target test_charge-mmff94 > [ 87%] Built target test_cistrans > [ 87%] Built target test_conversion > [ 88%] Built target test_datatest > [ 88%] Built target test_ffgaff > [ 88%] Built target test_ffghemical > [ 89%] Built target test_ffmmff94 > [ 89%] Built target test_ffuff > [ 89%] Built target test_formalcharge > [ 90%] Built target test_format > [ 90%] Built target test_formula > [ 90%] Built target test_graphsym > [ 90%] Built target test_implicitH > [ 91%] Built target test_inchiwrite > [ 91%] Built target test_internalcoord > [ 92%] Built target test_invalidsmarts > [ 92%] Built target test_invalidsmiles > [ 92%] Built target test_isomorphism > [ 93%] Built target test_iterators > [ 93%] Built target test_logp_psa > [ 93%] Built target test_lssr > [ 94%] Built target test_math > [ 94%] Built target test_mol > [ 94%] Built target test_phmodel > [ 95%] Built target test_residue > [ 95%] Built target test_ringtest > [ 95%] Built target test_rotor > [ 96%] Built target test_shuffle > [ 96%] Built target test_smartsparse > [ 96%] Built target test_smartstest > [ 97%] Built target test_smiles > [ 97%] Built target test_smilesmatch > [ 97%] Built target test_spectrophore > [ 98%] Built target test_squareplanar > [ 98%] Built target test_stereo > [ 98%] Built target test_stereoperception > [ 99%] Built target test_tetrahedral > [ 99%] Built target test_tetranonplanar > [ 99%] Built target test_tetraplanar > [100%] Built target test_uniqueid > [100%] Built target test_unitcell > running build > running build_py > copying openbabel.py -> > /Users/kws/Documents/code/openbabel_svn/build/scripts/pybuild > copying pybel.py -> > /Users/kws/Documents/code/openbabel_svn/build/scripts/pybuild > running build_ext > [100%] Built target _openbabel > Install the project... > -- Install configuration: "RelWithDebInfo" > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/babelconfig.h > -- Up-to-date: /usr/local/lib/pkgconfig/openbabel-2.0.pc > -- Up-to-date: /usr/local/lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake > -- Up-to-date: > /usr/local/lib/cmake/openbabel2/OpenBabel2_EXPORTS-relwithdebinfo.cmake > -- Up-to-date: /usr/local/lib/cmake/openbabel2/OpenBabel2Config.cmake > -- Up-to-date: /usr/local/lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake > -- Up-to-date: /usr/local/include/inchi/inchi_api.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/chemdrawcdx.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/alias.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/atom.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/atomclass.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/base.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/bitvec.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/bond.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/bondtyper.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/builder.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/canon.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/chains.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/chargemodel.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/chiral.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/conformersearch.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/data.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/descriptor.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/dlhandler.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/fingerprint.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/forcefield.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/format.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/generic.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/graphsym.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/grid.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/griddata.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/groupcontrib.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/inchiformat.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/internalcoord.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/isomorphism.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/kinetics.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/lineend.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/locale.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/matrix.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/mcdlutil.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/mol.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/molchrg.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/obconversion.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/oberror.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/obiter.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/obmolecformat.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/obutil.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/op.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/optransform.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/parsmart.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/patty.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/phmodel.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/plugin.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/pointgroup.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/query.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/rand.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/reaction.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/residue.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/ring.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/rotamer.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/rotor.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/shared_ptr.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/spectrophore.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/text.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/tokenst.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/typer.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/xml.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/math/align.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/math/erf.