We are trying to install rdkit using the default MacOS X system Python instead of homebrew brewed Python. (Most other recipes work both ways, and in general hombrew supports both options).

We used to succeed with this, but since commit 49aafe9 it doesn't work - I think the python_executable = "#{HOMEBREW_PREFIX}/bin/python" line is the problem.

c.c. @rwest @pierrelb

Ive installed with:
brew tap rdkit/rdkit
brew install rdkit --with-python3

and using like:
from rdkit import Chem

Im getting:
Traceback (most recent call last):
File "data_structs.py", line 5, in <module>
from rdkit import Chem
ModuleNotFoundError: No module named 'rdkit'

I am using this command to install a package:

brew install rdkit --with-python3 --with-inchi --without-numpy
But I'm getting this error:

Updating Homebrew...
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2020_03_4.tar.gz
==> Downloading from https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2020_03_4
######################################################################## 100.0%
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
==> cmake -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DBoost_NO_BOOST_CMAKE=ON -DPYTHON_EXECUTABLE='/usr/local/opt/[email protected]/bin/pytho
==> make -j4
Last 15 lines from /Users/macbook/Library/Logs/Homebrew/rdkit/02.make:
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMarchingSquares.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerMarchingSquares.cpp
[ 23%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerMolecule.cpp
[ 24%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerResidue.cpp
[ 24%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerResidueInteraction.cpp
[ 24%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerRing.cpp
[ 24%] Linking CXX shared library ../../lib/libRDKitcoordgen.dylib
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Cellar/cmake/3.17.3/bin/cmake -E cmake_link_script CMakeFiles/coordgen.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2020.3.4 -o ../../lib/libRDKitcoordgen.2020.03.4.dylib -install_name @rpath/libRDKitcoordgen.1.dylib CMakeFiles/coordgen.dir/coordgen/CoordgenFragmentBuilder.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenFragmenter.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenMacrocycleBuilder.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenMinimizer.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenTemplates.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizer.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerAtom.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerBond.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerFragment.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMarchingSquares.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o  -Wl,-rpath,/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/lib ../../lib/libRDKitmaeparser.2020.03.4.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_iostreams-mt.dylib /usr/local/lib/libboost_regex-mt.dylib 
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Cellar/cmake/3.17.3/bin/cmake -E cmake_symlink_library ../../lib/libRDKitcoordgen.2020.03.4.dylib ../../lib/libRDKitcoordgen.1.dylib ../../lib/libRDKitcoordgen.dylib
[ 24%] Built target coordgen
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/rdkit/homebrew-rdkit/issues

Could you suggest, please, what can be done?

[  8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o
cd /tmp/rdkit-20171120-3302-1k7arke/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -I/tmp/rdkit-20171120-3302-1k7arke/rdkit-Release_2017_03_3/Code -I/usr/local/include/eigen3  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.12 -fPIC   -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /tmp/rdkit-20171120-3302-1k7arke/rdkit-Release_2017_03_3/Code/DataStructs/MultiFPBReader.cpp
[  8%] Linking CXX shared library ../../lib/libRDKitDataStructs.dylib
cd /tmp/rdkit-20171120-3302-1k7arke/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Cellar/cmake/3.9.6/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.12 -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2017.3.3 -o ../../lib/libRDKitDataStructs.2017.03.3.dylib -install_name /tmp/rdkit-20171120-3302-1k7arke/rdkit-Release_2017_03_3/lib/libRDKitDataStructs.1.dylib CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.2017.03.3.dylib /usr/local/lib/libboost_thread.dylib /usr/local/lib/libboost_system.dylib /usr/local/lib/libboost_thread.dylib /usr/local/lib/libboost_system.dylib
cd /tmp/rdkit-20171120-3302-1k7arke/rdkit-Release_2017_03_3/Code/DataStructs && /usr/local/Cellar/cmake/3.9.6/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.2017.03.3.dylib ../../lib/libRDKitDataStructs.1.dylib ../../lib/libRDKitDataStructs.dylib
[  8%] Built target DataStructs
make: *** [all] Error 2

brew install rdkit fails on High Sierra

Hi I tried to install rdkit this morning with this command ( homebrew install rdkit) but it failed... The error msg came back as : No available formula for rdkit :( Is it something wrong with my end or there is a new formula? Many thanks!

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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950K .......... .......... .......... .......... .......... 37% 419K 4s
1000K .......... .......... .......... .......... .......... 39% 423K 4s
1050K .......... .......... .......... .......... .......... 41% 409K 4s
1100K .......... .......... .......... .......... .......... 43% 286K 4s
1150K .......... .......... .......... .......... .......... 45% 114K 4s
1200K .......... .......... .......... .......... .......... 47% 217K 4s
1250K .......... .......... .......... .......... .......... 49% 362K 4s
1300K .......... .......... .......... .......... .......... 51% 384K 4s
1350K .......... .......... .......... .......... .......... 53% 376K 4s
1400K .......... .......... .......... .......... .......... 54% 394K 4s
1450K .......... .......... .......... .......... .......... 56% 383K 3s
1500K .......... .......... .......... .......... .......... 58% 387K 3s
1550K .......... .......... .......... .......... .......... 60% 385K 3s
1600K .......... .......... .......... .......... .......... 62% 286K 3s
1650K .......... .......... .......... .......... .......... 64% 391K 3s
1700K .......... .......... .......... .......... .......... 66% 386K 3s
1750K .......... .......... .......... .......... .......... 68% 391K 2s
1800K .......... .......... .......... .......... .......... 70% 385K 2s
1850K .......... .......... .......... .......... .......... 72% 372K 2s
1900K .......... .......... .......... .......... .......... 73% 393K 2s
1950K .......... .......... .......... .......... .......... 75% 399K 2s
2000K .......... .......... .......... .......... .......... 77% 399K 2s
2050K .......... .......... .......... .......... .......... 79% 397K 2s
2100K .......... .......... .......... .......... .......... 81% 401K 1s
2150K .......... .......... .......... .......... .......... 83% 395K 1s
2200K .......... .......... .......... .......... .......... 85% 397K 1s
2250K .......... .......... .......... .......... .......... 87% 302K 1s
2300K .......... .......... .......... .......... .......... 89% 582K 1s
2350K .......... .......... .......... .......... .......... 90% 302K 1s
2400K .......... .......... .......... .......... .......... 92% 399K 1s
2450K .......... .......... .......... .......... .......... 94% 403K 0s
2500K .......... .......... .......... .......... .......... 96% 323K 0s
2550K .......... .......... .......... .......... .......... 98% 302K 0s
2600K .......... .......... .......... ........ 100% 493K=7.5s

