shashj199
commented
7 years ago Hey,
I was able to install rdkit successfully by following commands:
- brew uninstall python
- brew uninstall boost
- brew reinstall python
- brew link --overwrite python
- brew install rdkit
Please close this and thank you
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 https://github.com/rdkit/homebrew-rdkit/issues/39 Installing RDKit on Mac OSX 10.10.2 with java and inchi https://github.com/rdkit/homebrew-rdkit/issues/25