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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0") #89

Closed aravind1338 closed 3 years ago

aravind1338 commented 4 years ago

Configuration:

RDKit Version: with Python3 Operating system: macOS 10.15.5 Python version (if relevant): how did you install the RDKit? Using the command

brew install --with-python3 rdkit

Description:

The installation downloads all the dependencies, but it throws an error "Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0")".

I'm new to downloading stuff with brew, so I'm not quite sure what to do.

UnixJunkie commented 4 years ago

probably related to https://github.com/rdkit/homebrew-rdkit/issues/87

UnixJunkie commented 4 years ago

probably also related to https://github.com/rdkit/rdkit/issues/3030

whymauri commented 4 years ago

Try this:

cd /usr/local/lib
sudo ln -s $(ls | grep -Eo libboost_python3[0-9].dylib) libboost_python3.dylib

Based on: https://github.com/rdkit/rdkit/issues/1995#issuecomment-411263663 Cheers.

UnixJunkie commented 4 years ago

@whymauri this fixes the compilation, however, you cannot import rdkit from python after that.

# python3 --version
Python 3.7.7
# python3   
Python 3.7.7 (default, Mar 10 2020, 15:43:03) 
[Clang 11.0.0 (clang-1100.0.33.17)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.7/site-packages/rdkit/__init__.py", line 2, in <module>
    from .rdBase import rdkitVersion as __version__
ImportError: dlopen(/usr/local/lib/python3.7/site-packages/rdkit/rdBase.so, 2): Symbol not found: __Py_tracemalloc_config
  Referenced from: /usr/local/opt/boost-python3/lib/libboost_python38.dylib
  Expected in: flat namespace
 in /usr/local/opt/boost-python3/lib/libboost_python38.dylib
UnixJunkie commented 3 years ago

You might try this:

# backup your brew installed packages list
brew list --formula > my_brew_packages.txt
# uninstall all of them
brew uninstall --force $(cat my_brew_packages.txt)
# install rdkit from scratch
brew install rdkit --with-python3