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

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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
[ 0%] Scanning dependencies of target inchi_support
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[ 0%] Built target inchi_support
[ 0%] [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o
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[ 0%] [ 0%] [ 1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichicans.c.o
Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichican2.c.o
Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichicano.c.o
Linking C shared library ../../../../lib/libhc.dylib
[ 1%] Built target hc
[ 1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiisot.c.o
[ 1%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichilnct.c.o
[ 2%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimak2.c.o
[ 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
[ 3%] [ 4%] [ 4%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichimap4.c.o
Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichinorm.c.o
Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiparm.c.o
[ 4%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt1.c.o
[ 5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt2.c.o
[ 5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiprt3.c.o
[ 5%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiqueu.c.o
[ 6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiring.c.o
[ 6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichisort.c.o
[ 6%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichister.c.o
[ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichitaut.c.o
[ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichi_bns.c.o
[ 7%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/inchi_dll.c.o
[ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichiread.c.o
[ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr1.c.o
[ 8%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr2.c.o
[ 9%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr3.c.o
[ 9%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr4.c.o
Scanning dependencies of target ChemicalFeatures
[ 10%] Scanning dependencies of target RDGeneral
Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o
[ 10%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o
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[ 10%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o
[ 11%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o
[ 11%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o
[ 11%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o
[ 12%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o
[ 12%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr5.c.o
[ 13%] [ 13%] Building C object External/INCHI-API/CMakeFiles/Inchi.dir/src/ichirvr6.c.o
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
Linking CXX shared library ../../lib/libChemicalFeatures.dylib
[ 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/libRDBoost.dylib
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Linking CXX shared library ../../lib/libRDGeneral.dylib
[ 17%] Built target RDGeneral
Scanning dependencies of target EigenSolvers
Scanning dependencies of target SimDivPickers
[ 17%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o
[ 18%] [ 18%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o
Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o
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[ 18%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o
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[ 20%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o
[ 20%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o
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[ 21%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o
[ 22%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o
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Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o
[ 22%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o
[ 23%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o
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[ 23%] Built target Catalogs
[ 23%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o
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[ 23%] Built target Clustering
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[ 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
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[ 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
[ 24%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o
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/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o
[ 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
[ 28%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.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
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[ 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

I was able to build rdkit fine but I had problems with the boost libraries having been built against a different Python.

When I tried python -c 'import rdkit.Chem' I got
Fatal Python error: Interpreter not initialized (version mismatch?)

This is indicative of different libraries having been built against different versions of Python. I am using a 2.7.3 Framework build (brew install python --framework), and getting rdkit to link against this was the first issue (see #3), but the next problem was the "bottle" version of boost installed by default by brew install boost (or as a dependency of rdkit) is linked against the system python. To get rdkit to work I had to rebuild boost from source and have it link against the correct Python (the one I actually use, and the one I linked rdkit against):

brew uninstall boost
brew install boost --build-from-source

Then rebuild rdkit, and I was golden! (I think)
Not sure what can be done to this rdkit formula, but I thought I'd report this in case the workaround helps other people.

Hi,
I just use your homebrew-rdkit method to install rdkit cpp library. While installing, the brew shows a warning in this message:

==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/liyiyuian/Library/Caches/Homebrew/downloads/dbc78c6529381ce39a1c4765d1b16ec83572d3c1ad3cfde3d65efc15a6bfc66f--rdkit-Release_2019_09_1.tar.gz
==> cmake -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DBoost_NO_BOOST_CMAKE=ON -DPYTHON_EXECUTABLE='/usr/local/opt/[email protected]/bin/python3' -DPYTHON
==> make -j16
==> make install
Warning: rdkit/rdkit/rdkit dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
==> Caveats
      You may need to add RDBASE to your environment variables.
      For Bash, put something like this in your $HOME/.bashrc:
        export RDBASE=/usr/local/share/RDKit
==> Summary
🍺  /usr/local/Cellar/rdkit/2019.09.1: 1,561 files, 58MB, built in 4 minutes 45 seconds

I included the header but the g++ cannot find it, so I use the following command instead:
$ g++ -std=c++14 -I/usr/local/include/rdkit sample.cpp -o sample

And then it gives the following error:

Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
 "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.15.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -discard-value-names -main-file-name seq2RiPP.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -fno-strict-return -masm-verbose -munwind-tables -target-sdk-version=10.15 -target-cpu penryn -dwarf-column-info -debugger-tuning=lldb -ggnu-pubnames -target-linker-version 512.4 -v -resource-dir /Library/Developer/CommandLineTools/usr/lib/clang/11.0.0 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I /usr/local/include/rdkit -I/usr/local/include -stdlib=libc++ -internal-isystem /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1 -Wno-framework-include-private-from-public -Wno-atimport-in-framework-header -Wno-extra-semi-stmt -Wno-quoted-include-in-framework-header -std=c++14 -fdeprecated-macro -fdebug-compilation-dir /Users/liyiyuian/Documents/seq2ripp/orf2RiPP/code -ferror-limit 19 -fmessage-length 185 -stack-protector 1 -fstack-check -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fobjc-runtime=macosx-10.15.0 -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -o /var/folders/sr/sm8963pd4q5gwnv8gy0f5z4h0000gn/T/seq2RiPP-8fe82d.o -x c++ seq2RiPP.cpp
clang -cc1 version 11.0.0 (clang-1100.0.33.8) default target x86_64-apple-darwin19.3.0
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/local/include"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/include/rdkit
 /usr/local/include
 /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1
 /Library/Developer/CommandLineTools/usr/lib/clang/11.0.0/include
 /Library/Developer/CommandLineTools/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
End of search list.
 "/Library/Developer/CommandLineTools/usr/bin/ld" -demangle -lto_library /Library/Developer/CommandLineTools/usr/lib/libLTO.dylib -no_deduplicate -dynamic -arch x86_64 -macosx_version_min 10.15.0 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -o seq2RiPP /var/folders/sr/sm8963pd4q5gwnv8gy0f5z4h0000gn/T/seq2RiPP-8fe82d.o -L/usr/local/lib -lc++ -lSystem /Library/Developer/CommandLineTools/usr/lib/clang/11.0.0/lib/darwin/libclang_rt.osx.a
Undefined symbols for architecture x86_64:
  "RDKit::SmilesToMol(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, RDKit::SmilesParserParams const&)", referenced from:
      RDKit::SmilesToMol(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, bool, std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > >*) in seq2RiPP-8fe82d.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Could anyone please help me with this? Thank you!

This is the system Python:

file /usr/bin/Python
/usr/bin/Python: Mach-O universal binary with 2 architectures
/usr/bin/Python (for architecture x86_64): Mach-O 64-bit executable x86_64
/usr/bin/Python (for architecture i386): Mach-O executable i386

The gist is: https://gist.github.com/anonymous/642d2eac204664149543

Ideas welcome....

Currently the versions that gets installed is Release_2016_03_3.
Are there plans to switch to the latest release?

I might have a look soon.
Especially: remove old things related to Python 2.
Create a troubleshooting section and move many things in there.

I got this while installing rdkit on Mac:

Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb:96:in `caveats'
Please report this to the rdkit/rdkit tap!

I think this can avoid several issues we met before in the future like #62. By default, homebrew formula will install latest boost. By pinning the version, we can make sure rdkit will be installed by specific boost/boost-python/boost-python3 version. I am currently working on submitting the patches that provide formulas like [email protected].

