[Rdkit-discuss] installation problem

[Wong, S. E. <wo...@ll...>]

Hi;

   I am trying to install the CDKit, and in particular, the python wrapper on a redhat x86_64 desktop from source.  The cmake command I used is:

cmake -DBOOST_ROOT=/home/wong105/usr/boost_1_47_0 -D PYTHON_LIBRARY=/usr/lib64/python2.4/config/libpython2.4.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.4 -D PYTHON_EXECUTABLE=/usr/bin/python2.4 -D RDK_BUILD_SWIG_WRAPPERS=ON -D PYTHON_NUMPY_INCLUDE_PATH=/usr/lib64/python2.4/site-packages/numpy/core/include  -D SWIG_DIR=/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/ -D SWIG_EXECUTABLE=/home/wong105/usr/swig-3.0.2/bin/swig ../

and at the very end, the following set of warnings/errors occur:

[ 97%] Built target rdChemicalFeatures
[ 97%] Swig source
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:67: Warning 302: Identifier 'int64_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:21: Warning 302: previous definition of 'int64_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:68: Warning 302: Identifier 'uint64_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:31: Warning 302: previous definition of 'uint64_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:69: Warning 302: Identifier 'int_least64_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:44: Warning 302: previous definition of 'int_least64_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:70: Warning 302: Identifier 'uint_least64_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:54: Warning 302: previous definition of 'uint_least64_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:71: Warning 302: Identifier 'int_fast64_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:67: Warning 302: previous definition of 'int_fast64_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:72: Warning 302: Identifier 'uint_fast64_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:79: Warning 302: previous definition of 'uint_fast64_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:73: Warning 302: Identifier 'intmax_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:99: Warning 302: previous definition of 'intmax_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/GraphMolJava.i:74: Warning 302: Identifier 'uintmax_t' redefined (ignored),
/home/wong105/usr/swig-3.0.2/share/swig/3.0.2/stdint.i:100: Warning 302: previous definition of 'uintmax_t'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/../BitOps.i:47: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'),
/home/wong105/usr/RDKit/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/../BitOps.i:48: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'),
/home/wong105/usr/RDKit/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'.
/home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/../BitOps.i:60: Warning 302: Identifier 'NumBitsInCommon' redefined (ignored) (Renamed from 'NumBitsInCommon< ExplicitBitVect,ExplicitBitVect >'),
/home/wong105/usr/RDKit/Code/DataStructs/BitOps.h:219: Warning 302: previous definition of 'NumBitsInCommon'.
/home/wong105/usr/RDKit/Code/RDBoost/Exceptions.h:18: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored.
/home/wong105/usr/RDKit/Code/RDBoost/Exceptions.h:31: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored.
/home/wong105/usr/RDKit/Code/RDBoost/Exceptions.h:46: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored.
/home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:347: Warning 401: Nothing known about base class 'Queries::EqualityQuery< int,ConstAtomPtr,true >'. Ignored.
/home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:347: Warning 401: Maybe you forgot to instantiate 'Queries::EqualityQuery< int,ConstAtomPtr,true >' using %template.
/home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:387: Warning 401: Nothing known about base class 'Queries::SetQuery< int,Atom const *,true >'. Ignored.
/home/wong105/usr/RDKit/Code/GraphMol/QueryOps.h:387: Warning 401: Maybe you forgot to instantiate 'Queries::SetQuery< int,Atom const *,true >' using %template.
/home/wong105/usr/RDKit/Code/GraphMol/SanitException.h:26: Warning 520: Base class 'std::exception' of 'MolSanitizeException' is not similarly marked as a smart pointer.
/home/wong105/usr/RDKit/Code/GraphMol/SmilesParse/SmilesParse.h:58: Warning 520: Base class 'std::exception' of 'SmilesParseException' is not similarly marked as a smart pointer.
/home/wong105/usr/RDKit/Code/RDGeneral/versions.h:8: Warning 451: Setting a const char * variable may leak memory.
/home/wong105/usr/RDKit/Code/RDGeneral/versions.h:13: Warning 451: Setting a const char * variable may leak memory.
Unable to open file /home/wong105/usr/RDKit/Code/JavaWrappers/gmwrapper/src/org/RDKit/SWIGTYPE_p_std__pairT_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_boost__shared_ptrT_RDKit__Atom_t_boost__shared_ptrT_RDKit__Bond_t_t__adjacency_iterator_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_boost__shared_ptrT_RDKit__Atom_t_boost__shared_ptrT_RDKit__Bond_t_t__adjacency_iterator_t.java: File name too long
make[2]: *** [Code/JavaWrappers/gmwrapper/GraphMolJavaJAVA_wrap.cxx] Error 1
make[1]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2
make: *** [all] Error 2

Any ideas on what I may be doing wrong?

Thanks!
-Sergio