Eigen2 is required for building the bindings. See the docs you link to.
- Noel
On 9 April 2012 07:03, Park Hyerin <parkh...@gmail.com> wrote:
> I installed Openbabel on Fedora with Python.
> And also I followed
> http://openbabel.org/docs/2.3.1/Installation/install.html#compiling-open-babel
> after
> building.
> But I got some errors at here.
>
> $ cmake ../openbabel-2.3.1 -DPYTHON_BINDINGS=ON*$ make <- Here.*# make
> install$ export PYTHONPATH=/usr/local/lib/python2.6/site-packages:$PYTHONPATH
>
> And here are the errors.
>
>
> [root@---- build]# make
> [ 20%] Built target openbabel
> [ 21%] Built target plugin_charges
> [ 23%] Built target plugin_descriptors
> [ 24%] Built target plugin_fingerprints
> [ 25%] Built target plugin_forcefields
> [ 31%] Built target plugin_ops
> [ 44%] Built target inchi
> [ 44%] Built target APIInterface
> [ 44%] Built target CSRformat
> [ 45%] Built target MCDLformat
> [ 45%] Built target MNAformat
> [ 45%] Built target PQSformat
> [ 46%] Built target abinitformat
> [ 46%] Built target acrformat
> [ 46%] Built target adfformat
> [ 46%] Built target alchemyformat
> [ 47%] Built target amberformat
> [ 47%] Built target balstformat
> [ 47%] Built target bgfformat
> [ 48%] Built target boxformat
> [ 48%] Built target cacaoformat
> [ 48%] Built target cacheformat
> [ 49%] Built target carformat
> [ 49%] Built target castepformat
> [ 49%] Built target cccformat
> [ 50%] Built target cdxmlformat
> [ 50%] Built target chem3dformat
> [ 51%] Built target chemdrawcdx
> [ 51%] Built target chemdrawct
> [ 51%] Built target chemkinformat
> [ 52%] Built target chemtoolformat
> [ 52%] Built target cifformat
> [ 53%] Built target cmlformat
> [ 53%] Built target cmlreactformat
> [ 54%] Built target copyformat
> [ 54%] Built target crkformat
> [ 54%] Built target cssrformat
> [ 55%] Built target dlpolyformat
> [ 55%] Built target dmolformat
> [ 55%] Built target fastaformat
> [ 56%] Built target fastsearchformat
> [ 56%] Built target fchkformat
> [ 56%] Built target featformat
> [ 57%] Built target fhformat
> [ 57%] Built target fhiaimsformat
> [ 57%] 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 groformat
> [ 60%] Built target gromos96format
> [ 61%] Built target gulpformat
> [ 61%] Built target hinformat
> [ 62%] Built target inchiformat
> [ 62%] Built target jaguarformat
> [ 63%] 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
> [ 67%] Built target outformat
> [ 68%] Built target pcmodelformat
> [ 68%] Built target pdbformat
> [ 68%] Built target pdbqtformat
> [ 69%] Built target pngformat
> [ 69%] Built target povrayformat
> [ 69%] Built target pqrformat
> [ 70%] Built target pubchem
> [ 70%] Built target pwscfformat
> [ 71%] Built target qchemformat
> [ 71%] Built target reportformat
> [ 71%] Built target rsmiformat
> [ 72%] Built target rxnformat
> [ 72%] Built target shelxformat
> [ 72%] Built target smilesformat
> [ 73%] Built target svgformat
> [ 73%] Built target textformat
> [ 73%] Built target thermoformat
> [ 74%] Built target tinkerformat
> [ 74%] Built target titleformat
> [ 74%] Built target turbomoleformat
> [ 75%] Built target unichemformat
> [ 75%] Built target vaspformat
> [ 75%] Built target viewmolformat
> [ 76%] Built target xedformat
> [ 76%] Built target xmlformat
> [ 77%] Built target xsfformat
> [ 77%] Built target xtcformat
> [ 77%] Built target xyzformat
> [ 78%] Built target yasaraformat
> [ 78%] Built target zindoformat
> [ 78%] Built target babel
> [ 79%] Built target obabel
> [ 79%] Built target obchiral
> [ 79%] Built target obconformer
> [ 80%] Built target obenergy
> [ 80%] Built target obfit
> [ 80%] Built target obgen
> [ 81%] Built target obgrep
> [ 81%] Built target obminimize
> [ 81%] Built target obprobe
> [ 82%] Built target obprop
> [ 82%] Built target obrotamer
> [ 82%] Built target obrotate
> [ 83%] Built target obspectrophore
> [ 83%] Built target roundtrip
> [ 83%] Built target test_aromatest
> [ 83%] Built target test_atom
> [ 84%] Built target test_automorphism
> [ 84%] Built target test_bond
> [ 84%] Built target test_builder
> [ 85%] Built target test_canonconsistent
> [ 85%] Built target test_canonstable
> [ 85%] Built target test_cansmi
> [ 86%] Built target test_charge-gasteiger
> [ 86%] Built target test_charge-mmff94
> [ 86%] Built target test_cistrans
> [ 87%] Built target test_conversion
> [ 87%] Built target test_datatest
> [ 87%] Built target test_ffgaff
> [ 88%] Built target test_ffghemical
> [ 88%] Built target test_ffmmff94
> [ 88%] Built target test_ffuff
> [ 89%] Built target test_formalcharge
> [ 89%] Built target test_format
> [ 89%] Built target test_formula
> [ 90%] Built target test_graphsym
> [ 90%] Built target test_implicitH
> [ 91%] Built target test_inchiwrite
> [ 91%] Built target test_internalcoord