Hi,

Is there a problem with the formula. I'm using Yosemite OSX 10.10.2? See below for output:

(venv)MacBook-Pro:~ $ brew tap rdkit/rdkit
Cloning into '/usr/local/Library/Taps/rdkit/homebrew-rdkit'...
remote: Counting objects: 221, done.
remote: Total 221 (delta 0), reused 0 (delta 0), pack-reused 221
Receiving objects: 100% (221/221), 35.39 KiB | 0 bytes/s, done.
Resolving deltas: 100% (53/53), done.
Checking connectivity... done.
Tapped 1 formula

(venv)MacBook-Pro:~ $ brew install --HEAD rdkit
==> Installing rdkit from rdkit/homebrew-rdkit
rdkit: Unsatisfied dependency: numpy
Homebrew does not provide Python dependencies; install with:
pip install numpy
Error: An unsatisfied requirement failed this build.

(venv)MacBook-Pro:~ $ pip install numpy
Collecting numpy
Downloading numpy-1.9.2-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7MB)
100% |################################| 3.7MB 127kB/s
Installing collected packages: numpy

Successfully installed numpy-1.9.2

(venv)MacBook-Pro:~ $ brew install --HEAD rdkit
==> Installing rdkit from rdkit/homebrew-rdkit
==> Installing dependencies for rdkit: cmake, wget, boost, boost-python
==> Installing rdkit dependency: cmake
==> Downloading https://homebrew.bintray.com/bottles/cmake-3.2.1.yosemite.bottle

################################################################## 100.0%

==> Pouring cmake-3.2.1.yosemite.bottle.2.tar.gz
🍺 /usr/local/Cellar/cmake/3.2.1: 1847 files, 32M
==> Installing rdkit dependency: wget
==> Downloading https://homebrew.bintray.com/bottles/wget-1.16.3.yosemite.bottle

################################################################## 100.0%

==> Pouring wget-1.16.3.yosemite.bottle.tar.gz
🍺 /usr/local/Cellar/wget/1.16.3: 9 files, 1.5M
==> Installing rdkit dependency: boost
==> Downloading https://homebrew.bintray.com/bottles/boost-1.57.0.yosemite.bottl

################################################################## 100.0%

==> Pouring boost-1.57.0.yosemite.bottle.tar.gz
🍺 /usr/local/Cellar/boost/1.57.0: 10572 files, 439M
==> Installing rdkit dependency: boost-python
==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.57.0/boo

###################### 39.6%^C

(venv)Huws-MacBook-Pro:~ huwdjones$ brew install --HEAD rdkit
==> Installing rdkit from rdkit/homebrew-rdkit
==> Installing rdkit dependency: boost-python
==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.57.0/boo

################################################################## 100.0%

==> ./bootstrap.sh --prefix=/usr/local/Cellar/boost-python/1.57.0 --libdir=/usr/
==> ./b2 --build-dir=build-python --stagedir=stage-python python=2.7 --prefix=/u
🍺 /usr/local/Cellar/boost-python/1.57.0: 5 files, 11M, built in 90 seconds
==> Installing rdkit
==> Cloning https://github.com/rdkit/rdkit.git
Cloning into '/Library/Caches/Homebrew/rdkit--git'...
remote: Counting objects: 2632, done.
remote: Compressing objects: 100% (2169/2169), done.
remote: Total 2632 (delta 543), reused 1541 (delta 387), pack-reused 0
Receiving objects: 100% (2632/2632), 23.32 MiB | 683.00 KiB/s, done.
Resolving deltas: 100% (543/543), done.
Checking connectivity... done.
==> Checking out branch master
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TY
==> make
Linking CXX shared library ../../lib/libCatalogs.dylib
[ 10%] Built target Catalogs
Linking CXX shared library ../../lib/libDataStructs.dylib
[ 10%] Built target DataStructs
make: *** [all] Error 2

READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

(venv)MacBook-Pro:~ $ brew doctor
Your system is ready to brew.
(venv)MacBook-Pro:~ $ brew update
Already up-to-date.
(venv)MacBook-Pro:~ $ brew install --HEAD rdkit
==> Installing rdkit from rdkit/homebrew-rdkit
==> Cloning https://github.com/rdkit/rdkit.git
Updating /Library/Caches/Homebrew/rdkit--git
==> Checking out branch master
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TY
==> make
Linking CXX shared library ../../lib/libCatalogs.dylib
[ 10%] Built target Catalogs
Linking CXX shared library ../../lib/libDataStructs.dylib
[ 10%] Built target DataStructs
make: *** [all] Error 2

READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

(venv)MacBook-Pro:~ $ brew install --HEAD rdkit --with-java
==> Installing rdkit from rdkit/homebrew-rdkit
==> Installing dependencies for rdkit: pcre, swig
==> Installing rdkit dependency: pcre
==> Downloading https://homebrew.bintray.com/bottles/pcre-8.36.yosemite.bottle.t

################################################################## 100.0%

==> Pouring pcre-8.36.yosemite.bottle.tar.gz
🍺 /usr/local/Cellar/pcre/8.36: 146 files, 5.9M
==> Installing rdkit dependency: swig
==> Downloading https://homebrew.bintray.com/bottles/swig-3.0.5.yosemite.bottle.

################################################################## 100.0%

==> Pouring swig-3.0.5.yosemite.bottle.tar.gz
🍺 /usr/local/Cellar/swig/3.0.5: 727 files, 7.1M
==> Installing rdkit
==> Cloning https://github.com/rdkit/rdkit.git
Updating /Library/Caches/Homebrew/rdkit--git
==> Checking out branch master
==> mkdir External/java_lib
==> curl http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TY
==> make
^
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: *** [all] Error 2

READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

(venv)Huws-MacBook-Pro:~ huwdjones$ brew --version
0.9.5
(venv)Huws-MacBook-Pro:~ huwdjones$ brew install rdkit
==> Installing rdkit from rdkit/homebrew-rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_2.tar.gz

################################################################## 100.0%

==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.09.2' -DCMAKE_BUI
==> make
Linking CXX shared library ../../lib/libCatalogs.dylib
[ 12%] Built target Catalogs
Linking CXX shared library ../../lib/libDataStructs.dylib
[ 12%] Built target DataStructs
make: *** [all] Error 2

READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

Building with:

$ brew install rdkit

works fine. However, building with:

$ brew install rdkit --with-java

fails:

$ brew install rdkit --with-java
==> Installing rdkit from rdkit/homebrew-rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_1.tar.gz
Already downloaded: /Library/Caches/Homebrew/rdkit-2014.09.1.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
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.09.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_SWIG_WRAPPERS=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' .


-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-EQwcuu/rdkit-Release_2014_09_1/CMakeFiles/CMakeOutput.log".
See also "/tmp/rdkit-EQwcuu/rdkit-Release_2014_09_1/CMakeFiles/CMakeError.log".

READ THIS: http://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/rdkit/homebrew-rdkit/issues

Neither cited log file exists.

$ java -version
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

Ideas?

Hi,

I previously had no trouble brewing rdkit but now I'm getting the following message:

CMake Error at /usr/local/Cellar/cmake/2.8.12.2/share/cmake/Modules/FindBoost.cmake:1111 (message):
Unable to find the requested Boost libraries.