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/math/matrix3x3.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/math/spacegroup.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/math/transform3d.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/math/vector3.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/stereo/cistrans.h > -- Up-to-date: > /usr/local/include/openbabel-2.0/openbabel/stereo/squareplanar.h > -- Up-to-date: /usr/local/include/openbabel-2.0/openbabel/stereo/stereo.h > -- Up-to-date: > /usr/local/include/openbabel-2.0/openbabel/stereo/tetrahedral.h > -- Up-to-date: > /usr/local/include/openbabel-2.0/openbabel/stereo/tetranonplanar.h > -- Up-to-date: > /usr/local/include/openbabel-2.0/openbabel/stereo/tetraplanar.h > -- Up-to-date: /usr/local/share/openbabel/2.3.0/aromatic.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/atomtyp.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/bondtyp.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/element.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/fragments.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/gaff.dat > -- Up-to-date: /usr/local/share/openbabel/2.3.0/gaff.prm > -- Up-to-date: /usr/local/share/openbabel/2.3.0/ghemical.prm > -- Up-to-date: /usr/local/share/openbabel/2.3.0/isotope-small.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/isotope.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/logp.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/MACCS.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmff94.ff > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmff94s.ff > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffang.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffbndk.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffbond.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffchg.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffdef.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffdfsb.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffoop.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffpbci.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffprop.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffstbn.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmfftor.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffvdw.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffs_oop.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mmffs_tor.par > -- Up-to-date: /usr/local/share/openbabel/2.3.0/mr.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/patterns.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/phmodel.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/plugindefines.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/psa.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/qeq.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/resdata.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/ringtyp.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/SMARTS_InteLigand.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/space-groups.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/superatom.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/svgformat.script > -- Up-to-date: /usr/local/share/openbabel/2.3.0/torlib.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/types.txt > -- Up-to-date: /usr/local/share/openbabel/2.3.0/UFF.prm > -- Up-to-date: /usr/local/share/man/man1/babel.1 > -- Up-to-date: /usr/local/share/man/man1/obchiral.1 > -- Up-to-date: /usr/local/share/man/man1/obconformer.1 > -- Up-to-date: /usr/local/share/man/man1/obenergy.1 > -- Up-to-date: /usr/local/share/man/man1/obfit.1 > -- Up-to-date: /usr/local/share/man/man1/obgen.1 > -- Up-to-date: /usr/local/share/man/man1/obgrep.1 > -- Up-to-date: /usr/local/share/man/man1/obminimize.1 > -- Up-to-date: /usr/local/share/man/man1/obprobe.1 > -- Up-to-date: /usr/local/share/man/man1/obprop.1 > -- Up-to-date: /usr/local/share/man/man1/obrotamer.1 > -- Up-to-date: /usr/local/share/man/man1/obrotate.1 > -- Up-to-date: /usr/local/share/man/man1/roundtrip.1 > -- Installing: /usr/local/lib/libopenbabel.4.0.0.dylib > -- Up-to-date: /usr/local/lib/libopenbabel.4.dylib > -- Up-to-date: /usr/local/lib/libopenbabel.dylib > -- Installing: /usr/local/lib/openbabel/2.3.0/plugin_descriptors.so > -- Installing: /usr/local/lib/openbabel/2.3.0/plugin_fingerprints.so > -- Installing: /usr/local/lib/openbabel/2.3.0/plugin_forcefields.so > -- Installing: /usr/local/lib/openbabel/2.3.0/plugin_ops.so > -- Installing: /usr/local/lib/openbabel/2.3.0/plugin_charges.so > -- Installing: /usr/local/lib/openbabel/2.3.0/smilesformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mdlformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mol2format.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pdbformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/inchiformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/copyformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/MNAformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/molreport.so > -- Installing: /usr/local/lib/openbabel/2.3.0/nulformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/povrayformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/reportformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/svgformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/textformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/titleformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pngformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/adfformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/castepformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/dmolformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/fchkformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/fhiaimsformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gamessformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gaussformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gausscubeformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gausszmatformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gulpformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/hinformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/jaguarformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/molproformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mopacformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/nwchemformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pwscfformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/qchemformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/turbomoleformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/vaspformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/zindoformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gamessukformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/APIInterface.so > -- Installing: /usr/local/lib/openbabel/2.3.0/CSRformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/PQSformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/MCDLformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/alchemyformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/acrformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/amberformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/balstformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/bgfformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/boxformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cacaoformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cacheformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/carformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cccformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/chem3dformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/chemdrawct.so > -- Installing: /usr/local/lib/openbabel/2.3.0/chemtoolformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cifformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/crkformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cssrformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/dlpolyformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/fastsearchformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/fastaformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/featformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/fhformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/fingerprintformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/freefracformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/ghemicalformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/gromos96format.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mmcifformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mmodformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/moldenformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mpdformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/mpqcformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/msiformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/msmsformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/opendxformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/outformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pcmodelformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pdbqtformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pqrformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/shelxformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/thermoformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/tinkerformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/unichemformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/viewmolformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/xedformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/xyzformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/yasaraformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/rxnformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/chemdrawcdx.so > -- Installing: /usr/local/lib/openbabel/2.3.0/chemkinformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/rsmiformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cdxmlformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cmlformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/pubchem.so > -- Installing: /usr/local/lib/openbabel/2.3.0/xmlformat.so > -- Installing: /usr/local/lib/openbabel/2.3.0/cmlreactformat.so > -- Installing: /usr/local/lib/libinchi.0.3.1.dylib > -- Up-to-date: /usr/local/lib/libinchi.0.dylib > -- Up-to-date: /usr/local/lib/libinchi.dylib > -- Installing: /usr/local/bin/babel > -- Installing: /usr/local/bin/obabel > -- Installing: /usr/local/bin/obchiral > -- Installing: /usr/local/bin/obconformer > -- Installing: /usr/local/bin/obenergy > -- Installing: /usr/local/bin/obfit > -- Installing: /usr/local/bin/obgen > -- Installing: /usr/local/bin/obminimize > -- Installing: /usr/local/bin/obprobe > -- Installing: /usr/local/bin/obprop > -- Installing: /usr/local/bin/obrotamer > -- Installing: /usr/local/bin/obrotate > -- Installing: /usr/local/bin/obspectrophore > -- Installing: /usr/local/bin/obgrep > -- Installing: /usr/local/bin/roundtrip > running install > running build > running build_py > copying openbabel.py -> build/lib.macosx-10.3-fat-2.5 > copying pybel.py -> build/lib.macosx-10.3-fat-2.5 > running build_ext > building '_openbabel' extension > gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk > -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd > -fno-common -dynamic -DNDEBUG -g -O3 > -I/Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include > -I../include > -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/openbabel-python.cpp > -o > build/temp.macosx-10.3-fat-2.5/Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/openbabel-python.o > In file included from > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/openbabel-python.cpp:3100: > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:26:22: > error: Eigen/Core: No such file or directory > In file included from > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/openbabel-python.cpp:3100: > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:26:22: > error: Eigen/Core: No such file or directory > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:177: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:177: > error: ‘MatrixXd’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:178: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:178: > error: ‘Vector3d’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:183: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:183: > error: ‘MatrixXd’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:184: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:184: > error: ‘MatrixXd’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:185: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:185: > error: ‘MatrixXd’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:186: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:186: > error: ‘Vector3d’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:187: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:187: > error: expected ‘,’ or ‘...’ before ‘&’ token > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:187: > error: ISO C++ forbids declaration of ‘MatrixXd’ with no type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:177: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:177: > error: ‘MatrixXd’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:178: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:178: > error: ‘Vector3d’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:183: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:183: > error: ‘MatrixXd’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:184: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:184: > error: ‘MatrixXd’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:185: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:185: > error: ‘MatrixXd’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:186: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:186: > error: ‘Vector3d’ does not name a type > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:187: > error: ‘Eigen’ has not been declared > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:187: > error: expected ‘,’ or ‘...’ before ‘&’ token > /Users/kws/Documents/code/openbabel_svn/src/openbabel/scripts/python/../../include/openbabel/math/align.h:187: > error: ISO C++ forbids declaration of ‘MatrixXd’ with no type > lipo: can't figure out the architecture type of: /var/tmp//cc2zIqd1.out > error: command 'gcc' failed with exit status 1 > > > > > > > > On 25 Jan 2011, at 10:00, Noel O'Boyle wrote: > >> Are you compiling the release (i.e. the .tar.gz) or the development >> version (from SVN)? If the development version, then you need Swig 2.0 >> at least: >> >> -- Found SWIG: /usr/bin/swig (found version "1.3.31") >> -- SWIG version is 1.3.31 >> -- SWIG version 2.0.0 exactly is required >> >> - Noel >> >> On 24 January 2011 23:29, Ken Smith <k.w.sm...@qub.ac.uk> wrote: >>> >>> Folks >>> >>> I've successfully installed OpenBabel and its python bindings several >>> times from the development source code on a unix box >>> >>> However, I'm having difficulty the Python Bindings on a Mac. There's >>> no sign of any python module after the installation. >>> >>> Any ideas? >>> >>> Thanks in advance, >>> >>> Ken >>> >>> >>> cmake ../src/openbabel -DCMAKE_INSTALL_PREFIX=/usr/local/ - >>> DRUN_SWIG=ON -DPYTHON_BINDINGS=ON >>> -- The C compiler identification is GNU >>> -- The CXX compiler identification is GNU >>> -- Checking whether C compiler has -isysroot >>> -- Checking whether C compiler has -isysroot - yes >>> -- Checking whether C compiler supports OSX deployment target flag >>> -- Checking whether C compiler supports OSX deployment target flag - yes >>> -- Check for working C compiler: /usr/bin/cc >>> -- Check for working C compiler: /usr/bin/cc -- works >>> -- Detecting C compiler ABI info >>> -- Detecting C compiler ABI info - done >>> -- Checking whether CXX compiler has -isysroot >>> -- Checking whether CXX compiler has -isysroot - yes >>> -- Checking whether CXX compiler supports OSX deployment target flag >>> -- Checking whether CXX compiler supports OSX deployment target flag - >>> yes >>> -- Check for working CXX compiler: /usr/bin/c++ >>> -- Check for working CXX compiler: /usr/bin/c++ -- works >>> -- Detecting CXX compiler ABI info >>> -- Detecting CXX compiler ABI info - done >>> Using included inchi library. >>> -- Found LibXml2: /usr/lib/libxml2.dylib >>> -- Found ZLIB: /usr/include (found version "1.2.3") >>> -- Found wxWidgets: TRUE >>> -- Looking for conio.h >>> -- Looking for conio.h - not found >>> -- Looking for sys/time.h >>> -- Looking for sys/time.h - found >>> -- Looking for time.h >>> -- Looking for time.h - found >>> -- Looking for strings.h >>> -- Looking for strings.h - found >>> -- Looking for rpc/xdr.h >>> -- Looking for rpc/xdr.h - not found >>> -- Looking for regex.h >>> -- Looking for regex.h - found >>> -- Looking for C++ include sstream >>> -- Looking for C++ include sstream - found >>> -- Looking for rint >>> -- Looking for rint - found >>> -- Looking for snprintf >>> -- Looking for snprintf - found >>> -- Looking for sranddev >>> -- Looking for sranddev - found >>> -- Looking for strcasecmp >>> -- Looking for strcasecmp - found >>> -- Looking for strncasecmp >>> -- Looking for strncasecmp - found >>> -- Looking for dlopen in dl >>> -- Looking for dlopen in dl - found >>> -- Looking for sys/types.h >>> -- Looking for sys/types.h - found >>> -- Looking for stdint.h >>> -- Looking for stdint.h - found >>> -- Looking for stddef.h >>> -- Looking for stddef.h - found >>> -- Check size of clock_t >>> -- Check size of clock_t - done >>> -- Performing Test SCANDIR_NEEDS_CONST >>> -- Performing Test SCANDIR_NEEDS_CONST - Failed >>> -- Found Eigen2: /usr/local/include/eigen2 >>> -- Looking for getopt >>> -- Looking for getopt - found >>> GUI will not be built >>> -- Found PythonInterp: /Library/Frameworks/Python.framework/Versions/ >>> 2.5/bin/python2.5 >>> -- Found SWIG: /usr/bin/swig (found version "1.3.31") >>> -- SWIG version is 1.3.31 >>> -- SWIG version 2.0.0 exactly is required >>> -- Configuring done >>> -- Generating done >>> -- Build files have been written to: /Users/kws/Documents/code/ > > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
