Comments (6)
UnixJunkie
commented on June 22, 2024
Try removing all the --with options.
I guess one of them is breaking the build.
I know --with-java is broken #38, for example.
The bare minimum would be:
brew install --with-python3 --with-inchi
from homebrew-rdkit.
Adafede
commented on June 22, 2024
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!
from homebrew-rdkit.
Adafede
commented on June 22, 2024
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
from homebrew-rdkit.
UnixJunkie
commented on June 22, 2024
Ok. Just an idea you might try:
brew uninstall numpy
pip3 install numpy
brew install --with-python3 --with-inchi
from homebrew-rdkit.
Adafede
commented on June 22, 2024
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
/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py
/usr/local/lib/python3.7/site-packages/numpy/core/_multiarray_tests.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/_operand_flag_tests.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/_rational_tests.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/_string_helpers.py
/usr/local/lib/python3.7/site-packages/numpy/core/_struct_ufunc_tests.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/_type_aliases.py
/usr/local/lib/python3.7/site-packages/numpy/core/_ufunc_config.py
/usr/local/lib/python3.7/site-packages/numpy/core/_umath_tests.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/core/arrayprint.py
/usr/local/lib/python3.7/site-packages/numpy/core/cversions.py
/usr/local/lib/python3.7/site-packages/numpy/core/defchararray.py
/usr/local/lib/python3.7/site-packages/numpy/core/einsumfunc.py
/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py
/usr/local/lib/python3.7/site-packages/numpy/core/function_base.py
/usr/local/lib/python3.7/site-packages/numpy/core/generate_numpy_api.py
/usr/local/lib/python3.7/site-packages/numpy/core/getlimits.py
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/__ufunc_api.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/_neighborhood_iterator_imp.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/_numpyconfig.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayscalars.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/halffloat.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/multiarray_api.txt
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/noprefix.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_3kcompat.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_common.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_cpu.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_endian.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_interrupt.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_math.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_no_deprecated_api.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_os.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/numpyconfig.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/old_defines.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/oldnumeric.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/random/bitgen.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ufunc_api.txt
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ufuncobject.h
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/utils.h
/usr/local/lib/python3.7/site-packages/numpy/core/info.py
/usr/local/lib/python3.7/site-packages/numpy/core/lib/libnpymath.a
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/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_recfunctions.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_regression.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_shape_base.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_stride_tricks.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_twodim_base.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_type_check.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_ufunclike.py
/usr/local/lib/python3.7/site-packages/numpy/lib/tests/test_utils.py
/usr/local/lib/python3.7/site-packages/numpy/lib/twodim_base.py
/usr/local/lib/python3.7/site-packages/numpy/lib/type_check.py
/usr/local/lib/python3.7/site-packages/numpy/lib/ufunclike.py
/usr/local/lib/python3.7/site-packages/numpy/lib/user_array.py
/usr/local/lib/python3.7/site-packages/numpy/lib/utils.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/_umath_linalg.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/linalg/info.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/lapack_lite.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/linalg/linalg.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/setup.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/tests/test_build.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/tests/test_deprecations.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/tests/test_linalg.py
/usr/local/lib/python3.7/site-packages/numpy/linalg/tests/test_regression.py
/usr/local/lib/python3.7/site-packages/numpy/ma/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/ma/bench.py
/usr/local/lib/python3.7/site-packages/numpy/ma/core.py
/usr/local/lib/python3.7/site-packages/numpy/ma/extras.py
/usr/local/lib/python3.7/site-packages/numpy/ma/mrecords.py
/usr/local/lib/python3.7/site-packages/numpy/ma/setup.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_core.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_deprecations.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_extras.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_mrecords.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_old_ma.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_regression.py
/usr/local/lib/python3.7/site-packages/numpy/ma/tests/test_subclassing.py
/usr/local/lib/python3.7/site-packages/numpy/ma/testutils.py
/usr/local/lib/python3.7/site-packages/numpy/ma/timer_comparison.py
/usr/local/lib/python3.7/site-packages/numpy/ma/version.py
