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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Configuration errors occurred installing brew rdkit #12

Closed dr-frozenarm closed 10 years ago

dr-frozenarm commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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.