Installing on MacBook Air running Mojave failed

rdkit / homebrew-rdkit

Homebrew formula for rdkit

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Installing on MacBook Air running Mojave failed #83

Closed pducrot closed 4 years ago

pducrot commented 4 years ago

Hi, Installing on MacBook Air running Mojave 10.14.6 failed with both commands, see error message below. Cheers

brew install --HEAD --with-inchi --with-postgresql --with-avalon rdkit and brew install rdkit

CMake Error at /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message): Could NOT find Boost (missing: Boost_INCLUDE_DIR python) (Required is at least version "1.56.0") Call Stack (most recent call first): /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE) /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindBoost.cmake:2161 (find_package_handle_standard_args) CMakeLists.txt:262 (find_package)

-- Configuring incomplete, errors occurred! See also "/tmp/rdkit-20191123-477-1laiqx0/CMakeFiles/CMakeOutput.log".

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core): https://github.com/rdkit/homebrew-rdkit/issues

UnixJunkie commented 4 years ago

You should try adding '--with-python3' to your options. I guess it will force installing the missing dependency.

pducrot commented 4 years ago

brew install --HEAD --with-inchi --with-postgresql --with-avalon --with-python3 rdkit

still failing: CMake Error at /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message): Could NOT find Boost (missing: Boost_INCLUDE_DIR python) (Required is at least version "1.56.0") Call Stack (most recent call first): /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE) /usr/local/Cellar/cmake/3.15.5/share/cmake/Modules/FindBoost.cmake:2161 (find_package_handle_standard_args) CMakeLists.txt:262 (find_package)

UnixJunkie commented 4 years ago

Maybe you do have boost, but it is too old. Try this:

brew reinstall boost boost-python3

If this work, check the version that was installed, then retry to install rdkit.

pducrot commented 4 years ago

For those who might have similar issues:

/usr/local/lib/cmake folder had wrong access rights due to former installations (2014!)
boost didn't link properly and was probably absent of rdkit 2018 install Error: Could not symlink lib/cmake/boost_numpy-1.71.0
some dependencies were built with different standard Warning boost-python3 dependency gcc was built with a different C++ standard

Solution

updated cmake access rights
reinstalled rdkit from scratch, with neither the --HEAD nor the --with-postgresql options

UnixJunkie commented 4 years ago

Thanks for documenting your solution. Brew builds are not super reproducible...