Re: [Rdkit-discuss] installing on mac with --with-java

Sun, 06 Jul 2014 12:39:52 -0700 

here's the output:

Last login: Sun Jul  6 12:13:22 on console
timbomac:~ timbo$ 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 102k 0 0:00:02 0:00:02 --:--:-- 102k ==> 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: /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)


-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-ewWj/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log". See also "/tmp/rdkit-ewWj/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log". 
/usr/local/Library/Homebrew/formula.rb:556: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_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' . 
1. raise
2. ignore
3. backtrace
4. irb
5. shell
Choose an action:


Not obvious what action I should choose.

Tim


On 06/07/2014 17:43, Matthew Swain wrote:

Hi Tim,

Could you try running

    brew install rdkit --with-java --verbose --debug
That should give more detailed error messages in the Terminal, and also holds off from deleting the log files right away. 

Matt
On 6 Jul 2014, at 11:53, Tim Dudgeon <tdudgeon...@gmail.com <mailto:tdudgeon...@gmail.com>> wrote: 


I'm trying to install on Mac with the instructions here:
https://github.com/rdkit/homebrew-rdkit
The basic install:
brew install rdkit
works fine, but I want the Java wrappers so that I can run with Jython.
And I get this:

$ brew install --with-java rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2014_03_1.tar.gz 
Already downloaded: /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 ==> 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 


-- Configuring incomplete, errors occurred!
See also "/tmp/rdkit-tZ3q/rdkit-Release_2014_03_1/CMakeFiles/CMakeOutput.log". See also "/tmp/rdkit-tZ3q/rdkit-Release_2014_03_1/CMakeFiles/CMakeError.log". 

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

$
The mentioned CMakeOutput.log and CMakeError.log files do not exist (not in the location mentioned and not anywhere). 

Any ideas what's wrong?

Thanks
Tim


------------------------------------------------------------------------------
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
Rdkit-discuss@lists.sourceforge.net
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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to