Hi Samuel, 'm' is not a molecule object. If you can show us the rest of your code we might be able to help you further.
Ciao, Bjoern Am 09.06.2014 15:13, schrieb [email protected]: > Hello, > > Could some kindly explain why I am getting error message when I run this > line of my code (what is the correction): > > Code: num_ha = m.GetNumHeavyAtoms() > > Message: AttributeError: 'module' object has no attribute GetNumHeavyAtoms. > > > Thank you. > > Kind regards > > Samuel > >> Send Rdkit-discuss mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rdkit-discuss digest..." >> >> >> Today's Topics: >> >> 1. Re: installation problem (Matthew Lardy) >> 2. Re: installation problem (Greg Landrum) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 5 Jun 2014 17:12:09 -0700 >> From: Matthew Lardy <[email protected]> >> Subject: Re: [Rdkit-discuss] installation problem >> To: "Wong, Sergio E." <[email protected]> >> Cc: "[email protected]" >> <[email protected]> >> Message-ID: >> <CAESmxqxiAhUT-ShhREYe3HqL7YQUxixw7ooyg4KW+Vd=m1o...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Sergio, >> >> I was having errors like that up until I found my working combination of >> cmake, boost, and swig (again for CentOS 6.x). A former colleague of mine >> also struggled to build the wrappers until he switched to those exact >> versions I enumerated earlier. >> >> I wish that I had a more descriptive answer, but I simply tried >> combination >> after combination of those three applications until I found one that >> worked. >> >> Let me know if upgrading your version of boost helps! >> Matt >> >> >> >> On Thu, Jun 5, 2014 at 3:29 PM, Wong, Sergio E. <[email protected]> wrote: >> >>> 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]> >>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 6 Jun 2014 05:54:26 +0200 >> From: Greg Landrum <[email protected]> >> Subject: Re: [Rdkit-discuss] installation problem >> To: "Wong, Sergio E." <[email protected]> >> Cc: "[email protected]" >> <[email protected]> >> Message-ID: >> <CAD4fdRR2-711NBad984eT83CB-iDEMBn2KjrcC1vV3Oq=uh...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> The errors below are from the java compiler, something I don't think I've >> seen before. >> >> In the theory that this might be due to an initial attempt with a newer >> version of SWIG: You might try removing everything in the >> directory $RDBASE/Code/JavaWrappers/gmwrapper/src/org/RDKit, "touch"ing >> the >> file $RDBASE/Code/JavaWrappers/gmwrapper/GraphMolJava.i to force a >> rebuild, then rebuilding. >> >> Note: in your original message you said that you were interested in using >> the Python wrappers. If this is the case, you don't actually need to be >> building the java wrappers (where these errors are happening) at all. If >> you set RDK_BUILD_SWIG_WRAPPERS to OFF in your cmake command line, the >> java >> wrapper will be disabled. >> >> -greg >> >> >> >> On Fri, Jun 6, 2014 at 12:29 AM, Wong, Sergio E. <[email protected]> wrote: >> >>> 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]> >>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> ------------------------------------------------------------------------------ >> 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> End of Rdkit-discuss Digest, Vol 80, Issue 7 >> ******************************************** >> > > > > ------------------------------------------------------------------------------ > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions > Find What Matters Most in Your Big Data with HPCC Systems > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. > Leverages Graph Analysis for Fast Processing & Easy Data Exploration > http://www.hpccsystems.com > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://www.hpccsystems.com _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