> [ 91%] Built target test_invalidsmarts
> [ 92%] Built target test_invalidsmiles
> [ 92%] Built target test_isomorphism
> [ 92%] Built target test_iterators
> [ 93%] Built target test_logp_psa
> [ 93%] Built target test_lssr
> [ 93%] Built target test_math
> [ 94%] Built target test_mol
> [ 94%] Built target test_phmodel
> [ 94%] Built target test_residue
> [ 95%] Built target test_ringtest
> [ 95%] Built target test_rotor
> [ 95%] Built target test_shuffle
> [ 96%] Built target test_smartsparse
> [ 96%] Built target test_smartstest
> [ 96%] Built target test_smiles
> [ 97%] Built target test_smilesmatch
> [ 97%] Built target test_spectrophore
> [ 97%] Built target test_squareplanar
> [ 98%] Built target test_stereo
> [ 98%] Built target test_stereoperception
> [ 98%] Built target test_tetrahedral
> [ 99%] Built target test_tetranonplanar
> [ 99%] Built target test_tetraplanar
> [ 99%] Built target test_uniqueid
> [100%] Built target test_unitcell
> running build
> running build_py
> copying openbabel.py -> /root/Download/build/scripts/pybuild
> copying pybel.py -> /root/Download/build/scripts/pybuild
> running build_ext
> building '_openbabel' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC
> -I/root/Download/openbabel-2.3.1/scripts/python/../../include -I../include
> -I/usr/include/python2.6 -c
> /root/Download/openbabel-2.3.1/scripts/python/openbabel-python.cpp -o
> build/temp.linux-x86_64-2.6/root/Download/openbabel-2.3.1/scripts/python/openbabel-python.o
> In file included from
> /root/Download/openbabel-2.3.1/scripts/python/openbabel-python.cpp:3358:
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:26:22:
> error: Eigen/Core: No such file or directory
> In file included from
> /root/Download/openbabel-2.3.1/scripts/python/openbabel-python.cpp:3353:
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryAtom::Matches(const
> OpenBabel::OBAtom*) const’:
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/query.h:101:
> warning: comparison between signed and unsigned integer expressions
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/query.h:
> In member function ‘virtual bool OpenBabel::OBQueryBond::Matches(const
> OpenBabel::OBBond*) const’:
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/query.h:179:
> warning: comparison between signed and unsigned integer expressions
> In file included from
> /root/Download/openbabel-2.3.1/scripts/python/openbabel-python.cpp:3358:
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:
> At global scope:
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:177:
> error: ‘Eigen’ has not been declared
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:177:
> error: ISO C++ forbids declaration of ‘MatrixXd’ with no type
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:177:
> error: expected ‘;’ before ‘_rotMatrix’
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:178:
> error: ‘Eigen’ has not been declared
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:178:
> error: ISO C++ forbids declaration of ‘Vector3d’ with no type
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:178:
> error: expected ‘;’ before ‘_ref_centr’
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:183:
> error: ‘Eigen’ has not been declared
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:183:
> error: ISO C++ forbids declaration of ‘MatrixXd’ with no type
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:183:
> error: expected ‘;’ before ‘_result’
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:184:
> error: ‘Eigen’ has not been declared
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:184:
> error: ISO C++ forbids declaration of ‘MatrixXd’ with no type
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:184:
> error: expected ‘;’ before ‘_mref’
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:185:
> error: ‘Eigen’ has not been declared
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:185:
> error: expected ‘,’ or ‘...’ before ‘&’ token
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:186:
> error: ‘Eigen’ has not been declared
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:186:
> error: ISO C++ forbids declaration of ‘Vector3d’ with no type
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:186:
> error: expected ‘;’ before ‘MoveToOrigin’
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:187:
> error: ISO C++ forbids declaration of ‘Eigen’ with no type
> /root/Download/openbabel-2.3.1/scripts/python/../../include/openbabel/math/align.h:187:
> error: expected ‘,’ or ‘...’ before ‘::’ token
> 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
> [root@lage build]#
>
>
> I don't know why these errors occur :(
> Please help me!
>
>
>
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