Hi;
So I switched down to swig 2.0, up to boost 1.47 and up to cmake v.2.8 and
got further, but now have other errors :
....
[ 98%] Built target GraphMolWrap
Scanning dependencies of target BuildJavaWrapperTests
[ 98%] jar cf org.RDKitDoc.jar -d doc
----------
1. ERROR in src/org/RDKit/AtomColors.java (at line 11)
public enum AtomColors {
^^^^
Syntax error on token "enum", interface expected
----------
....
162. ERROR in src/org/RDKit/SanitizeFlags.java (at line 22)
SANITIZE_ADJUSTHS(RDKFuncsJNI.SANITIZE_ADJUSTHS_get()),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Syntax error on token(s), misplaced construct(s)
----------
163. ERROR in src/org/RDKit/SanitizeFlags.java (at line 22)
SANITIZE_ADJUSTHS(RDKFuncsJNI.SANITIZE_ADJUSTHS_get()),
^
Syntax error, insert ";" to complete InvalidConstructorDeclaration
----------
164. ERROR in src/org/RDKit/SanitizeFlags.java (at line 23)
SANITIZE_ALL(RDKFuncsJNI.SANITIZE_ALL_get());
^^^^^^^^^^^^^^^^^^^^^^^^^
Syntax error on token(s), misplaced construct(s)
----------
165. ERROR in src/org/RDKit/SanitizeFlags.java (at line 23)
SANITIZE_ALL(RDKFuncsJNI.SANITIZE_ALL_get());
^
Syntax error on token ")", delete this token
----------
166. ERROR in src/org/RDKit/SanitizeFlags.java (at line 39)
@SuppressWarnings("unused")
^^^^^^^^^^^^^^^^^
Syntax error, annotations are only available if source level is 5.0
----------
167. ERROR in src/org/RDKit/SanitizeFlags.java (at line 44)
@SuppressWarnings("unused")
^^^^^^^^^^^^^^^^^
Syntax error, annotations are only available if source level is 5.0
----------
168. ERROR in src/org/RDKit/SanitizeFlags.java (at line 50)
@SuppressWarnings("unused")
^^^^^^^^^^^^^^^^^
Syntax error, annotations are only available if source level is 5.0
----------
169. ERROR in src/org/RDKit/SanitizeFlags.java (at line 58)
private static class SwigNext {
^^^^^^^^
The type SwigNext is already defined
----------
169 problems (163 errors, 6 warnings)make[2]: ***
[../Code/JavaWrappers/gmwrapper/org.RDKit.jar] Error 255
make[1]: ***
[Code/JavaWrappers/gmwrapper/CMakeFiles/BuildJavaWrapperTests.dir/all] Error 2
make: *** [all] Error 2
Any ideas?
Thanks!
-Sergio
________________________________
From: Matthew Lardy [[email protected]]
Sent: Thursday, June 05, 2014 1:58 PM
To: Wong, Sergio E.
Cc: [email protected]
Subject: Re: [Rdkit-discuss] installation problem
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]<mailto:[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
_______________________________________________
Rdkit-discuss mailing list
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https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