/usr/local/lib/python3.7/site-packages/numpy/matlib.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/defmatrix.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/setup.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_defmatrix.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_interaction.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_masked_matrix.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_matrix_linalg.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_multiarray.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_numeric.py
/usr/local/lib/python3.7/site-packages/numpy/matrixlib/tests/test_regression.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/_polybase.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/chebyshev.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/hermite.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/hermite_e.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/laguerre.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/legendre.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/polynomial.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/polyutils.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/setup.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_chebyshev.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_classes.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_hermite.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_hermite_e.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_laguerre.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_legendre.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_polynomial.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_polyutils.py
/usr/local/lib/python3.7/site-packages/numpy/polynomial/tests/test_printing.py
/usr/local/lib/python3.7/site-packages/numpy/random/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/random/_pickle.py
/usr/local/lib/python3.7/site-packages/numpy/random/bit_generator.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/bit_generator.pxd
/usr/local/lib/python3.7/site-packages/numpy/random/bounded_integers.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/common.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/common.pxd
/usr/local/lib/python3.7/site-packages/numpy/random/generator.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/info.py
/usr/local/lib/python3.7/site-packages/numpy/random/mt19937.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/mtrand.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/pcg64.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/philox.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/setup.py
/usr/local/lib/python3.7/site-packages/numpy/random/sfc64.cpython-37m-darwin.so
/usr/local/lib/python3.7/site-packages/numpy/random/tests/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/mt19937-testset-1.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/mt19937-testset-2.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/pcg64-testset-1.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/pcg64-testset-2.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/philox-testset-1.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/philox-testset-2.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/sfc64-testset-1.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/data/sfc64-testset-2.csv
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_direct.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_generator_mt19937.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_generator_mt19937_regressions.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_random.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_randomstate.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_randomstate_regression.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_regression.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_seed_sequence.py
/usr/local/lib/python3.7/site-packages/numpy/random/tests/test_smoke.py
/usr/local/lib/python3.7/site-packages/numpy/setup.py
/usr/local/lib/python3.7/site-packages/numpy/testing/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/__init__.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/decorators.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/noseclasses.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/nosetester.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/parameterized.py
/usr/local/lib/python3.7/site-packages/numpy/testing/_private/utils.py
/usr/local/lib/python3.7/site-packages/numpy/testing/decorators.py
/usr/local/lib/python3.7/site-packages/numpy/testing/noseclasses.py
/usr/local/lib/python3.7/site-packages/numpy/testing/nosetester.py
/usr/local/lib/python3.7/site-packages/numpy/testing/print_coercion_tables.py
/usr/local/lib/python3.7/site-packages/numpy/testing/setup.py
/usr/local/lib/python3.7/site-packages/numpy/testing/tests/__init__.py
/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
from homebrew-rdkit.
UnixJunkie
commented on June 22, 2024
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...
from homebrew-rdkit.
Related Issues (20)
- update to latest release HOT 2
- Add build with Cairo flag HOT 1
- Installs RDKit/Code into the wrong directory HOT 3
- Failing make at "[ 14%] Built target rdBase" HOT 2
- RDKit installation problem on macOS Big Sur HOT 7
- Installation Not Working HOT 1
- rdpath in dylibs is not set (10.15.7 intel) HOT 11
- Invalid option: --with-python3 HOT 16
- rdkit with pyenv HOT 2
- Invalid option --with-python3 HOT 4
- Installation Error on Mac 10.15.2 HOT 4
- Update README to reflect python3 only
- Failure to install on macOS Mojave HOT 12
- Problem with linker while compiling HOT 5
- Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0") HOT 5
- Failed to install on MacOS Mojave 10.14.6 HOT 6
- Build error in Ubuntu 16.04.6 LTS HOT 9
- Add rdkit.egg-info directory HOT 7
- rdkit installation problem in mac os catelina HOT 2
- RDKIt PostgreSQL cartrdige via brew HOT 8
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from homebrew-rdkit.