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. * 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)! 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