Hi Sergio,
What version of Swig, Boost and Cmake are you using? I found that
switching to Swig (v2.0.10), Boost (v1.55), and Cmake (v 2.8.10.2) resolved
those types of errors when I was having them.
At least that worked on CentOS 6.x. :)
Matt
On Thu, Jun 5, 2014 at 1:09 PM, Wong, Sergio E. <[email protected]> wrote:
> 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
>
>
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Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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