OSX 10.10.2 Issue? about homebrew-rdkit HOT 4 CLOSED

I think the --with-java option hasn't worked for a while. But brew install rdkit and brew install rdkit --HEAD should both work fine.

Could you try doing brew install rdkit --HEAD --verbose --debug and post the full output?

from homebrew-rdkit.

(venv)MacBook-Pro:~ $ brew install rdkit --HEAD --verbose --debug
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
==> Installing rdkit from rdkit/homebrew-rdkit
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb
/usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb
/usr/bin/env python -c import numpy
/usr/local/Library/Homebrew/build.rb (Formulary::FromPathLoader): loading /usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/boost-python.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/cmake.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/wget.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/git.rb
/usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/python.rb
/usr/bin/env python -c import numpy
==> Cloning https://github.com/rdkit/rdkit.git
git --git-dir /Library/Caches/Homebrew/rdkit--git/.git status -s
Updating /Library/Caches/Homebrew/rdkit--git
git config remote.origin.url https://github.com/rdkit/rdkit.git
git config remote.origin.fetch +refs/heads/master:refs/remotes/origin/master
git fetch origin
git checkout -f master --
Already on 'master'
Your branch is up-to-date with 'origin/master'.
git reset --hard origin/master
HEAD is now at d3d362a merge master
==> Checking out branch master
==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -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_EXECUTABLE='/venv/bin/python' -DPYTHON_INCLUDE_DIR='/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7' -DPYTHON_LIBRARY='/venv/bin/../lib/libpython2.7.dylib' -DPYTHON_NUMPY_INCLUDE_PATH='/venv/lib/python2.7/site-packages/numpy/core/include' .
-- The C compiler identification is AppleClang 6.0.0.6000057
-- The CXX compiler identification is AppleClang 6.0.0.6000057
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - 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 PythonInterp: /venv/bin/python (found version "2.7.9")
-- Found PythonLibs: /venv/lib/libpython2.7.dylib (found version "2.7.9")
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- python
Python Install directory /usr/local/Cellar/rdkit/HEAD/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
-- Build files have been written to: /tmp/rdkit20150404-6468-ri0mgh
==> make
Scanning dependencies of target inchi_support
Scanning dependencies of target hc
[ 1%] [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o
[ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o
Built target inchi_support
Linking C shared library ../../../../lib/libhc.dylib
Scanning dependencies of target ChemicalFeatures
Scanning dependencies of target RDGeneral
[ 2%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o
Scanning dependencies of target RDBoost
[ 2%] [ 3%] [ 3%] [ 3%] [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o
Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o
Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o
Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o
Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o
[ 4%] Built target hc
make[2]: *** No rule to make target /venv/lib/libpython2.7.dylib', needed bylib/libRDBoost.2015.03.1pre.dylib'. Stop.
make[2]: *** Waiting for unfinished jobs....
[ 5%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o
Linking CXX shared library ../../lib/libChemicalFeatures.dylib
[ 5%] Built target ChemicalFeatures
Linking CXX shared library ../../lib/libRDGeneral.dylib
[ 5%] Built target RDGeneral
Scanning dependencies of target EigenSolvers
Scanning dependencies of target SimDivPickers
Scanning dependencies of target DataStructs
[ 5%] [ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o
[ 6%] [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o
Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o
Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o
Scanning dependencies of target Catalogs
make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 6%] [ 7%] [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o
[ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o
[ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o
[ 9%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o
[ 9%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o
Linking CXX shared library ../../lib/libSimDivPickers.dylib
[ 9%] Built target SimDivPickers
[ 9%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o
[ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o
Linking CXX shared library ../../../lib/libEigenSolvers.dylib
[ 10%] [ 10%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o
Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o
[ 10%] Built target EigenSolvers
Linking CXX shared library ../../lib/libCatalogs.dylib
[ 10%] Built target Catalogs
Linking CXX shared library ../../lib/libDataStructs.dylib
[ 10%] Built target DataStructs
make: *** [all] Error 2
/usr/local/Library/Homebrew/debrew.rb:11:in `raise'
BuildError: Failed executing: make

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
   ORIGIN: https://github.com/Homebrew/homebrew
   HEAD: 3e2a79a38e459b3e85dcc50fdb1864c4fc9e6a1e
   Last commit: 12 hours ago
   HOMEBREW_PREFIX: /usr/local
   HOMEBREW_CELLAR: /usr/local/Cellar
   CPU: 8-core 64-bit haswell
   OS X: 10.10.2-x86_64
   Xcode: N/A
   CLT: 6.2.0.0.1.1424975374
   Clang: 6.0 build 600
   X11: N/A
   System Ruby: 2.0.0-p481
   Perl: /usr/bin/perl
   Python: /venv/bin/python => /venv/bin/python2.7
   Ruby: /usr/bin/ruby
   Java: 1.6.0_65
   ==> ENV
   HOMEBREW_CC: clang
   HOMEBREW_CXX: clang++
   MAKEFLAGS: -j8
   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/10.10
   ACLOCAL_PATH: /usr/local/share/aclocal
   PATH: /venv/bin:/venv/bin:/usr/local/Library/ENV/4.3:/usr/local/opt/cmake/bin:/usr/local/opt/wget/bin:/usr/local/opt/python/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: rdkit HEAD did not build
Logs:
/Library/Logs/Homebrew/rdkit/01.cmake
/Library/Logs/Homebrew/rdkit/01.cmake.cc
/Library/Logs/Homebrew/rdkit/02.make
/Library/Logs/Homebrew/rdkit/02.make.cc
/Library/Logs/Homebrew/rdkit/CMakeCache.txt

from homebrew-rdkit.

Ah, I think the problem is caused by the virtualenv. See #20 for a workaround that might help.

from homebrew-rdkit.

Ah yes thanks. I found I had to use the native python when installing the RDKit formula. Then create the virtualenv and then copy the libraries into the new virtualenv. I found that installing python with brew and attempting this failed. Thanks for your help.

from homebrew-rdkit.