I certainly do have java installed, JAVA_HOME is set, and it looks like
it is being found under
/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home/
This is the Apple provided JDK for Java 6.
The version being used is 1.6.0_65.
MacOS is version 10.9.4.
I tried using Oracle supplied Java 7 and get further but still hit problems.
$ brew install rdkit --with-java --verbose --debug
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/cmake.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/wget.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/openssl.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/makedepend.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/swig.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/pcre.rb
/usr/local/Library/brew.rb (Formulary::StandardLoader): loading
/usr/local/Library/Formula/boost.rb
/usr/bin/env python -c import numpy
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/boost.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/cmake.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/wget.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/openssl.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading
/usr/local/Library/Formula/makedepend.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading
/usr/local/Library/Formula/pkg-config.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/swig.rb
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/pcre.rb
/usr/bin/env python -c import numpy
/usr/local/Library/Taps/rdkit/homebrew-rdkit/Formula/rdkit.rb
(Formulary::StandardLoader): loading /usr/local/Library/Formula/python.rb
==> 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
==> mkdir External/java_lib
==> curl
http://search.maven.org/remotecontent?filepath=junit/junit/4.11/junit-4.11.jar
-o External/java_lib/junit.jar
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left Speed
100 239k 100 239k 0 0 126k 0 0:00:01 0:00:01 --:--:--
126k
==> 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_SWIG_WRAPPERS=ON
-DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF
-DPYTHON_LIBRARY='/System/Library/Frameworks/Python.framework/Versions/2.7/Python'
-DPYTHON_INCLUDE_DIR='/System/Library/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:
/System/Library/Frameworks/Python.framework/Versions/2.7/Python (found
version "2.7.5")
-- Found PythonInterp: /usr/bin/python (found version "2.7.5")
-- 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
-- Found SWIG: /usr/local/bin/swig (found version "3.0.2")
-- Found Java:
/Library/Java/JavaVirtualMachines/jdk1.7.0_55.jdk/Contents/Home/bin/java
(found version "1.7.0.55")
-- Found JNI:
/Library/Java/JavaVirtualMachines/jdk1.7.0_55.jdk/Contents/Home/jre/lib/libjawt.dylib
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/rdkit-T7Ao/rdkit-Release_2014_03_1
==> make
Scanning dependencies of target inchi_support
Scanning dependencies of target hc
[ 0%] [ 0%] Building C object
Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o
Built target inchi_support
[ 1%] Building C object
Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o
Linking C shared library ../../../../lib/libhc.dylib
Scanning dependencies of target InfoTheory
[ 1%] Building CXX object
Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o
[ 1%] Built target hc
Scanning dependencies of target RDBoost
[ 1%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o
Scanning dependencies of target RDGeneral
Scanning dependencies of target ChemicalFeatures
[ 1%] Building CXX object
Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o
[ 2%] Building CXX object
Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o
[ 3%] Building CXX object
Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o
Linking CXX static library libInfoTheory.a
[ 3%] Built target InfoTheory
[ 4%] Swig source
/usr/local/include/boost/smart_ptr/shared_array.hpp:60: Error: Syntax
error in input(3).
make[2]: ***
[Code/JavaWrappers/gmwrapper/src/org/RDKit/GraphMolJavaJAVA_wrap.cxx]
Error 1
make[1]: ***
[Code/JavaWrappers/gmwrapper/CMakeFiles/GraphMolWrap.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 4%] Building CXX object
Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o
[ 5%] Building CXX object
Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o
Linking CXX shared library ../../lib/libChemicalFeatures.dylib
Linking CXX shared library ../../lib/libRDBoost.dylib
[ 5%] [ 5%] Built target RDBoost
Built target ChemicalFeatures
[ 5%] Building CXX object
Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o
Linking CXX shared library ../../lib/libRDGeneral.dylib
[ 5%] Built target RDGeneral
make: *** [all] Error 2
/usr/local/Library/Homebrew/formula.rb:556:in `block in system'
BuildError: Failed executing: make
1. raise
2. ignore
3. backtrace
4. irb
5. shell
Choose an action:
Tim
On 07/07/2014 08:23, Greg Landrum wrote:
Hi Tim,
On Sun, Jul 6, 2014 at 9:38 PM, Tim Dudgeon <[email protected]
<mailto:[email protected]>> wrote:
here's the output:
Last login: Sun Jul 6 12:13:22 on console
timbomac:~ timbo$ brew install rdkit --with-java --verbose --debug
<snip>
==> 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
<snip>
-- Found SWIG: /usr/local/bin/swig (found version "3.0.2")
Just an FYI: even after the problem below is solved, the java wrappers
for the last release of the RDKit will probably not build with SWIG
v3.x. This has been fixed in github. You can either go back to an
older version of SWIG or install the trunk version with: brew install
--HEAD rdkit
-- Found Java:
/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home/bin/java
(found version "1.6.0.65")
CMake Error at
/usr/local/Cellar/cmake/3.0.0/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:136
(message):
Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
Call Stack (most recent call first):
/usr/local/Cellar/cmake/3.0.0/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:343
(_FPHSA_FAILURE_MESSAGE)
/usr/local/Cellar/cmake/3.0.0/share/cmake/Modules/FindJNI.cmake:286
(FIND_PACKAGE_HANDLE_STANDARD_ARGS)
Code/JavaWrappers/gmwrapper/CMakeLists.txt:6 (find_package)
This is the actual problem. cmake is unable to find the required
components of the JDK.
Do you have the JDK installed? Which version of OS/X are you using?
-greg
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