Boost version: 1.55.0

Boost include path: /usr/local/include

Could not find the following Boost libraries:

      boost_python

No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the
directory containing Boost libraries or BOOST_ROOT to the location of
Boost.

I tried uninstalling boost and then building from source; did not help.

Hi,

Thank you for your nice formula!
However, it gets stuck at this step, hope you can help:

==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/rdkit/2019.09.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev 
==> make -j12
Last 15 lines from /Users/rutza/Library/Logs/Homebrew/rdkit/02.make:
[ 34%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.dylib
cd /tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/Code/Geometry && /usr/local/Cellar/cmake/3.15.4/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2019.9.1 -o ../../lib/libRDKitRDGeometryLib.2019.09.1.dylib -install_name @rpath/libRDKitRDGeometryLib.1.dylib CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -Wl,-rpath,/tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/lib ../../lib/libRDKitDataStructs.2019.09.1.dylib ../../lib/libRDKitRDGeneral.2019.09.1.dylib 
cd /tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/Code/Geometry && /usr/local/Cellar/cmake/3.15.4/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.2019.09.1.dylib ../../lib/libRDKitRDGeometryLib.1.dylib ../../lib/libRDKitRDGeometryLib.dylib
[ 34%] Built target RDGeometryLib
make[1]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2
[ 34%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/Code/RDBoost/Wrap && /usr/local/Cellar/cmake/3.15.4/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -bundle -Wl,-headerpad_max_install_names -bundle -undefined dynamic_lookup -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o -Wl,-rpath,/tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/lib ../../../lib/libRDKitRDBoost.2019.09.1.dylib /opt/local/lib/libboost_python-mt.dylib /opt/local/lib/libboost_serialization-mt.dylib ../../../lib/libRDKitRDGeneral.2019.09.1.dylib 
[ 34%] Built target rdBase
/tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/Code/RDGeneral/versions.h:22: Warning 451: Setting a const char * variable may leak memory.
/tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/Code/RDGeneral/versions.h:23: Warning 451: Setting a const char * variable may leak memory.
/tmp/rdkit-20191031-28476-1hpww73/rdkit-Release_2019_09_1/Code/RDGeneral/versions.h:24: Warning 451: Setting a const char * variable may leak memory.
[ 34%] Built target GraphMolWrap_swig_compilation
make: *** [all] Error 2

(Launched it with following command: brew install --with-python3 --with-java --with-inchi --with-avalon --with-postgresql rdkit)

The error is more or less reproducible, sometimes crashing at 34%, sometimes 33, et cætera.

Best

After running brew install rdkit, I'm getting the following errors. Any help is appreciated.

Note: I'm on OSX 10.13.3, and I've completely uninstalled everything (python@2, python, boost, boost-python, bumpy) before starting. My path variable is set in my .bashrc as export PATH=~/.local/bin:/usr/local/sbin:$PATH

$ brew install rdkit
==> Installing rdkit from rdkit/rdkit
==> Installing dependencies for rdkit/rdkit/rdkit: boost, python, boost-python, python@2, numpy
==> Installing rdkit/rdkit/rdkit dependency: boost
==> Downloading https://homebrew.bintray.com/bottles/boost-1.67.0_1.high_sierra.bottle.tar.gz
Already downloaded: /Users/cthoyt/Library/Caches/Homebrew/boost-1.67.0_1.high_sierra.bottle.tar.gz
==> Pouring boost-1.67.0_1.high_sierra.bottle.tar.gz
🍺  /usr/local/Cellar/boost/1.67.0_1: 13,506 files, 450.9MB
==> Installing rdkit/rdkit/rdkit dependency: python
==> Downloading https://homebrew.bintray.com/bottles/python-3.6.5.high_sierra.bottle.1.tar.gz
Already downloaded: /Users/cthoyt/Library/Caches/Homebrew/python-3.6.5.high_sierra.bottle.1.tar.gz
==> Pouring python-3.6.5.high_sierra.bottle.1.tar.gz
==> /usr/local/Cellar/python/3.6.5/bin/python3 -s setup.py --no-user-cfg install --force --verbose --in
==> /usr/local/Cellar/python/3.6.5/bin/python3 -s setup.py --no-user-cfg install --force --verbose --in
==> /usr/local/Cellar/python/3.6.5/bin/python3 -s setup.py --no-user-cfg install --force --verbose --in
==> Caveats
Python has been installed as
  /usr/local/bin/python3

Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
  /usr/local/opt/python/libexec/bin

If you need Homebrew's Python 2.7 run
  brew install python@2

Pip, setuptools, and wheel have been installed. To update them run
  pip3 install --upgrade pip setuptools wheel

You can install Python packages with
  pip3 install <package>
They will install into the site-package directory
  /usr/local/lib/python3.6/site-packages

See: https://docs.brew.sh/Homebrew-and-Python
==> Summary
🍺  /usr/local/Cellar/python/3.6.5: 4,736 files, 99.2MB
==> Installing rdkit/rdkit/rdkit dependency: boost-python
==> Downloading https://homebrew.bintray.com/bottles/boost-python-1.67.0.high_sierra.bottle.tar.gz
Already downloaded: /Users/cthoyt/Library/Caches/Homebrew/boost-python-1.67.0.high_sierra.bottle.tar.gz
==> Pouring boost-python-1.67.0.high_sierra.bottle.tar.gz
🍺  /usr/local/Cellar/boost-python/1.67.0: 459 files, 17.3MB
==> Installing rdkit/rdkit/rdkit dependency: python@2
==> Downloading https://homebrew.bintray.com/bottles/[email protected]_3.high_sierra.bottle.2.tar.gz
Already downloaded: /Users/cthoyt/Library/Caches/Homebrew/[email protected]_3.high_sierra.bottle.2.tar.gz
==> Pouring [email protected]_3.high_sierra.bottle.2.tar.gz
==> /usr/local/Cellar/python@2/2.7.14_3/bin/python -s setup.py --no-user-cfg install --force --verbose 
==> /usr/local/Cellar/python@2/2.7.14_3/bin/python -s setup.py --no-user-cfg install --force --verbose 
==> /usr/local/Cellar/python@2/2.7.14_3/bin/python -s setup.py --no-user-cfg install --force --verbose 
==> Caveats
Pip and setuptools have been installed. To update them
  pip install --upgrade pip setuptools

You can install Python packages with
  pip install <package>

They will install into the site-package directory
  /usr/local/lib/python2.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python
==> Summary
🍺  /usr/local/Cellar/python@2/2.7.14_3: 4,669 files, 82.4MB
==> Installing rdkit/rdkit/rdkit dependency: numpy
==> Downloading https://homebrew.bintray.com/bottles/numpy-1.14.3.high_sierra.bottle.tar.gz
Already downloaded: /Users/cthoyt/Library/Caches/Homebrew/numpy-1.14.3.high_sierra.bottle.tar.gz
==> Pouring numpy-1.14.3.high_sierra.bottle.tar.gz
🍺  /usr/local/Cellar/numpy/1.14.3: 939 files, 24.9MB
==> Installing rdkit/rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2017_09_3.tar.gz
Already downloaded: /Users/cthoyt/Library/Caches/Homebrew/rdkit-2017.09.3.tar.gz
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/u
Last 15 lines from /Users/cthoyt/Library/Logs/Homebrew/rdkit/01.cmake:
-- Boost version: 1.67.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.67.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-20180429-30726-jbbbb9/rdkit-Release_2017_09_3/CMakeFiles/CMakeOutput.log".

