Matt: thanks for that. Your pull request is merged.
Tim: if you get the newest version of the RDKit homebrew recipe you should
be able to try it.
-greg
On Mon, Jul 7, 2014 at 10:56 AM, Matthew Swain <[email protected]> wrote:
> The problem with the Oracle-supplied Java 7 is unreleated I think -
> possibly it's the issue with SWIG v3.x that Greg mentioned.
>
> With regards to the Apple-provided Java 6 - it looks like the problem is
> that it puts the JNI headers in a different location that cmake isn't aware
> of.
>
> I think I have a solution -
> https://github.com/rdkit/homebrew-rdkit/pull/11
>
> On 7 Jul 2014, at 09:04, Tim Dudgeon <[email protected]> wrote:
>
> 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]> 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
>
>
>
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
>
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
