Installing RDKit on Mac OSX 10.10.2 with java and inchi #25

ChristopherFowler · 2015-04-27T17:33:49Z

This issue may have already been brought up in issue #23 but I wanted to post it here since I've had no luck fixing the problem. I can compile RDKit just fine without using --with-java but I need the java wrappers for my work. Below is the full console print-out with --debug and --verbose.

The familiar error statement is this:

[ 40%] Built target cDataStructs
Linking CXX shared library ../../lib/libGraphMol.dylib
[ 40%] Built target GraphMol
make: *** [all] Error 2

I'm not exactly sure how to resolve this issue. There has been mention around the web about adding some command to the cmake call but I'm not sure how to do that.

Here's the full story:

$ brew install rdkit --with-java --with-inchi --debug --verbose
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
==> Installing rdkit from rdkit/homebrew-rdkit
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/swig.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pcre.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb
/usr/bin/env python -c import numpy
/usr/local/Library/Homebrew/build.rb (Formulary::FromPathLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/swig.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pcre.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/python.rb
/usr/bin/env python -c import numpy
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_2.tar.gz
Already downloaded: /Library/Caches/Homebrew/rdkit-2014.09.2.tar.gz
==> Verifying rdkit-2014.09.2.tar.gz checksum
tar xf /Library/Caches/Homebrew/rdkit-2014.09.2.tar.gz
==> mkdir External/java_lib
==> curl http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar -o External/java_lib/junit.jar
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 161 100 161 0 0 401 0 --:--:-- --:--:-- --:--:-- 401

==> cd External/INCHI-API; bash download-inchi.sh

Downloading InChI software distribution version 1.04
http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip
====>

/var/folders/rt/s9lnxk2x2jv81c2_6f8ll6rw0000gn/T/rdkit-inchi-XXX.tmQVIw8g

--2015-04-27 13:13:22-- http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/INCHI-1-API.zip
Resolving www.inchi-trust.org... 91.151.214.89
Connecting to www.inchi-trust.org|91.151.214.89|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2701930 (2.6M) [application/zip]
Saving to: 'INCHI-1-API.zip'

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2015-04-27 13:13:29 (354 KB/s) - 'INCHI-1-API.zip' saved [2701930/2701930]

Unarchiving

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Copying files

Removing temporary files

Done!