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/rdkit/homebrew-rdkit/issues

These open issues may also help:
MacOS: ModuleNotFoundError: No module named 'rdkit' https://github.com/rdkit/homebrew-rdkit/issues/50
Installing RDKit on Mac OSX 10.10.2 with java and inchi https://github.com/rdkit/homebrew-rdkit/issues/25

I'm also having the issue that the log file it references, /tmp/rdkit-20180429-30726-jbbbb9/rdkit-Release_2017_09_3/CMakeFiles/CMakeOutput.log doesn't exist.

Everything builds, but the Python wrappers are not fully functional due to a bug in boost 1.60

We need to figure out how to use boost 1.59

Hi,

I'm having trouble installing RDKit on a Mac running Yosemite 10.10.3.

I first built a Python virtualenv based on my system installation and
activated it.

The first effort to "brew install rdkit" seemd to implicate boost as the
cause of failure, so I uninstalled and rebuilt boost, which appeared to
succeed.

When trying again to intall rdkit, it failed with the following in
~/Library/Logs/Homebrew/rdkit/02.make:

[  8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o
[  9%] [  9%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o
Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o
[ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o
Linking CXX shared library ../../lib/libSimDivPickers.dylib
[ 10%] [ 11%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o
[ 11%] Built target SimDivPickers
[ 11%] Linking CXX shared library ../../../lib/libEigenSolvers.dylib
[ 12%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o
[ 12%] Built target EigenSolvers
Linking CXX shared library ../../lib/libCatalogs.dylib
[ 12%] Built target Catalogs
Linking CXX shared library ../../lib/libDataStructs.dylib
[ 12%] Built target DataStructs
make: *** [all] Error 2

When I run the commands:

python-config --prefix
find /usr/local/Cellar/rdkit -name rdBase.so -exec otool -L {} \;
find /usr/local/Cellar/boost -name libboost_python-mt.dylib -exec otool -L {} \;

I get:

> python-config --prefix
/System/Library/Frameworks/Python.framework/Versions/2.7
> find /usr/local/Cellar/rdkit -name rdBase.so -exec otool -L {} \;
find: /usr/local/Cellar/rdkit: No such file or directory
> find /usr/local/Cellar/boost -name libboost_python-mt.dylib -exec otool -L {} \;
> 

Any suggestions?

I had previously been able to install this formulae, I just reinstalled my os and tried to install it again. I wonder if its related with changes on home-brew, there was another issue mentioning it.

$ brew install rdkit --with-python3 --without-numpy
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> Updated Formulae
consul kubernetes-cli libpq packer pilosa

==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2017_09_2.tar.gz
Already downloaded: /Users/nicolas/Library/Caches/Homebrew/rdkit-2017.09.2.tar.gz
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/rdkit/2017.09.2 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOS
==> make -j4
Last 15 lines from /Users/nicolas/Library/Logs/Homebrew/rdkit/02.make:
cd /tmp/rdkit-20180210-16665-1iqo56f/rdkit-Release_2017_09_2/Code/DataStructs && /usr/local/Cellar/cmake/3.10.2/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2017.9.2 -o ../../lib/libRDKitDataStructs.2017.09.2.dylib -install_name /tmp/rdkit-20180210-16665-1iqo56f/rdkit-Release_2017_09_2/lib/libRDKitDataStructs.1.dylib CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.2017.09.2.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib
cd /tmp/rdkit-20180210-16665-1iqo56f/rdkit-Release_2017_09_2/Code/DataStructs && /usr/local/Cellar/cmake/3.10.2/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.2017.09.2.dylib ../../lib/libRDKitDataStructs.1.dylib ../../lib/libRDKitDataStructs.dylib
[ 11%] Built target DataStructs
[ 11%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20180210-16665-1iqo56f/rdkit-Release_2017_09_2/Code/RDBoost/Wrap && /usr/local/Cellar/cmake/3.10.2/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -bundle -Wl,-headerpad_max_install_names -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.2017.09.2.dylib /usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/Python /usr/local/lib/libboost_python-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_chrono-mt.dylib /usr/local/lib/libboost_date_time-mt.dylib /usr/local/lib/libboost_atomic-mt.dylib /usr/local/lib/libboost_serialization-mt.dylib ../../../lib/libRDKitRDGeneral.2017.09.2.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib
Undefined symbols for architecture x86_64:
"boost::python::detail::init_module(PyModuleDef&, void (*)())", referenced from:
_PyInit_rdBase in RDBase.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [rdkit/rdBase.so] Error 1
make[1]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all] Error 2
make: *** [all] Error 2

When trying to install on Mac OS X 10.7.5 with brew 0.9.3 I get the following problem.

$ brew install rdkit --with-java --with-inchi
==> Downloading http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2012/RDKit_2012_09_1.tgz
Already downloaded: /Library/Caches/Homebrew/rdkit-2012.09.1.tgz
==> mkdir External/java_lib
==> curl http://cloud.github.com/downloads/KentBeck/junit/junit-4.10.jar -o External/java_lib/junit.jar
==> cd External/INCHI-API; bash download-inchi.sh
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2012.09.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS
==> make
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [lib/libGraphMol.2012.09.1beta.dylib] Error 1
make[1]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/all] Error 2
make: *** [all] Error 2

As title, I think that will make us find the problem faster.
As I remember, it can be setup like running every day.
@greglandrum Can you setup this for us ?

As we seen in numpy and boost-python, there are two different way to handle the installation.

In boost-python, there are two different version of formulas.

https://github.com/Homebrew/homebrew-core/blob/master/Formula/boost-python.rb
https://github.com/Homebrew/homebrew-core/blob/master/Formula/boost-python3.rb

In numpy, there are only one formula and install on python and python3 at the same time.
It also has a option to install on python3 only.

https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb

The following is the run code.
Somehow after downloading, cmake is unable to build.
I thought it is a python version issue with the directories, but the documentation says that it is automatically installed under the python 2.

