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30 changes: 0 additions & 30 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -31,35 +31,5 @@ If you want to stay on the edge and use the latest and greatest from GitHub:

By default, Homebrew will attempt to install and manage numpy for you, like all other dependencies. You may alternatively install and manage numpy separately, via `pip`. However, when installing rdkit with python 3, a pip-installed numpy for python 2 can prevent homebrew properly installing numpy for python 3. To solve this, make sure you use `pip` in both python 2 and 3:

pip install numpy
pip3 install numpy
brew install rdkit --with-python3 --without-numpy

Or use homebrew in both python 2 and 3:

pip uninstall numpy
pip3 uninstall numpy
brew install rdkit --with-python3

- *Fatal Python error: Interpreter not initialized (version mismatch?)*

This indicates that rdkit or one of its dependencies (e.g. boost) was linked
against a different version of Python than the one you are using it with.
Try rebuilding boost from source:

brew uninstall boost
brew install boost --build-from-source

If that doesn't fix it, try comparing the output of these three commands:

python-config --prefix
find /usr/local/Cellar/rdkit -name rdBase.so -exec otool -L {} \;
find /usr/local/Cellar/boost -name libboost_python-mt.dylib -exec otool -L {} \;

- *TypeError: No to_python (by-value) converter found for C++ type: boost::shared_ptr<RDKit::ROMol>*

This is likely due to a bug in boost-python v1.60, which has now been patched in the boost homebrew formula. To get the patch, run:

brew reinstall boost
brew reinstall rdkit