Make sure you (re)run cmake before running make

==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.09.2' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DJAVA_AWT_INCLUDE_DIRECTORIES=/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/include -DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_EXECUTABLE='/usr/bin/python' -DPYTHON_INCLUDE_DIR='/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7' -DPYTHON_LIBRARY='/System/Library/Frameworks/Python.framework/Versions/2.7/Python' -DPYTHON_NUMPY_INCLUDE_PATH='/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include' .
-- The C compiler identification is AppleClang 6.1.0.6020049
-- The CXX compiler identification is AppleClang 6.1.0.6020049
-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang
-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++
-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Found PythonInterp: /usr/bin/python (found version "2.7.6")
-- Found PythonLibs: /System/Library/Frameworks/Python.framework/Versions/2.7/Python (found version "2.7.6")
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- python
Python Install directory /usr/local/Cellar/rdkit/2014.09.2/lib/python2.7/site-packages
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR)
-- Found InChI software locally
-- Found SWIG: /usr/local/bin/swig (found version "3.0.5")
-- Found Java: /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/bin/java (found version "1.8.0.25")
-- Found JNI: /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/libjawt.dylib
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2
==> make
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[ 2%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimake.c.o
../BitOps.i:47: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'),
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'.
../BitOps.i:48: Warning 302: Identifier 'AllProbeBitsMatch' redefined (ignored) (Renamed from 'AllProbeBitsMatch< ExplicitBitVect >'),
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:72: Warning 302: previous definition of 'AllProbeBitsMatch'.
../BitOps.i:60: Warning 302: Identifier 'NumBitsInCommon' redefined (ignored) (Renamed from 'NumBitsInCommon< ExplicitBitVect,ExplicitBitVect >'),
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/DataStructs/BitOps.h:219: Warning 302: previous definition of 'NumBitsInCommon'.
[ 3%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap1.c.o
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDBoost/Exceptions.h:18: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDBoost/Exceptions.h:31: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDBoost/Exceptions.h:46: Warning 401: Nothing known about base class 'std::runtime_error'. Ignored.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:375: Warning 401: Nothing known about base class 'Queries::EqualityQuery< int,ConstAtomPtr,true >'. Ignored.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:375: Warning 401: Maybe you forgot to instantiate 'Queries::EqualityQuery< int,ConstAtomPtr,true >' using %template.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:415: Warning 401: Nothing known about base class 'Queries::SetQuery< int,Atom const *,true >'. Ignored.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/QueryOps.h:415: Warning 401: Maybe you forgot to instantiate 'Queries::SetQuery< int,Atom const *,true >' using %template.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/SanitException.h:26: Warning 520: Base class 'std::exception' of 'MolSanitizeException' is not similarly marked as a smart pointer.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/GraphMol/SmilesParse/SmilesParse.h:58: Warning 520: Base class 'std::exception' of 'SmilesParseException' is not similarly marked as a smart pointer.
[ 3%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap2.c.o
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Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiparm.c.o
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[ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_bns.c.o
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[ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiread.c.o
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[ 10%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o
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[ 12%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr5.c.o
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Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr7.c.o
[ 14%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll_main.c.o
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[ 14%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/runichi.c.o
[ 14%] Built target ChemicalFeatures
[ 14%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll_a.c.o
[ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll_a2.c.o
[ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ikey_dll.c.o
[ 15%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ikey_base26.c.o
[ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_io.c.o
[ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/sha2.c.o
[ 16%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/strutil.c.o
[ 17%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/util.c.o
Linking C shared library ../../lib/libInchi.dylib
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Linking CXX shared library ../../lib/libRDGeneral.dylib
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Scanning dependencies of target EigenSolvers
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[ 17%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o
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Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o
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Linking CXX shared library ../../lib/libCatalogs.dylib
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[ 23%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o
Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so
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Linking CXX shared library ../../lib/libDataStructs.dylib
[ 23%] Built target DataStructs
Scanning dependencies of target InfoTheory
[ 23%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o
Scanning dependencies of target RDGeometryLib
Scanning dependencies of target rdMetricMatrixCalc
[ 23%] [ 23%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o
Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o
[ 23%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o
Scanning dependencies of target rdSimDivPickers
Scanning dependencies of target cDataStructs
[ 23%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o
[ 23%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDGeneral/versions.h:8: Warning 451: Setting a const char * variable may leak memory.
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/RDGeneral/versions.h:13: Warning 451: Setting a const char * variable may leak memory.
[ 23%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o
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Linking CXX shared library ../../../lib/libInfoTheory.dylib
Scanning dependencies of target GraphMolWrap
[ 24%] Built target InfoTheory
[ 25%] Building CXX object Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o
Scanning dependencies of target rdInfoTheory
[ 25%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o
[ 25%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o
[ 25%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o
Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so
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[ 26%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o
Scanning dependencies of target cQuantize
[ 27%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o
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Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138655:31: error: use of undeclared identifier 'arg1'; did you mean 'jarg1'?
boost::detail::sp_nullptr_t arg1 ;
^~~~
jarg1
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here
SWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138655:18: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'
boost::detail::sp_nullptr_t arg1 ;

