rJava is not picking up the correct Java version

Question

I've been struggling with this problem for a while now. When I install rJava from R, it takes Java 1.6 instead of 1.8. I am using MAC OS 10.8.5 and these are the steps that I've already done.

I've installed R.
I have both Java 1.6 and 1.8 on my machine.
I've reconfigures R from terminal using: sudo R CMD javareconf -n.
Here is what the output looks like:

Java interpreter : /usr/bin/java
Java version     : 1.8.0_25
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on OS X

trying to compile and link a JNI progam

detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c conftest.c -o conftest.o
gcc -arch x86_64 -std=gnu99 -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 -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm

Then I went on to R and installed rJava package as source like this: install.packages("rJava", type="source") and I get to DONE(rJava)

then when I check the version using:

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

I still get 1.6.0_25-b17 instead of 1.8

Please let me know if you know the solution to this.

Answer 1

Latest version of rJava has fixed this issue. I installed latest version from site using command

install.packages("rJava",,"http://rforge.net/",type="source")

Now the output by calling jvm is as:

> library(rJava)
> .jinit()
> .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.7.0_75-b13"

Note: I have java 1.7 and 1.6 installed, and not java 1.8

Answer 2

What helped me in this case was 2 things (following advice from here: https://www3.ntu.edu.sg/home/ehchua/programming/howto/JDK_Howto.html)

• Informing Ubuntu of the java installation that you want to use.

For this I ran:

$ sudo update-alternatives --install "/usr/bin/java" "java" "/usr/java/jdk1.8.0_201/bin/java" 1

$ sudo update-alternatives --install "/usr/bin/javac" "javac" "/usr/java/jdk1.8.0_201/bin/javac" 1

$ sudo update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/java/jdk1.8.0_201/bin/javaws" 1

followed by

$ sudo update-alternatives --set java /usr/java/jdk1.8.0_201/bin/java

$ sudo update-alternatives --set javac /usr/java/jdk1.8.0_201/bin/javac

$ sudo update-alternatives --set javaws /usr/java/jdk1.8.0_201/bin/javaws

Then I could finally see my java in the alternatives in

sudo update-alternatives --config java

where I selected the newly installed java. Then I ran

 sudo R CMD javareconf JAVA_HOME=/usr/java/jdk1.8.0_201/bin/