rJava uses 1.6 instead of the current Java version

[blernermhc]

I am running rJava 0.9-8 on a Mac OSX 10.10.5. The current version of Java installed is 1.8:

~ -> java -version
java version "1.8.0_72"
Java(TM) SE Runtime Environment (build 1.8.0_72-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.72-b15, mixed mode)

However, rJava is using 1.6:

> .jcall("java/lang/System", "S", "getProperty", "java.version")
[1] "1.6.0_65"

I have followed advice found on stackoverflow to resolve this, including running javareconf and installing rJava from source. I have also tried rJava 0.9-9. I get the same error in RStudio and the R command line and R gui. I have also tried restarting RStudio and rebooting. None of these have helped.

This is what ldpaths contains:

: ${JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_72.jdk/Contents/Home/jre}
: ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/server}
if test -n ""; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:}
else
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
fi
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
  R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
fi
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (OS X) and LD_LIBRARY_PATH elsewhere
if test -z "${DYLD_FALLBACK_LIBRARY_PATH}"; then
  DYLD_FALLBACK_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
else
  DYLD_FALLBACK_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${DYLD_FALLBACK_LIBRARY_PATH}"
fi
export DYLD_FALLBACK_LIBRARY_PATH

This is what is in javaconf

## Versions from settings when configure was run
: ${JAVA_HOME=}
: ${JAVA_CPPFLAGS=~autodetect~}
: ${JAVA_LD_LIBRARY_PATH=~autodetect~}
: ${JAVA_LIBS=~autodetect~}

Thanks for your help!

[scottschreckengaust]

I forked and now only difference is https://github.com/s-u/rJava/pull/16/files

[s-u]

rJava uses whatever you link it against. Make sure you link against the correct jvm and that it contains the path in the id and/or it can be found on the library path. All of this is automatic if you use regular R distribution - but note that only the R script sets the library path so in other cases you may want to fix the jvm id location if your'e using the Oracle binaries which often don't do that.

[gwerbin]

Are you still having issues? Can you say you "ran javareconf" what exactly did you run?

There is a note about this issue in the Homebrew formula for R It says:

To enable rJava support, run the following command:

R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers

If you've installed a version of Java other than the default, you might need to instead use:

        R CMD javareconf JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers -I/Library/Java/JavaVirtualMachines/jdk<version>.jdk/"

      (where <version> can be found by running `java -version`, `/usr/libexec/java#{'_'}home`, or `locate jni.h`), or:

        R CMD javareconf JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers -I$(/usr/libexec/java#{'_'}home | grep -o '.*jdk')"

[blernermhc]

Thanks for checking back. We are no longer using rJava and instead communicating via a socket.