[ 28%] Built target rdSimDivPickers
[ 29%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138656:18: error: no type named 'sp_nullptr_t' in namespace 'boost::detail'
  boost::detail::sp_nullptr_t *argp1 ;
  ~~~~~~~~~~~~~~~^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138661:28: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'
  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; 
            ~~~~~~~~~~~~~~~^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138661:43: error: expected expression
  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; 
                                          ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138666:3: error: use of undeclared identifier 'arg1'
  arg1 = *argp1; 
  ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138669:77: error: use of undeclared identifier 'arg1'
      result = (boost::shared_array< int > *)new boost::shared_array< int >(arg1);
                                                                            ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139268:31: error: use of undeclared identifier 'arg1'; did you mean 'jarg1'?
  boost::detail::sp_nullptr_t arg1 ;
                              ^~~~
                              jarg1
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here
SWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
                                                                                                                        ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139268:31: error: reference to local variable 'jarg1' declared in enclosing function 'Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11'
  boost::detail::sp_nullptr_t arg1 ;
                              ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:138653:121: note: 'jarg1' declared here
SWIGEXPORT jlong JNICALL Java_org_RDKit_RDKFuncsJNI_new_1Shared_1Int_1Array_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
                                                                                                                        ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139268:18: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'
  boost::detail::sp_nullptr_t arg1 ;
  ~~~~~~~~~~~~~~~^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139269:18: error: no type named 'sp_nullptr_t' in namespace 'boost::detail'
  boost::detail::sp_nullptr_t *argp1 ;
  ~~~~~~~~~~~~~~~^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139274:28: error: no member named 'sp_nullptr_t' in namespace 'boost::detail'
  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; 
            ~~~~~~~~~~~~~~~^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139274:43: error: expected expression
  argp1 = *(boost::detail::sp_nullptr_t **)&jarg1; 
                                          ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139279:3: error: use of undeclared identifier 'arg1'
  arg1 = *argp1; 
  ^
/tmp/rdkit20150427-32910-le799c/rdkit-Release_2014_09_2/Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx:139282:83: error: use of undeclared identifier 'arg1'
      result = (boost::shared_array< double > *)new boost::shared_array< double >(arg1);
                                                                                  ^
Linking CXX shared module ../../../rdkit/rdBase.so
[ 29%] Built target rdBase
Scanning dependencies of target Alignment
[ 29%] Scanning dependencies of target rdGeometry
Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o
[ 29%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o
15 errors generated.
make[2]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o] Error 1
make[1]: *** [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 29%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o
Scanning dependencies of target GraphMol
[ 29%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o
Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so
[ 29%] Built target cQuantize
[ 29%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o
Linking CXX shared library ../../../lib/libAlignment.dylib
[ 29%] Built target Alignment
[ 29%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o
[ 30%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o
Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so
[ 30%] Built target rdInfoTheory
[ 31%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o
[ 31%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o
[ 31%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o
[ 32%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o
[ 33%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o
[ 33%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o
[ 33%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o
Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so
[ 33%] Built target rdGeometry
[ 33%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o
[ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o
[ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o
[ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o
[ 35%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o
[ 35%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o
[ 35%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o
[ 36%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o
[ 36%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o
[ 36%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o
[ 37%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o
[ 37%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o
[ 38%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o
[ 38%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o
[ 38%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RankAtoms.cpp.o
[ 39%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o
[ 39%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o
[ 39%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o
[ 40%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o
[ 40%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o
Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so
[ 40%] Built target cDataStructs
Linking CXX shared library ../../lib/libGraphMol.dylib
[ 40%] Built target GraphMol
make: *** [all] Error 2
/usr/local/Library/Homebrew/debrew.rb:11:in `raise'
BuildError: Failed executing: make 
1. raise
2. ignore
3. backtrace
4. irb
5. shell
Choose an action: 1
==> Formula
Tap: rdkit/homebrew-rdkit
Path: /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
==> Configuration
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew
HEAD: 7731e73cc532a4c9919c019c697e443b1cf70334
Last commit: 4 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: 8-core 64-bit sandybridge
OS X: 10.10.2-x86_64
Xcode: 6.3.1
CLT: 6.2.0.0.1.1424975374
Clang: 6.1 build 602
X11: 2.7.7 => /opt/X11
System Ruby: 2.0.0-p481
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /usr/bin/ruby
Java: 1.8.0_25
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j8
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.10
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Library/ENV/4.3:/usr/local/opt/cmake/bin:/usr/local/opt/wget/bin:/usr/local/opt/swig/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: rdkit 2014.09.2 did not build
Logs:
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/01.java_lib
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/02.junit.jar
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/03.INCHI-API;
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/04.cmake
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/04.cmake.cc
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/05.make
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/05.make.cc
     /Users/christopherfowler/Library/Logs/Homebrew/rdkit/CMakeCache.txt

The text was updated successfully, but these errors were encountered:

greglandrum · 2015-04-28T04:04:02Z

Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?

ChristopherFowler · 2015-04-28T12:14:34Z

Hi Greg. Thanks for the quick reply. I have tried both --HEAD and without when compiling rdkit --with-java and I got the same error both times.

Does this mean that the --with-java
functionality is indeed not working right now?

Best,
Chris

On Apr 28, 2015, at 12:04 AM, Greg Landrum notifications@github.com wrote:

Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?

—
Reply to this email directly or view it on GitHub.

ChristopherFowler · 2015-04-28T12:34:10Z

Oh and one other thing. We will need Java working for Mac OSX 10.8.5 to current (I'm on 10.10.2 currently). Some of our machines aren't allowed to be upgraded here yet for security purposes.

In general, we really need the Java bindings for windows 7, 8, RHEL 5, 6, and the aforementioned Mac versions. There may be other architectures in the future but we know of these for now.

If all you can do for the moment is the Mac versions that's enough for a start.

Just to give you a heads up, my group is at the National Center for Computational Toxicology at the EPA in Research Triangle Park, NC. We are working on developing a public web application that extensively used rdkit which is why we are needing these architectures.

The cheminformatics community is small, so I figured I would introduce myself and let you know where our group is.

Best,
Chris Fowler

On Apr 28, 2015, at 12:04 AM, Greg Landrum notifications@github.com wrote:

Just to be sure that this isn't something that has "accidentally" been fixed, can you please try installing the dev version of the rdkit with "brew install --HEAD rdkit"?

—
Reply to this email directly or view it on GitHub.

greglandrum · 2015-11-18T13:53:11Z

@GreNIX apologies that this has taken me so long to track down/reproduce, but I finally managed to reproduce the problem (accidentally, of course), and then, after some struggling, reproduce it.

The problem seems to be a bad interaction between SWIG, boost, and recent versions of clang on the Mac.
