Configuration errors occurred installing brew rdkit

[dr-frozenarm]

Hi I am trying to install rdkit on mac os 10.9.4 using the brew installation process and I get the error bellow.
Could you walk me through the error as I am not sure what's the problem.
Thanks in advance.

used as include directory in directory /tmp/rdkit-qaDg/rdkit-Release_2014_03_1/Code/ChemicalFeatures/Wrap

-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-qaDg/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log".
See also "/tmp/rdkit-qaDg/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log".

READ THIS: https://github.com/Homebrew/homebrew/wiki/troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/rdkit/homebrew-rdkit/issues

[mcs07]

Can you re-run the same install command but add --debug --verbose to the end? So something like:

brew install rdkit --debug --verbose

This makes the error message a bit more descriptive.

[dr-frozenarm]

Hi Matt thanks for the quick reply.
I did run the
brew install rdkit --debug --verbose

This is what I am getting:

-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-2YH9/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log".
See also "/tmp/rdkit-2YH9/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log".
/usr/local/Library/Homebrew/formula.rb:559:in `block in system'
BuildError: Failed executing: cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.03.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_LIBRARY='/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Python' -DPYTHON_INCLUDE_DIR='/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Headers' .

1. raise
2. ignore
3. backtrace
4. irb
5. shell
   Choose an action: 1
   ==> Formula
   Tap: rdkit/homebrew-rdkit
   Path: /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
   ==> Configuration
   HOMEBREW_VERSION: 0.9.5
   HEAD: e8448bba8d6e79f4aa75f1e36fcb1b9ada8c75f2
   CPU: quad-core 64-bit ivybridge
   OS X: 10.9.4-x86_64
   Xcode: 5.1.1
   CLT: 6.0.0.0.1.1405597879
   X11: N/A
   ==> ENV
   HOMEBREW_CC: clang
   HOMEBREW_CXX: clang++
   MAKEFLAGS: -j4
   CMAKE_PREFIX_PATH: /usr/local
   CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
   CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
   CMAKE_FRAMEWORK_PATH: /usr/local/opt/python/Frameworks
   PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.9
   ACLOCAL_PATH: /usr/local/share/aclocal
   PATH: /Users/frozenarm/Virtualenvs/chemoinf/bin:/usr/local/Library/ENV/4.3:/usr/local/opt/cmake/bin:/usr/local/opt/wget/bin:/usr/local/opt/swig/bin:/usr/local/opt/python/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: rdkit 2014.03.1 did not build
Logs:
/Users/frozenarm/Library/Logs/Homebrew/rdkit/01.cmake
/Users/frozenarm/Library/Logs/Homebrew/rdkit/01.cmake.cc
/Users/frozenarm/Library/Logs/Homebrew/rdkit/CMakeCache.txt

Hope that helps.

[mcs07]

Hmm. The cmake command itself looks OK. Did cmake print any output above that error that might give a clue? The "correct" output should look something like this:

==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.03.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_LIBRARY='/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Python' -DPYTHON_INCLUDE_DIR='/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Headers' .
-- The C compiler identification is AppleClang 5.1.0.5030040
-- The CXX compiler identification is AppleClang 5.1.0.5030040
-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang
-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++
-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Found PythonLibs: /usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Python (found version "2.7.8") 
-- Found PythonInterp: /usr/local/bin/python (found version "2.7.8") 
-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/local/Cellar/rdkit/2014.03.1/lib/python2.7/site-packages
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Configuring done
-- Generating done

If your output looks the same, the next step would be to look at the content of those cmake log files listed at the end of the error output.

[dr-frozenarm]

This is what I am getting:

==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_03_1.tar.gz
Already downloaded: /Library/Caches/Homebrew/rdkit-2014.03.1.tar.gz
==> Verifying rdkit-2014.03.1.tar.gz checksum
tar xf /Library/Caches/Homebrew/rdkit-2014.03.1.tar.gz
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.03.1' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_LIBRARY='/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Python' -DPYTHON_INCLUDE_DIR='/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Headers' .
-- The C compiler identification is AppleClang 5.1.0.5030040
-- The CXX compiler identification is AppleClang 5.1.0.5030040
-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang
-- Check for working C compiler: /usr/local/Library/ENV/4.3/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++
-- Check for working CXX compiler: /usr/local/Library/ENV/4.3/clang++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Found PythonLibs: /usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/Python (found version "2.7.8")
-- Found PythonInterp: /usr/local/bin/python (found version "2.7.8")
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- python
Python Install directory /usr/local/Cellar/rdkit/2014.03.1/lib/python2.7/site-packages
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
PYTHON_NUMPY_INCLUDE_PATH
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/External/INCHI-API
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/RDGeneral
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/RDBoost
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/RDBoost/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/DataStructs
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/DataStructs/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Geometry
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Geometry/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Numerics/Alignment
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Numerics/Alignment/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Numerics/EigenSolvers
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Numerics/Optimizer
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ForceField
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ForceField/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/DistGeom
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/DistGeom/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/Catalogs
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Depictor
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Depictor/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/SmilesParse
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/FileParsers
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Substruct
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ChemReactions
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ChemReactions/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ChemTransforms
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Subgraphs
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/FragCatalog
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/FragCatalog/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Descriptors
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Descriptors/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Fingerprints
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/PartialCharges
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/PartialCharges/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolTransforms
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolTransforms/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ForceFieldHelpers
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ForceFieldHelpers/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/DistGeomHelpers
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/DistGeomHelpers/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolAlign
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolAlign/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolChemicalFeatures
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolChemicalFeatures/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ShapeHelpers
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/ShapeHelpers/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolCatalog
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/MolCatalog/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/GraphMol/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/DataManip/MetricMatrixCalc/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/SimDivPickers
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/SimDivPickers/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ML/Cluster/Murtagh
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ML/Cluster/Murtagh
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ML/InfoTheory
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ML/InfoTheory/Wrap
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ML/Data
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ChemicalFeatures
used as include directory in directory /tmp/rdkit-2YH9/rdkit-Release_2014_03_1/Code/ChemicalFeatures/Wrap

If it helps numpy works fine.

[mcs07]

cmake isn't finding numpy for some reason. I have submitted an update to the rdkit homebrew formula (#13) that I think should fix the problem (although it's hard to be sure, as I can't replicate your issue).

Once @greglandrum takes a look, if he approves and merges, you will need to run a brew update to pull down the changes before trying to install again.