Comments (27)
I fixed it by running:
mkdir -p /Users/nico/Library/Python/3.6/lib/python/site-packages
echo 'import site; site.addsitedir("/usr/local/lib/python3.6/site-packages")' >> /Users/<username>/Library/Python/3.6/lib/python/site-packages/homebrew.pth
Note: this is using python 3.6, change to your version, same with the username of your account
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I will try at home
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This is still an issue for me and my colleague, even with the suggestion from @UnixJunkie above.
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same thing for em on my Mac...
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Why isn't the formula doing all this stuffs!!!
How am I supposed to know about those...
I'm really annoyed by this formula, it's not automatic.
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I discovered it by looking into others trying to install python modules with brew, the commands came from the "caveats" in the brew install output from one of the dependencies... so no particularly obvious
from homebrew-rdkit.
Interesting. This really shouldn't be necessary. By any chance are you trying to import rdkit from a different python installation than the homebrew one?
which python3
should give something like /usr/local/bin/python3
And if you run import sys;print(sys.path)
in the python interpreter, you should see /usr/local/lib/python3.6/site-packages
already in there.... (without needing to add the homebrew.pth file)
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Thanks, I will try this.
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One thing I found is that when I tried to brew install rdkit --with-python3
. I got this:
Warning: rdkit: this formula has no --with-python3 option so it will be ignored!
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Forget that, it seems that my homebrew
has some problem.
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My python3 works for Homebrew-rdkit
, but I need to install through brew install rdkit/rdkit/rdkit --with-python3
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@UnixJunkie Is there any update of this ?
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This can be closed.
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I can repeatedly install rdkit using these steps:
pip3 install numpy
brew install --HEAD rdkit --with-python3 --with-inchi
This is no panacea, because it does not install a tagged release, but I can live with that for the moment.
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@Astrovicis did the brew install work? Can you paste the full log of it.
What is the output of 'which python3'?
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These days, you can even install a recently tagged version of rdkit:
brew tap rdkit/rdkit
which python3 || brew install python3
pip3 install numpy
brew install rdkit --with-inchi
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brew install log:
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2019_03_2.tar.gz
Already downloaded: /Users/maxhoward/Library/Caches/Homebrew/downloads/bfc63b18873a7e4cd38cb0629faa183240367686eef85d2251f3351efc03903e--rdkit-Release_2019_03_2.tar.gz
==> cmake -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG -D
Last 15 lines from /Users/maxhoward/Library/Logs/Homebrew/rdkit/01.cmake:
boost_pythonConfig.cmake
boost_python-config.cmake
Add the installation prefix of "boost_python" to CMAKE_PREFIX_PATH or set
"boost_python_DIR" to a directory containing one of the above files. If
"boost_python" provides a separate development package or SDK, be sure it
has been installed.
Call Stack (most recent call first):
/usr/local/lib/cmake/Boost-1.71.0/BoostConfig.cmake:182 (boost_find_component)
/usr/local/Cellar/cmake/3.15.3/share/cmake/Modules/FindBoost.cmake:443 (find_package)
CMakeLists.txt:255 (find_package)
-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-20190917-17742-10u5rc/rdkit-Release_2019_03_2/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
which python3 output:
/usr/local/bin/python3
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ok, the problem is that the current version of boost/boost-python in homebrew is not compatible with rdkit.
I don't know how to fix this easily.
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This one would be nice to prevent this problem in the future:
#65
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There was a related fix in the past:
rdkit/rdkit@738fc04
by @mcs07
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I suspect the previous version in homebrew was working.
I looked the history of this file:
https://github.com/Homebrew/homebrew-core/commits/master/Formula/boost.rb
That would be boost 1.70.0 or the one just before: boost 1.69.0_2.
And I guess the boost-python3 formula's version must also match.
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I fixed it by running:
mkdir -p /Users/nico/Library/Python/3.6/lib/python/site-packages
echo 'import site; site.addsitedir("/usr/local/lib/python3.6/site-packages")' >> /Users/<username>/Library/Python/3.6/lib/python/site-packages/homebrew.pth
Note: this is using python 3.6, change to your version, same with the username of your account
with this I still have the same error. MacOS: ModuleNotFoundError: No module named 'rdkit' #50
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@chenwenjie95 try to use the rdkit install recipe from this PR:
#73
You need to do a git checkout, checkout the correct branch then add this as a tap to your homebrew.
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@chenwenjie95 try this and tell us how it goes (with full log attached as a gist, if necessary):
brew update
which python3 || brew install python3
pip3 install numpy
brew unlink boost || echo boost_not_installed
brew unlink boost-python3 || echo boost-python3_not_installed
brew install rdkit --with-python3
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Long time without new feedback so closing.
If the problem persists, ask us the reopen the issue.
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I still have this problem
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Install the new rdkit recipe, not from this tap:
brew uninstall --force rdkit
brew untap rdkit/rdkit
brew update
brew install rdkit
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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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