Having trouble installing rdkit on Mac OS X 10.10.3

[shenkin]

Hi,

I'm having trouble installing RDKit on a Mac running Yosemite 10.10.3.

I first built a Python virtualenv based on my system installation and activated it.

The first effort to "brew install rdkit" seemd to implicate boost as the cause of failure, so I uninstalled and rebuilt boost, which appeared to succeed.

When trying again to intall rdkit, it failed with the following in ~/Library/Logs/Homebrew/rdkit/02.make:

[  8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o
[  9%] [  9%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o
Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o
[ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o
Linking CXX shared library ../../lib/libSimDivPickers.dylib
[ 10%] [ 11%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o
[ 11%] Built target SimDivPickers
[ 11%] Linking CXX shared library ../../../lib/libEigenSolvers.dylib
[ 12%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o
[ 12%] Built target EigenSolvers
Linking CXX shared library ../../lib/libCatalogs.dylib
[ 12%] Built target Catalogs
Linking CXX shared library ../../lib/libDataStructs.dylib
[ 12%] Built target DataStructs
make: *** [all] Error 2

When I run the 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 {} \;

I get:

> python-config --prefix
/System/Library/Frameworks/Python.framework/Versions/2.7
> find /usr/local/Cellar/rdkit -name rdBase.so -exec otool -L {} \;
find: /usr/local/Cellar/rdkit: No such file or directory
> find /usr/local/Cellar/boost -name libboost_python-mt.dylib -exec otool -L {} \;
> 

Any suggestions?

[mcs07]

Probably caused by the virtualenv. See https://github.com/rdkit/homebrew-rdkit/issues/20 for more info.

[shenkin]

Sounds good. I will try Anaconda. Reponse appreciated. I will report back after trying, which won't be for a few days.

[shenkin]

I have given up on virtualenv-like things and just want to try brew with the system Python. I am still encountering problems, but will post them elsewhere following a search. Closing this case in the meantime.