Comments (5)
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.
from homebrew-rdkit.
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' .
- raise
- ignore
- backtrace
- irb
- 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.
from homebrew-rdkit.
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.
from homebrew-rdkit.
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.
from homebrew-rdkit.
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.
from homebrew-rdkit.
Related Issues (20)
- update to latest release HOT 2
- Add build with Cairo flag HOT 1
- Installs RDKit/Code into the wrong directory HOT 3
- Failing make at "[ 14%] Built target rdBase" HOT 2
- RDKit installation problem on macOS Big Sur HOT 7
- Installation Not Working HOT 1
- rdpath in dylibs is not set (10.15.7 intel) HOT 11
- Invalid option: --with-python3 HOT 16
- rdkit with pyenv HOT 2
- Invalid option --with-python3 HOT 4
- Installation Error on Mac 10.15.2 HOT 4
- Update README to reflect python3 only
- Failure to install on macOS Mojave HOT 12
- Problem with linker while compiling HOT 5
- Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0") HOT 5
- Failed to install on MacOS Mojave 10.14.6 HOT 6
- Build error in Ubuntu 16.04.6 LTS HOT 9
- Add rdkit.egg-info directory HOT 7
- rdkit installation problem in mac os catelina HOT 2
- RDKIt PostgreSQL cartrdige via brew HOT 8
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from homebrew-rdkit.