172-0-2-103:~ lesteryang$ brew install rdkit
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2017_03_3.tar.gz
Already downloaded: /Users/lesteryang/Library/Caches/Homebrew/rdkit-2017.03.3.tar.gz
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/rdkit/2017.03.3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEW
==> make
Last 15 lines from /Users/lesteryang/Library/Logs/Homebrew/rdkit/02.make:
[ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o
cd /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/Geometry && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -I/tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code -I/usr/local/include/eigen3  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -fPIC   -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/Geometry/UniformGrid3D.cpp
[ 14%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o
cd /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/Geometry && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -DRDGeometryLib_EXPORTS -DRDK_64BIT_BUILD -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -isystem /usr/local/include -I/tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code -I/usr/local/include/eigen3  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -fPIC   -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/Geometry/GridUtils.cpp
[ 14%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/RDBoost/Wrap && /usr/local/Cellar/cmake/3.9.2/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -bundle -Wl,-headerpad_max_install_names  -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.2017.03.3.dylib /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/lib/libboost_python-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_serialization-mt.dylib ../../../lib/libRDKitRDGeneral.2017.03.3.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib 
[ 14%] Built target rdBase
[ 14%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.dylib
cd /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/Geometry && /usr/local/Cellar/cmake/3.9.2/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++  -mpopcnt -std=c++11 -stdlib=libc++ -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.12 -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2017.3.3 -o ../../lib/libRDKitRDGeometryLib.2017.03.3.dylib -install_name /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/lib/libRDKitRDGeometryLib.1.dylib CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.2017.03.3.dylib ../../lib/libRDKitRDGeneral.2017.03.3.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib 
cd /tmp/rdkit-20170910-67701-adxb4v/rdkit-Release_2017_03_3/Code/Geometry && /usr/local/Cellar/cmake/3.9.2/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.2017.03.3.dylib ../../lib/libRDKitRDGeometryLib.1.dylib ../../lib/libRDKitRDGeometryLib.dylib
[ 14%] Built target RDGeometryLib
make[1]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2
make: *** [all] Error 2

Configuration:

RDKit Version: with Python3
Operating system: macOS 10.15.5
Python version (if relevant):
how did you install the RDKit? Using the command

brew install --with-python3 rdkit

Description:

The installation downloads all the dependencies, but it throws an error "Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0")".

I'm new to downloading stuff with brew, so I'm not quite sure what to do.

so that their install is way faster

Hi,

I am using conda and rdkit, so installed
https://github.com/rdkit/conda-rdkit
with
conda build boost
conda build rdkit

The installation seems to be successfull, at least in part, since I can import and use rdkit.

However, I think the version of RDKit is incomplete, since there are no fr_ functions in Chem.Descriptors and when I import rdkit.Chem.PandasTools I get:
[Errno 2] No such file or directory: '/home/.../Programme/anaconda/envs/_build/share/RDKit/Data/Salts.txt'

Is this version incomplete?

Hello,

Could the formula be updated to the latest release?

Thanks!
Francois.

Configuration:

• RDKit Version: HEAD (611c704)
• Operating system: macOS 10.14.6
• Python version (if relevant):
• Are you using conda? No
• If you are using conda, which channel did you install the rdkit from?
• If you are not using conda: how did you install the RDKit? Tried with brew.

Description:

Installation via Homebrew (2.2.15) fails with error ending: [ 15%] Built target coordge. I expected to be able to install using the instructions given at:

https://github.com/rdkit/homebrew-rdkit

None of the possible errors listed there appear to explain what I'm seeing. What am I missing?

A version of Boost had been installed. Also couldn't compile in that case. Deleted boost, and received the error below on attempt to install.

brew install --HEAD rdkit

Full output:

$ brew install --HEAD rdkit
==> Installing rdkit from rdkit/rdkit
==> Cloning https://github.com/rdkit/rdkit.git
Updating /Users/rich/Library/Caches/Homebrew/rdkit--git
==> Checking out branch master
Already on 'master'
Your branch is up to date with 'origin/master'.
HEAD is now at 611c704 Fixes #3131 (#3132)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: module 'numpy' has no attribute 'get_include'
==> cmake -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATI
==> make -j4
Last 15 lines from /Users/rich/Library/Logs/Homebrew/rdkit/02.make:
cd /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200505-74362-mnomh6/External/catch/catch/single_include/catch2 -I/tmp/rdkit-20200505-74362-mnomh6/External -I/tmp/rdkit-20200505-74362-mnomh6/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200505-74362-mnomh6/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.2/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200505-74362-mnomh6/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o -c /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen/coordgen/sketcherMinimizerResidue.cpp
[ 16%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o
cd /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200505-74362-mnomh6/External/catch/catch/single_include/catch2 -I/tmp/rdkit-20200505-74362-mnomh6/External -I/tmp/rdkit-20200505-74362-mnomh6/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200505-74362-mnomh6/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.2/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200505-74362-mnomh6/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o -c /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen/coordgen/sketcherMinimizerResidueInteraction.cpp
[ 16%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o
cd /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200505-74362-mnomh6/External/catch/catch/single_include/catch2 -I/tmp/rdkit-20200505-74362-mnomh6/External -I/tmp/rdkit-20200505-74362-mnomh6/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200505-74362-mnomh6/External/CoordGen -I/usr/local/Cellar/[email protected]/3.8.2/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200505-74362-mnomh6/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o -c /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen/coordgen/sketcherMinimizerRing.cpp
[ 16%] Linking CXX shared library ../../lib/libRDKitcoordgen.dylib
cd /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen && /usr/local/Cellar/cmake/3.17.2/bin/cmake -E cmake_link_script CMakeFiles/coordgen.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2020.9.1 -o ../../lib/libRDKitcoordgen.2020.09.1dev1.dylib -install_name @rpath/libRDKitcoordgen.1.dylib CMakeFiles/coordgen.dir/coordgen/CoordgenFragmentBuilder.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenFragmenter.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenMacrocycleBuilder.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenMinimizer.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenTemplates.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizer.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerAtom.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerBond.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerFragment.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMarchingSquares.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o  -Wl,-rpath,/tmp/rdkit-20200505-74362-mnomh6/lib ../../lib/libRDKitmaeparser.2020.09.1dev1.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_iostreams-mt.dylib /usr/local/lib/libboost_regex-mt.dylib 
cd /tmp/rdkit-20200505-74362-mnomh6/External/CoordGen && /usr/local/Cellar/cmake/3.17.2/bin/cmake -E cmake_symlink_library ../../lib/libRDKitcoordgen.2020.09.1dev1.dylib ../../lib/libRDKitcoordgen.1.dylib ../../lib/libRDKitcoordgen.dylib
[ 16%] Built target coordgen
[ 16%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20200505-74362-mnomh6/Code/RDBoost/Wrap && /usr/local/Cellar/cmake/3.17.2/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -bundle -Wl,-headerpad_max_install_names -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o  -Wl,-rpath,/tmp/rdkit-20200505-74362-mnomh6/lib ../../../lib/libRDKitRDBoost.2020.09.1dev1.dylib ../../../lib/libRDKitRDGeneral.2020.09.1dev1.dylib /usr/local/lib/libboost_python38-mt.dylib 
[ 16%] Built target rdBase
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/rdkit/homebrew-rdkit/issues

Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC.

When I try this formula as is, I've got this error:

g++-5: error: unrecognized command line option '-stdlib=libc++'

And after changing the related line into

'ENV['CXXFLAGS'] = -std=c++11 -Wno-parentheses -Wno-logical-op-parentheses -Wno-format'

build was successful. This might be related to the compiler. In my environment, homebrew used gcc, so the formula must check whether the compiler is gcc or clang.

related to #81

I encountered an error while installing rdkit via brew on osx 10.9.5. Here's what happened:

$ brew tap rdkit/rdkit
$ brew install rdkit

...some dependencies are installed, then

==> Installing rdki

...

