I'm running R 3.2.4 on OS X 10.5, with multiple Java installations. I currently have JDK 7 as my default installation. Using R CMD javareconf
it appears everything gets configured correctly:
guhar@NCATS-1850784-M:~/src/cdkr [master*]$ R CMD javareconf JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/include/'
Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/jre/bin/java
Java version : 1.7.0_71
Java home path : /Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home
Java compiler : /Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/bin/jar
System Java on OS X
trying to compile and link a JNI program
detected JNI cpp flags : -I/Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/include/
detected JNI linker flags : -framework JavaVM
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -framework JavaVM -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home
Java library path:
JNI cpp flags : -I/Library/Java/JavaVirtualMachines/jdk1.7.0_71.jdk/Contents/Home/include/
JNI linker flags : -framework JavaVM
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
I then install rJava 0.98 and no errors are reported. However, when I start R and use rJava
it indicates that the java.version
system property (which indicates the JRE version) is 1.6, even though JAVA_HOME
is set to my JDK 7 installation:
> library(rJava)
> .jinit()
> .jcall("java/lang/System","S","getProperty","java.version")
[1] "1.6.0_65"
Is there something I need to set on the rJava
side to make it recognize my JAVA_HOME
setting? Or is this something that needs to be set in the OS X environment?