OSX 10.10.2 Issue?

[huwdjones]

Hi,

Is there a problem with the formula. I'm using Yosemite OSX 10.10.2? See below for output:

(venv)MacBook-Pro:~ $ brew tap rdkit/rdkit Cloning into '/usr/local/Library/Taps/rdkit/homebrew-rdkit'... remote: Counting objects: 221, done. remote: Total 221 (delta 0), reused 0 (delta 0), pack-reused 221 Receiving objects: 100% (221/221), 35.39 KiB | 0 bytes/s, done. Resolving deltas: 100% (53/53), done. Checking connectivity... done. Tapped 1 formula

(venv)MacBook-Pro:~ $ brew install --HEAD rdkit ==> Installing rdkit from rdkit/homebrew-rdkit rdkit: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy Error: An unsatisfied requirement failed this build.

(venv)MacBook-Pro:~ $ pip install numpy Collecting numpy Downloading numpy-1.9.2-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7MB) 100% |################################| 3.7MB 127kB/s Installing collected packages: numpy

Successfully installed numpy-1.9.2

(venv)MacBook-Pro:~ $ brew install --HEAD rdkit ==> Installing rdkit from rdkit/homebrew-rdkit ==> Installing dependencies for rdkit: cmake, wget, boost, boost-python ==> Installing rdkit dependency: cmake ==> Downloading https://homebrew.bintray.com/bottles/cmake-3.2.1.yosemite.bottle

100.0%

==> Pouring cmake-3.2.1.yosemite.bottle.2.tar.gz 🍺 /usr/local/Cellar/cmake/3.2.1: 1847 files, 32M ==> Installing rdkit dependency: wget ==> Downloading https://homebrew.bintray.com/bottles/wget-1.16.3.yosemite.bottle

100.0%

==> Pouring wget-1.16.3.yosemite.bottle.tar.gz 🍺 /usr/local/Cellar/wget/1.16.3: 9 files, 1.5M ==> Installing rdkit dependency: boost ==> Downloading https://homebrew.bintray.com/bottles/boost-1.57.0.yosemite.bottl

100.0%

==> Pouring boost-1.57.0.yosemite.bottle.tar.gz 🍺 /usr/local/Cellar/boost/1.57.0: 10572 files, 439M ==> Installing rdkit dependency: boost-python ==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.57.0/boo

39.6%^C

(venv)Huws-MacBook-Pro:~ huwdjones$ brew install --HEAD rdkit ==> Installing rdkit from rdkit/homebrew-rdkit ==> Installing rdkit dependency: boost-python ==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.57.0/boo

100.0%

==> ./bootstrap.sh --prefix=/usr/local/Cellar/boost-python/1.57.0 --libdir=/usr/ ==> ./b2 --build-dir=build-python --stagedir=stage-python python=2.7 --prefix=/u 🍺 /usr/local/Cellar/boost-python/1.57.0: 5 files, 11M, built in 90 seconds ==> Installing rdkit ==> Cloning https://github.com/rdkit/rdkit.git Cloning into '/Library/Caches/Homebrew/rdkit--git'... remote: Counting objects: 2632, done. remote: Compressing objects: 100% (2169/2169), done. remote: Total 2632 (delta 543), reused 1541 (delta 387), pack-reused 0 Receiving objects: 100% (2632/2632), 23.32 MiB | 683.00 KiB/s, done. Resolving deltas: 100% (543/543), done. Checking connectivity... done. ==> Checking out branch master ==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TY ==> make 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

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

(venv)MacBook-Pro:~ $ brew doctor Your system is ready to brew. (venv)MacBook-Pro:~ $ brew update Already up-to-date. (venv)MacBook-Pro:~ $ brew install --HEAD rdkit ==> Installing rdkit from rdkit/homebrew-rdkit ==> Cloning https://github.com/rdkit/rdkit.git Updating /Library/Caches/Homebrew/rdkit--git ==> Checking out branch master ==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TY ==> make 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

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

(venv)MacBook-Pro:~ $ brew install --HEAD rdkit --with-java ==> Installing rdkit from rdkit/homebrew-rdkit ==> Installing dependencies for rdkit: pcre, swig ==> Installing rdkit dependency: pcre ==> Downloading https://homebrew.bintray.com/bottles/pcre-8.36.yosemite.bottle.t

100.0%

==> Pouring pcre-8.36.yosemite.bottle.tar.gz 🍺 /usr/local/Cellar/pcre/8.36: 146 files, 5.9M ==> Installing rdkit dependency: swig ==> Downloading https://homebrew.bintray.com/bottles/swig-3.0.5.yosemite.bottle.

100.0%

==> Pouring swig-3.0.5.yosemite.bottle.tar.gz 🍺 /usr/local/Cellar/swig/3.0.5: 727 files, 7.1M ==> Installing rdkit ==> Cloning https://github.com/rdkit/rdkit.git Updating /Library/Caches/Homebrew/rdkit--git ==> Checking out branch master ==> mkdir External/java_lib ==> curl http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4 ==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TY ==> make ^ 15 errors generated. make[2]: * [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx.o] Error 1 make[1]: * [Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2 make: *\ [all] Error 2

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

(venv)Huws-MacBook-Pro:~ huwdjones$ brew --version 0.9.5 (venv)Huws-MacBook-Pro:~ huwdjones$ brew install rdkit ==> Installing rdkit from rdkit/homebrew-rdkit ==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_2.tar.gz

100.0%

==> cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/2014.09.2' -DCMAKE_BUI ==> make 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

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

[mcs07]

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?

[huwdjones]

(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

[mcs07]

Ah, I think the problem is caused by the virtualenv. See https://github.com/rdkit/homebrew-rdkit/issues/20 for a workaround that might help.

[huwdjones]

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.