==> make
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Linking CXX shared library ../../lib/libRDGeneral.dylib
[  5%] Built target RDGeneral
make: *** [all] Error 2

brew gist-logs rdkit:
https://gist.github.com/a437c40ea71027f3d1a6

In case it matters, I use virtualenvwrapper and had one activated when I ran brew install rdkit

First, cheers to you devs for producing this delicious brew.

This is just a suggestion for the README. I got difficult-to-interpret errors installing because I was using a virtualenv. Also, it was not clear how to tell it to compile for py3. My commands that got it working:

deactivate
brew install python3
pip3 install --upgrade pip setuptools
pip3 install pandas    # simply pip3 install numpy would probably work
brew install --with-inchi --with-python3 rdkit
cd ~/.virtualenvs/myenv/lib/python3.5/site-packages   # "myenv is the name of the virtualenv
ln -s /usr/local/Cellar/rdkit/2015.09.2/lib/python3.5/site-packages/rdkit

Another note: in my virtualenv I did pip install pillow to get molecule drawing in jupyter to work.

I think it does not. But I should check.
If it does not, then remove the numpy dependency in the rdkit.rb file
and call pip3 in there to install it.

Hi,

I'm getting a failed install with
Mac OS X 10.10.5, brew 0.9.5, and Xcode7.0.1. Error messages below:

==> Installing rdkit/rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2015_03_1.tar.gz
==> Downloading from https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2015_03_1

################################################################## 100.0%

==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2015.03.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_I
==> make
Last 15 lines from /Users/scottrowland/Library/Logs/Homebrew/rdkit/02.make:

include <stdio.h>

     ^

1 error generated.
make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
1 error generated.
make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1
make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2
1 error generated.
make[2]: *** [Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o] Error 1
make[1]: *** [Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/all] Error 2
1 error generated.
make[2]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o] Error 1
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make: *** [all] Error 2

I thought rdkit is compiled with clang.

I installed this way:

brew tap rdkit/rdkit
pip3 install numpy
brew install --HEAD rdkit --with-python3 --with-inchi'

https://brew.sh/2018/01/19/homebrew-1.5.0/

On 1st March 2018 the python formula will be upgraded to Python 3.x and a python@2 formula will be added for installing Python 2.7 (although this will be keg-only so neither python nor python2 will be added to the PATH by default without a manual brew link --force). We will maintain python2, python3 and python@3 aliases. Any formulae that use depends_on "python" outside Homebrew/core will need to be updated at this point if they wish to keep using Python 2. Note: macOS has provided Python 2.7 since OS X Lion (10.7) so you can update formulae that need Python 2 today by removing depends_on "python" so they use the system python instead.

It will cause problem for current implementation.

Hi all,

I'm a little new to rdkit, so apologies if this is an issue that's either been noted before, or just a result of me doing something completely wrong!

Essentially, I'm just using substructure matching to compare two bonds, but the version that I acquired via home-brew seems to struggle with the following example. This has worked with other versions (e.g., the version I have on a linux VM, which I think I built from source), but not this one:

import rdkit
rdkit.version
'2016.03.3'
import rdkit.Chem as Chem
x = Chem.MolFromSmarts('[#15]-[#8-]')
y = Chem.MolFromSmarts('[#15]-[#8-]')
x.HasSubstructMatch(y)
False
y.HasSubstructMatch(x)
False

Unless I misunderstand how these functions are meant to work, I believe this should return True, not False?

Hi,
Installing on MacBook Air running Mojave 10.14.6 failed with both commands, see error message below.
Cheers

brew install --HEAD --with-inchi --with-postgresql --with-avalon rdkit
and
brew install rdkit

CMake Error at /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find Boost (missing: Boost_INCLUDE_DIR python) (Required is at
least version "1.56.0")
Call Stack (most recent call first):
/usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
/usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindBoost.cmake:2161 (find_package_handle_standard_args)
CMakeLists.txt:262 (find_package)

-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-20191123-477-1laiqx0/CMakeFiles/CMakeOutput.log".

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/rdkit/homebrew-rdkit/issues

When I installed the rdkit, following messages appear
Warning: SHA1 support is deprecated and will be removed in a future version. Please switch this formula to SHA256.

Hi I am trying to install rdkit on mac os 10.9.4 using the brew installation process and I get the error bellow.
Could you walk me through the error as I am not sure what's the problem.
Thanks in advance.

used as include directory in directory /tmp/rdkit-qaDg/rdkit-Release_2014_03_1/Code/ChemicalFeatures/Wrap

-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-qaDg/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log".
See also "/tmp/rdkit-qaDg/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log".

READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

Updating homebrew today with brew update gives me a few warnings about deprecated dependency parsing:

Warning: Calling 'depends_on :python3' is deprecated!
Use 'depends_on "python3"' instead.
/usr/local/Homebrew/Library/Homebrew/dependency_collector.rb:88:in `parse_spec'

Warning: Calling 'depends_on :postgresql' is deprecated!
Use 'depends_on "postgresql"' instead.
/usr/local/Homebrew/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb:24:in `<class:Rdkit>'
Please report this to the rdkit/rdkit tap!

Warning: Calling 'depends_on :python' is deprecated!
Use 'depends_on "python"' instead.
/usr/local/Homebrew/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb:32:in `<class:Rdkit>'
Please report this to the rdkit/rdkit tap!```

I am running into some post installation issues on my mac (OS 10.9.5). I was hoping to use brew install and then follow this post to use rdkit in a virtualenv.

From what I can tell my installation went ok:

==> Installing rdkit from rdkit/homebrew-rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2015_03_1.tar.gz
Already downloaded: /Library/Caches/Homebrew/rdkit-2015.03.1.tar.gz
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2015.03.1' -DCMAKE_BUI
==> make
==> make install
==> Caveats
You may need to add RDBASE to your environment variables.
For Bash, put something like this in your $HOME/.bashrc

export RDBASE=/usr/local/share/RDKit

When I CD to RDBASE I see the following directories:

Contrib
Data
Docs
Projects

I cd'd to the Projects directory and ran ctest but got the following:

Test project /usr/local/share/RDKit/Projects
Start 1: pythonTestDbCLI
1/1 Test #1: pythonTestDbCLI ..................**Failed 0.02 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 0.02 sec*

I also checked out the directory usr/local/Cellar/rdkit/2015.03.1/lib/python2.7/site-packages/rdkit and tried a ctest here

Start 1: pythonTestDirML
1/6 Test #1: pythonTestDirML .................._Failed 0.01 sec
Start 2: pythonTestDirDataStructs
2/6 Test #2: pythonTestDirDataStructs ........._Failed 0.01 sec
Start 3: pythonTestDirDbase
3/6 Test #3: pythonTestDirDbase ..............._Failed 0.01 sec
Start 4: pythonTestDirSimDivFilters
4/6 Test #4: pythonTestDirSimDivFilters ......._Failed 0.01 sec
Start 5: pythonTestDirVLib
5/6 Test #5: pythonTestDirVLib ................_Failed 0.01 sec
Start 6: pythonTestDirChem
6/6 Test #6: pythonTestDirChem ................_Failed 0.01 sec

0% tests passed, 6 tests failed out of 6

Total Test time (real) = 0.09 sec

Part of this may just be my ignorance of using a mac (transitioning from windows) but any help you can provide is much appreciated. Thank you again,

Dennis

Hey I'm unable to install rdkit on my Mac. I have no idea why this is happening. I tried brew install --HEAD rdkit as well. Please check if possible.

