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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Failing make at "[ 14%] Built target rdBase" #107

Closed rynecjohnston closed 3 years ago

rynecjohnston commented 3 years ago

I can't seem to install rdkit from the brew recipe on my MacOS Big Sur machine. I've had this issue for this rdkit release as well as the previous rdkit release/MacOS Catalina. I have tried uninstalling all the brew dependencies, but still this happens. Any ideas on what might be going on?


05:26:12 PM brew install rdkit --with-python3
Error:
  homebrew-core is a shallow clone.
To `brew update`, first run:
  git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch --unshallow
This restriction has been made on GitHub's request because updating shallow
clones is an extremely expensive operation due to the tree layout and traffic of
Homebrew/homebrew-core and Homebrew/homebrew-cask. We don't do this for you
automatically to avoid repeatedly performing an expensive unshallow operation in
CI systems (which should instead be fixed to not use shallow clones). Sorry for
the inconvenience!
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2020_09_1.tar.gz
Already downloaded: /Users/ryne/Library/Caches/Homebrew/downloads/377d0a717f4f8caf8be184a84798d57935742421c99a356ce30bd1222cb745f0--rdkit-Release_2020_09_1.tar.gz
detected clang C++ compiler
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_STATIC_LIBS=OFF -DBoost_NO_BOOST_CMAKE=ON -DPYTHON_EXECU
==> make -j4
Last 15 lines from /Users/ryne/Library/Logs/Homebrew/rdkit/02.make:
[ 13%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.dylib
cd /tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/Code/SimDivPickers && /usr/local/Cellar/cmake/3.19.2/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -stdlib=libc++ -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/MacOSX.sdk -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2020.9.1 -o ../../lib/libRDKitSimDivPickers.2020.09.1.dylib -install_name @rpath/libRDKitSimDivPickers.1.dylib CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o  -Wl,-rpath,/tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/lib ../../lib/libRDKithc.2020.09.1.dylib ../../lib/libRDKitRDGeneral.2020.09.1.dylib
cd /tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/Code/SimDivPickers && /usr/local/Cellar/cmake/3.19.2/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.2020.09.1.dylib ../../lib/libRDKitSimDivPickers.1.dylib ../../lib/libRDKitSimDivPickers.dylib
[ 13%] Built target SimDivPickers
[ 13%] Linking CXX shared library ../../lib/libRDKitDataStructs.dylib
cd /tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/Code/DataStructs && /usr/local/Cellar/cmake/3.19.2/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -stdlib=libc++ -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/MacOSX.sdk -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2020.9.1 -o ../../lib/libRDKitDataStructs.2020.09.1.dylib -install_name @rpath/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  -Wl,-rpath,/tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/lib ../../lib/libRDKitRDGeneral.2020.09.1.dylib
cd /tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/Code/DataStructs && /usr/local/Cellar/cmake/3.19.2/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.2020.09.1.dylib ../../lib/libRDKitDataStructs.1.dylib ../../lib/libRDKitDataStructs.dylib
[ 13%] Built target DataStructs
[ 14%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/Code/RDBoost/Wrap && /usr/local/Cellar/cmake/3.19.2/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 -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -stdlib=libc++ -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/MacOSX.sdk -bundle -Wl,-headerpad_max_install_names -bundle -undefined dynamic_lookup -L/usr/local/lib -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o  -Wl,-rpath,/tmp/rdkit-20201229-28334-12ha57z/rdkit-Release_2020_09_1/lib ../../../lib/libRDKitRDBoost.2020.09.1.dylib ../../../lib/libRDKitRDGeneral.2020.09.1.dylib /usr/local/lib/libboost_python39-mt.dylib
[ 14%] 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

These open issues may also help:
Installs RDKit/Code into the wrong directory https://github.com/rdkit/homebrew-rdkit/issues/106
RDKIt PostgreSQL cartrdige via brew https://github.com/rdkit/homebrew-rdkit/issues/99
Add rdkit.egg-info directory https://github.com/rdkit/homebrew-rdkit/issues/97
rdkit installation problem in mac os catelina https://github.com/rdkit/homebrew-rdkit/issues/98```
rynecjohnston commented 3 years ago

I nuked my entire OS, then reinstalled and it worked.

UnixJunkie commented 3 years ago

maybe nuking brew would have been enough