I was able to solve the problem by reverting to an older version of boost. I was able to get the rdkit java wrappers to build with an up-to-date XCode by using boost 1.48. I can confirm that neither 1.55 nor 1.56 work.

Is it possible to install boost 1.48 using homebrew?

-greg

greglandrum · 2015-11-18T14:41:26Z

hmm, looks like I spoke too soon.

The wrappers build, but the tests are failing to build for me. It looks like there may be an incompatibility with Java8 that is causing problems. <sigh>

ChristopherFowler · 2015-11-18T14:46:14Z

Can you try it on Java 7 and 6 just to see if you get the same result?

On Nov 18, 2015, at 9:41 AM, Greg Landrum notifications@github.com wrote:

hmm, looks like I spoke too soon.

The wrappers build, but the tests are failing to build for me. It looks like there may be an incompatibility with Java8 that is causing problems.

—
Reply to this email directly or view it on GitHub.

greglandrum · 2015-11-18T14:57:18Z

Easier said that done. I found a way to patch it so that the docs build under java8, but I will need to spend a bit more time to confirm that this also works back to java 6.

diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
index 461bce4..d099215 100644
--- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt
+++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
@@ -140,7 +140,7 @@ endif()
ADD_CUSTOM_COMMAND(
   OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class
-  COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
+  COMMAND ${JAVA_COMPILE} -Xdoclint:none -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
   DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar ${JAVA_TEST_FILES}
)

ChristopherFowler · 2015-11-18T17:28:34Z

Thanks for looking into this. I appreciate it.

Chris Fowler

On Wed, Nov 18, 2015 at 9:57 AM, Greg Landrum notifications@github.com
wrote:

Easier said that done. I found a way to patch it so that the docs build
under java8, but I will need to spend a bit more time to confirm that this
also works back to java 6.

diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
index 461bce4..d099215 100644
--- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt
+++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
@@ -140,7 +140,7 @@ endif()
ADD_CUSTOM_COMMAND(
OUTPUT ${CMAKE_JAVA_TEST_OUTDIR}/org/RDKit/WrapperTests.class

COMMAND ${JAVA_COMPILE} -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}

COMMAND ${JAVA_COMPILE} -Xdoclint:none -d ${CMAKE_JAVA_TEST_OUTDIR} -cp "${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar${PATH_SEP}${JUNIT_JAR}" ${JAVA_TEST_FILES}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar ${JAVA_TEST_FILES}
)

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#25 (comment)
.

nbateshaus · 2016-04-04T01:14:24Z

I've been looking into this. I have compile working with boost 1.60 and Java 1.8.0_77, but still no javadoc. I got this far via:

diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
index 2095d8e..ab55cce 100644
--- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt
+++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
@@ -48,6 +48,9 @@ endif()
 # Coax SWIG into playing nicely with Apple environments
 if(APPLE)
   SET(CMAKE_SIZEOF_VOID_P 4)
+  # Invocation of the compiler on swig-generated files somehow 'forgets' that
+  # we use a modern dialect of C++
+  ADD_COMPILE_OPTIONS(-std=c++14)
 endif(APPLE)

 if(CMAKE_SIZEOF_VOID_P MATCHES 4)

*** Edit:
After updating RDKit to HEAD, I can now build all the way through. W00t!

greglandrum · 2016-04-05T04:16:06Z

The problem that Nik is fixing with the --std=c++14 flag is a tricky one.
Recent versions of the OS X include at least two different versions of the C++ libraries: one for older flavors of C++ and one for modern C++ (=C++11/14). You pick which one to use at compile/link time with the -std and/or -stdlib arguments.
For the RDKit it doesn't matter (yet) which standard you pick, but I believe you can only use one at a time. So you cannot, for example, combine libraries that have been linked against stdc++ and libc++.

@bp-kelley posted some code to test for library versions on OS X here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html

Here's the test:

if otool -L "$PYROOT/lib/libboost_python.dylib"  | grep libc++ ; then
    FLAGS="-std=c++11 -stdlib=libc++"
else
    FLAGS="-stdlib=libstdc++"
fi

bp-kelley · 2016-04-05T16:24:51Z

I just make a pull request for CMake to pick the right version of libc++ on
OSX. You may want to try it out and see if it works for you:

rdkit/rdkit#845

This was hair-pulling for a while until we figured it out. The problem
isn't really that libc++ and stdlibc++ can't work together, they were
designed not to collide (except on osx 10.8), the problem is that boost was
compiled with libc++ and the symbols can't be found.

Cheers,
Brian

On Tue, Apr 5, 2016 at 12:16 AM, Greg Landrum notifications@github.com
wrote:

The problem that Nik is fixing with the --std=c++14 flag is a tricky one.
Recent versions of the OS X include at least two different versions of the
