Configuration: RDKit Version: with Python3 Oper

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Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0") about homebrew-rdkit HOT 5 CLOSED

aravind1338 commented on July 4, 2024

Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0")

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Comments (5)

whymauri commented on July 4, 2024 1

Try this:

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

Based on: rdkit/rdkit#1995 (comment)
Cheers.

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UnixJunkie commented on July 4, 2024

probably related to #87

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UnixJunkie commented on July 4, 2024

probably also related to rdkit/rdkit#3030

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UnixJunkie commented on July 4, 2024

@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

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UnixJunkie commented on July 4, 2024

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

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