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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Formula not building till the end #81

Closed Adafede closed 4 years ago

Adafede commented 4 years ago

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

UnixJunkie commented 4 years ago

Try removing all the --with options. I guess one of them is breaking the build. I know --with-java is broken https://github.com/rdkit/homebrew-rdkit/issues/38, for example. The bare minimum would be:

brew install --with-python3 --with-inchi
Adafede commented 4 years ago

Wow, quick reply!

1st trial:

Adriano:~ rutza$ brew install --with-python3 --with-inchi rdkit
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/rutza/Library/Caches/Homebrew/downloads/dbc78c6529381ce39a1c4765d1b16ec83572d3c1ad3cfde3d65efc15a6bfc66f--rdkit-Release_2019_09_1.tar.gz
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
==> 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:
         ^~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o] Error 1
make[1]: *** [Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/all] Error 2
[ 29%] Linking CXX shared library ../../lib/libRDKitcoordgen.dylib
cd /tmp/rdkit-20191031-40250-13fqueh/rdkit-Release_2019_09_1/External/CoordGen && /usr/local/Cellar/cmake/3.15.4/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 /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/libRDKitcoordgen.2019.09.1.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/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-20191031-40250-13fqueh/rdkit-Release_2019_09_1/lib ../../lib/libRDKitmaeparser.2019.09.1.dylib /opt/local/lib/libboost_system-mt.dylib /opt/local/lib/libboost_iostreams-mt.dylib /opt/local/lib/libboost_regex-mt.dylib 
cd /tmp/rdkit-20191031-40250-13fqueh/rdkit-Release_2019_09_1/External/CoordGen && /usr/local/Cellar/cmake/3.15.4/bin/cmake -E cmake_symlink_library ../../lib/libRDKitcoordgen.2019.09.1.dylib ../../lib/libRDKitcoordgen.1.dylib ../../lib/libRDKitcoordgen.dylib
[ 29%] Built target coordgen
make[1]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2
[ 29%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20191031-40250-13fqueh/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-20191031-40250-13fqueh/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 
[ 29%] Built target rdBase
make: *** [all] Error 2

2nd:

Adriano:~ rutza$ brew install --with-python3 --with-inchi --without-numpy rdkit 
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/rutza/Library/Caches/Homebrew/downloads/dbc78c6529381ce39a1c4765d1b16ec83572d3c1ad3cfde3d65efc15a6bfc66f--rdkit-Release_2019_09_1.tar.gz
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
==> 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:
cd /tmp/rdkit-20191031-42209-12lmrm4/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
[ 29%] Built target RDGeometryLib
In file included from /tmp/rdkit-20191031-42209-12lmrm4/rdkit-Release_2019_09_1/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:13:
/tmp/rdkit-20191031-42209-12lmrm4/rdkit-Release_2019_09_1/Code/RDBoost/import_array.h:6:10: fatal error: 'numpy/arrayobject.h' file not found
#include <numpy/arrayobject.h>
         ^~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o] Error 1
make[1]: *** [Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all] Error 2
make[1]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2
[ 29%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20191031-42209-12lmrm4/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-20191031-42209-12lmrm4/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 
[ 29%] Built target rdBase
make: *** [all] Error 2

Not there yet!

Adafede commented 4 years ago

Just did a quick step more by myself: 

Adriano:~ rutza$ brew reinstall numpy
==> Reinstalling numpy 
==> Downloading https://homebrew.bintray.com/bottles/numpy-1.17.2.catalina.bottle.tar.gz
Already downloaded: /Users/rutza/Library/Caches/Homebrew/downloads/85558c1300233c4616a3368b23f6eb4692823bdddd9acb24845a772936375afa--numpy-1.17.2.catalina.bottle.tar.gz
==> Pouring numpy-1.17.2.catalina.bottle.tar.gz
🍺  /usr/local/Cellar/numpy/1.17.2: 485 files, 15.6MB
Adriano:~ rutza$ brew install --with-python3 --with-inchi rdkit
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/rutza/Library/Caches/Homebrew/downloads/dbc78c6529381ce39a1c4765d1b16ec83572d3c1ad3cfde3d65efc15a6bfc66f--rdkit-Release_2019_09_1.tar.gz
Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/numpy/core/__init__.py", line 17, in <module>
    from . import multiarray
  File "/usr/local/lib/python3.7/site-packages/numpy/core/multiarray.py", line 14, in <module>
    from . import overrides
  File "/usr/local/lib/python3.7/site-packages/numpy/core/overrides.py", line 7, in <module>
    from numpy.core._multiarray_umath import (
ImportError: dlopen(/usr/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Symbol not found: ___addtf3
  Referenced from: /usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in /usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/usr/local/lib/python3.7/site-packages/numpy/core/__init__.py", line 47, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy c-extensions failed.
- Try uninstalling and reinstalling numpy.
- If you have already done that, then:
  1. Check that you expected to use Python3.7 from "/usr/local/opt/python/bin/python3.7",
     and that you have no directories in your PATH or PYTHONPATH that can
     interfere with the Python and numpy version "1.17.2" you're trying to use.
  2. If (1) looks fine, you can open a new issue at
     https://github.com/numpy/numpy/issues.  Please include details on:
     - how you installed Python
     - how you installed numpy
     - your operating system
     - whether or not you have multiple versions of Python installed
     - if you built from source, your compiler versions and ideally a build log

- If you're working with a numpy git repository, try `git clean -xdf`
  (removes all files not under version control) and rebuild numpy.

Note: this error has many possible causes, so please don't comment on
an existing issue about this - open a new one instead.