Thanks a ton

Last 15 lines from /Users/shashank/Library/Logs/Homebrew/rdkit/02.make:
[ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o
cd /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/DataStructs && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include -I/tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code -mpopcnt -std=c++11 -stdlib=libc++ -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.11 -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/DataStructs/DiscreteValueVect.cpp
[ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o
cd /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/DataStructs && /usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -DDataStructs_EXPORTS -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DUSE_BUILTIN_POPCOUNT -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include -I/tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code -mpopcnt -std=c++11 -stdlib=libc++ -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.11 -fPIC -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/DataStructs/FPBReader.cpp
[ 9%] Linking CXX shared library ../../lib/libSimDivPickers.dylib
cd /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/SimDivPickers && /usr/local/Cellar/cmake/3.7.2/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -mpopcnt -std=c++11 -stdlib=libc++ -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.11 -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2016.3.3 -o ../../lib/libSimDivPickers.2016.03.3.dylib -install_name /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/lib/libSimDivPickers.1.dylib CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libhc.2016.03.3.dylib ../../lib/libRDGeneral.2016.03.3.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib
cd /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/SimDivPickers && /usr/local/Cellar/cmake/3.7.2/bin/cmake -E cmake_symlink_library ../../lib/libSimDivPickers.2016.03.3.dylib ../../lib/libSimDivPickers.1.dylib ../../lib/libSimDivPickers.dylib
[ 9%] Built target SimDivPickers
[ 10%] Linking CXX shared library ../../lib/libDataStructs.dylib
cd /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/DataStructs && /usr/local/Cellar/cmake/3.7.2/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/super/clang++ -mpopcnt -std=c++11 -stdlib=libc++ -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -mmacosx-version-min=10.11 -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2016.3.3 -o ../../lib/libDataStructs.2016.03.3.dylib -install_name /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/lib/libDataStructs.1.dylib CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o ../../lib/libRDGeneral.2016.03.3.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_thread-mt.dylib /usr/local/lib/libboost_system-mt.dylib
cd /tmp/rdkit-20170327-4568-p4wyky/rdkit-Release_2016_03_3/Code/DataStructs && /usr/local/Cellar/cmake/3.7.2/bin/cmake -E cmake_symlink_library ../../lib/libDataStructs.2016.03.3.dylib ../../lib/libDataStructs.1.dylib ../../lib/libDataStructs.dylib
[ 10%] Built target DataStructs
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/rdkit/homebrew-rdkit/issues

These open issues may also help:
Homebrew installs old version of RDKit #39
Installing RDKit on Mac OSX 10.10.2 with java and inchi #25

inchi doesn't seem to be working, even though I did brew install --with-inchi rdkit. I pulled ethanol examples from wikipedia's inchi page, and generating the mol doesn't work.
All of these,

> mol = Chem.MolFromInchi(u'InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3')
> mol = Chem.MolFromInchi(u'InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3/m0/s1')
> mol = Chem.MolFromInchi(u'InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3')
> mol = Chem.MolFromInchi(u'InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3/m0/s1')
> mol = Chem.MolFromInchi(u'1/C2H6O/c1-2-3/h3H,2H2,1H3')
> mol = Chem.MolFromInchi(u'1/C2H6O/c1-2-3/h3H,2H2,1H3/m0/s1')
> mol = Chem.MolFromInchi(u'1S/C2H6O/c1-2-3/h3H,2H2,1H3')
> mol = Chem.MolFromInchi(u'1S/C2H6O/c1-2-3/h3H,2H2,1H3/m0/s1')

raise the same ArgumentError:

---------------------------------------------------------------------------
ArgumentError                             Traceback (most recent call last)
<ipython-input-30-32b267697aff> in <module>()
----> 1 mol = Chem.MolFromInchi(u'InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3')

/Users/nathan/.virtualenvs/A0/lib/python2.7/site-packages/rdkit/Chem/inchi.pyc in MolFromInchi(inchi, sanitize, removeHs, logLevel, treatWarningAsError)
     69     """
     70     try:
---> 71         mol, retcode, message, log = rdinchi.InchiToMol(inchi, sanitize, removeHs)
     72     except ValueError as e :
     73         logger.error(str(e))

ArgumentError: Python argument types in
    rdkit.Chem.rdinchi.InchiToMol(unicode, bool, bool)
did not match C++ signature:
    InchiToMol(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > inchi, bool sanitize=True, bool removeHs=True)

Other observations:
If I don't pass a unicode string (i.e. drop the "u"), it returns NoneType.
MolFromSmiles works.
I tried adding True, True as arguments and that got the same error.

I tried to install rdkit with brew and got an error:

$ brew install rdkit --with-python3 --with-inchi --with-avalon --with-postgresql --with-pycairo
==> Installing rdkit from rdkit/rdkit
Warning: A newer Command Line Tools release is available.
Update them from Software Update in System Preferences or
https://developer.apple.com/download/more/.

==> Installing dependencies for rdkit/rdkit/rdkit: py3cairo
==> Installing rdkit/rdkit/rdkit dependency: py3cairo
==> Downloading https://homebrew.bintray.com/bottles/py3cairo-1.18.2.catalina.bottle.tar.gz
######################################################################## 100.0%
==> Pouring py3cairo-1.18.2.catalina.bottle.tar.gz
�  /usr/local/Cellar/py3cairo/1.18.2: 16 files, 321.2KB
==> Installing rdkit/rdkit/rdkit --with-inchi --with-postgresql --with-avalon --with-pycairo --with-python3
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/jinserk/Library/Caches/Homebrew/downloads/dbc78c6529381ce39a1c4765d1b16ec83572d3c1ad3cfde3d65efc15a6bfc66f--rdkit-Release_2019_09_1.tar.gz
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/rdkit/2019.09.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev -DRDK_INSTA
==> make -j8
==> make install
Error: An exception occurred within a child process:
  Errno::ENOENT: No such file or directory @ rb_file_s_rename - (Code/PgSQL/rdkit/rdkit.sql91.in, Code/PgSQL/rdkit/rdkit--3.4.sql)

It's the same even though I don't give --with-postgresql option.

While installing RDKit through Homebrew it reports a deprecated call:

Warning: Calling Formula#std_cmake_parameters is deprecated!
Use Formula#std_cmake_args instead.
/usr/local/Homebrew/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb:36:in `install'
Please report this to the rdkit/rdkit tap!

I shall send a PR in a moment with a fix.

Installing with the --with-java option does not work for me:
https://gist.github.com/tdudgeon/5213f4b4342b298c26ad23296dd0871e
With plain:
brew install rdkit
it works fine.
This is on El Capitan 10.11.5