Ubuntu :: Cannot Compile Java-based Packages In R

I'm trying to compile JGR, rJava, etc. for use w/ my updated R. My configuration of Ubuntu (9.10 Karmic, kernel 2.6.31-22-generic) and R (version 2.11.1; from lib.stat.cmu.edu source) shouldn't be terribly unusual. But, all my efforts to compile Java programs for R fail, possibly because of something in my Ubuntu configuration of Java.First, I ran: R CMD javareconf. The output from that tells me that "JAVA_HOME is not a valid path, ignoring" and the cpp flags are set to nothing. The javareconf fills most of the variables with references to openjdk. JAVA_HOME, as far as I can tell, points to a properly installed copy of Sun Java. When I run update.packages(checkBuilt=T) with this, it unsurprisingly tells me that "One or more Java configuration variables are not set" and all of my Java based programs fail to compile.

I've tried switching the default Java to the Sun version using "sudo update-alternatives --config java". Now, javareconf fills in the cpp flag and variables point to the Sun version, though I still get the error msg that JAVA_HOME is not a valid path (though javareconf sets the home path to: /usr/lib/jvm/java-6-sun-1.6.0.20/jre). When I try to compile rJava, I get the error: rJava, "JNI types differ from the native type."Does anyone have any thoughts on how to fix this? Alternatively, is there somewhere I can report these problems so they might get fixed in future versions?I suspect I can't be the only person having these problems.