Original error was: dlopen(/usr/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Symbol not found: ___addtf3
  Referenced from: /usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in /usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib

==> 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:
cd /tmp/rdkit-20191031-44993-1x4gk8l/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
[ 29%] Built target RDGeometryLib
In file included from /tmp/rdkit-20191031-44993-1x4gk8l/rdkit-Release_2019_09_1/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:13:
/tmp/rdkit-20191031-44993-1x4gk8l/rdkit-Release_2019_09_1/Code/RDBoost/import_array.h:6:10: fatal error: 'numpy/arrayobject.h' file not found
#include <numpy/arrayobject.h>
         ^~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[2]: *** [Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o] Error 1
make[1]: *** [Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/all] Error 2
make[1]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2
[ 29%] Linking CXX shared module ../../../rdkit/rdBase.so
cd /tmp/rdkit-20191031-44993-1x4gk8l/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-20191031-44993-1x4gk8l/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 
[ 29%] Built target rdBase
make: *** [all] Error 2
UnixJunkie commented 4 years ago

Ok. Just an idea you might try:

brew uninstall numpy
pip3 install numpy
brew install --with-python3 --with-inchi
Adafede commented 4 years ago

Worked like a charm! 

Adriano:~ rutza$ brew uninstall numpy
Uninstalling /usr/local/Cellar/numpy/1.17.2... (485 files, 15.6MB)
Adriano:~ rutza$ pip3 install numpy
Collecting numpy
  Downloading https://files.pythonhosted.org/packages/ea/f4/acaa005b20777fc56a1dc0cae228ab2cb5a7f09a7e7fcb6d4619ce24a1b7/numpy-1.17.3-cp37-cp37m-macosx_10_9_x86_64.whl (15.1MB)
     |████████████████████████████████| 15.1MB 6.6MB/s 
Installing collected packages: numpy
Successfully installed numpy-1.17.3
Adriano:~ rutza$ brew install --with-python3 --with-inchi rdkit
==> Installing rdkit from rdkit/rdkit
==> Installing dependencies for rdkit/rdkit/rdkit: numpy
==> Installing rdkit/rdkit/rdkit dependency: numpy
==> Downloading https://homebrew.bintray.com/bottles/numpy-1.17.2.catalina.bottle.tar.gz
Already downloaded: /Users/rutza/Library/Caches/Homebrew/downloads/85558c1300233c4616a3368b23f6eb4692823bdddd9acb24845a772936375afa--numpy-1.17.2.catalina.bottle.tar.gz
==> Pouring numpy-1.17.2.catalina.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/f2py
Target /usr/local/bin/f2py
already exists. You may want to remove it:
  rm '/usr/local/bin/f2py'

To force the link and overwrite all conflicting files:
  brew link --overwrite numpy

To list all files that would be deleted:
  brew link --overwrite --dry-run numpy

Possible conflicting files are:
/usr/local/bin/f2py
/usr/local/bin/f2py3
/usr/local/bin/f2py3.7
/usr/local/lib/python3.7/site-packages/numpy/LICENSE.txt
/usr/local/lib/python3.7/site-packages/numpy/__config__.py
/usr/local/lib/python3.7/site-packages/numpy/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/_distributor_init.py
/usr/local/lib/python3.7/site-packages/numpy/_globals.py
/usr/local/lib/python3.7/site-packages/numpy/_pytesttester.py
/usr/local/lib/python3.7/site-packages/numpy/compat/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/compat/_inspect.py
/usr/local/lib/python3.7/site-packages/numpy/compat/py3k.py
/usr/local/lib/python3.7/site-packages/numpy/compat/setup.py
/usr/local/lib/python3.7/site-packages/numpy/compat/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/compat/tests/test_compat.py
/usr/local/lib/python3.7/site-packages/numpy/conftest.py
/usr/local/lib/python3.7/site-packages/numpy/core/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/core/_add_newdocs.py
/usr/local/lib/python3.7/site-packages/numpy/core/_aliased_types.py
/usr/local/lib/python3.7/site-packages/numpy/core/_asarray.py
/usr/local/lib/python3.7/site-packages/numpy/core/_dtype.py
/usr/local/lib/python3.7/site-packages/numpy/core/_dtype_ctypes.py
/usr/local/lib/python3.7/site-packages/numpy/core/_dummy.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/_exceptions.py
/usr/local/lib/python3.7/site-packages/numpy/core/_internal.py
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/usr/local/lib/python3.7/site-packages/numpy/testing/_private/parameterized.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/utils.py
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/usr/local/lib/python3.7/site-packages/numpy/testing/print_coercion_tables.py
/usr/local/lib/python3.7/site-packages/numpy/testing/setup.py
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/usr/local/lib/python3.7/site-packages/numpy/testing/tests/test_decorators.py
/usr/local/lib/python3.7/site-packages/numpy/testing/tests/test_doctesting.py
/usr/local/lib/python3.7/site-packages/numpy/testing/tests/test_utils.py
/usr/local/lib/python3.7/site-packages/numpy/testing/utils.py
/usr/local/lib/python3.7/site-packages/numpy/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_ctypeslib.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_matlib.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_numpy_version.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_public_api.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_reloading.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_scripts.py
/usr/local/lib/python3.7/site-packages/numpy/tests/test_warnings.py
/usr/local/lib/python3.7/site-packages/numpy/version.py
==> Summary
🍺  /usr/local/Cellar/numpy/1.17.2: 485 files, 15.6MB
==> Installing rdkit/rdkit/rdkit --with-inchi --with-python3
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_09_1.tar.gz
Already downloaded: /Users/rutza/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 
==> make -j12
==> 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: 1,569 files, 59.2MB, built in 4 minutes 26 seconds
==> Caveats
==> rdkit
      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

Many many thanks

UnixJunkie commented 4 years ago

I think the formula shouldn't install numpy, since there is one already installed by pip3. If you want to have a look at it one day...