C++ libraries: one for older flavors of C++ and one for modern C++
(=C++11/14). You pick which one to use at compile/link time with the -std
and/or -stdlib arguments.
For the RDKit it doesn't matter (yet) which standard you pick, but I
believe you can only use one at a time. So you cannot, for example, combine
libraries that have been linked against stdc++ and libc++.

@bp-kelley https://github.com/bp-kelley posted some code to test for
library versions on OS X here:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html

Here's the test:

if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then
FLAGS="-std=c++11 -stdlib=libc++"
else
FLAGS="-stdlib=libstdc++"
fi

—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
#25 (comment)

nbateshaus · 2016-04-05T21:30:06Z

I just tried that fix instead of mine, and can confirm that it works! Thanks!

bp-kelley · 2016-04-05T22:41:02Z

Great! Thanks for trying the build.

ChristopherFowler · 2016-04-06T02:48:43Z

RDKit folks,

So I really appreciate your diligence on this. I've actually left the EPA
for graduate school so I won't be needing any more correspondence. Thank
you guys very much for all of your hard work!

Best,
Chris Fowler

On Tue, Apr 5, 2016 at 12:24 PM, Brian Kelley notifications@github.com
wrote:

I just make a pull request for CMake to pick the right version of libc++ on
OSX. You may want to try it out and see if it works for you:

rdkit/rdkit#845

This was hair-pulling for a while until we figured it out. The problem
isn't really that libc++ and stdlibc++ can't work together, they were
designed not to collide (except on osx 10.8), the problem is that boost was
compiled with libc++ and the symbols can't be found.

Cheers,
Brian

On Tue, Apr 5, 2016 at 12:16 AM, Greg Landrum notifications@github.com
wrote:

The problem that Nik is fixing with the --std=c++14 flag is a tricky one.
Recent versions of the OS X include at least two different versions of
the
C++ libraries: one for older flavors of C++ and one for modern C++
(=C++11/14). You pick which one to use at compile/link time with the -std
and/or -stdlib arguments.
For the RDKit it doesn't matter (yet) which standard you pick, but I
believe you can only use one at a time. So you cannot, for example,
combine
libraries that have been linked against stdc++ and libc++.

@bp-kelley https://github.com/bp-kelley posted some code to test for
library versions on OS X here:

http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05322.html

Here's the test:

if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then
FLAGS="-std=c++11 -stdlib=libc++"
else
FLAGS="-stdlib=libstdc++"
fi

—
You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub
<
https://github.com/rdkit/homebrew-rdkit/issues/25#issuecomment-205635577>

—
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Reply to this email directly or view it on GitHub
#25 (comment)

UnixJunkie · 2019-07-09T07:12:40Z

this is so old, I guess it can be closed

mcs07 mentioned this issue Apr 18, 2016

Update for v2016.03.1 #31

Merged

shashj199 mentioned this issue Mar 27, 2017

Unable to install rdkit -- mac OS #41

Closed

shonfeder mentioned this issue Dec 12, 2017

fix for conf-rdkit to support upcoming version of rdkit ocaml/opam-repository#10926

Merged

Astrovicis mentioned this issue Sep 18, 2019

MacOS: ModuleNotFoundError: No module named 'rdkit' #50

Closed

UnixJunkie closed this as completed Sep 18, 2019

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Installing RDKit on Mac OSX 10.10.2 with java and inchi #25

Installing RDKit on Mac OSX 10.10.2 with java and inchi #25

ChristopherFowler commented Apr 27, 2015

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greglandrum commented Nov 18, 2015

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nbateshaus commented Apr 4, 2016

greglandrum commented Apr 5, 2016

bp-kelley commented Apr 5, 2016

nbateshaus commented Apr 5, 2016

bp-kelley commented Apr 5, 2016

ChristopherFowler commented Apr 6, 2016

UnixJunkie commented Jul 9, 2019

Installing RDKit on Mac OSX 10.10.2 with java and inchi #25

Installing RDKit on Mac OSX 10.10.2 with java and inchi #25

Comments

ChristopherFowler commented Apr 27, 2015

==> cd External/INCHI-API; bash download-inchi.sh

/var/folders/rt/s9lnxk2x2jv81c2_6f8ll6rw0000gn/T/rdkit-inchi-XXX.tmQVIw8g

Unarchiving

inflating: INCHI-1-API/readme2.txt

Copying files

Removing temporary files

Make sure you (re)run cmake before running make

greglandrum commented Apr 28, 2015

ChristopherFowler commented Apr 28, 2015

ChristopherFowler commented Apr 28, 2015

greglandrum commented Nov 18, 2015

greglandrum commented Nov 18, 2015

ChristopherFowler commented Nov 18, 2015

greglandrum commented Nov 18, 2015

ChristopherFowler commented Nov 18, 2015

nbateshaus commented Apr 4, 2016

greglandrum commented Apr 5, 2016

bp-kelley commented Apr 5, 2016

nbateshaus commented Apr 5, 2016

bp-kelley commented Apr 5, 2016

ChristopherFowler commented Apr 6, 2016

UnixJunkie commented Jul 9, 2019