[R-sig-Debian] Trouble compiling Java-based R packages

[Peter Muhlberger]

I seem to have fixed the problem, thanks to a number of suggestions
here--specifically, the suggestions were that I stick to openjdk and
perhaps to clean up my loaded versions of java.

I used synaptic to uninstall as many version of Java as I could,
though ultimately this may not have made a difference.  I could not
fully uninstall Sun's Java because two applications I need depend on
it: OpenOffice and JEdit.  I did eliminate Sun's jdk.  I did erase
some software associated with gij.  I also uninstalled and then
reinstalled openjdk.  Again, I'm not sure that mattered.

When I reran "sudo update-alternatives --config java", openjdk was the
default java and its status was 'auto'.  It may have been sufficient
to set these using update-alternatives.  Next, I gave JAVA_HOME a new
value (setting it to empty did not work; default setting was Sun):

export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/jre

I reran R CMD javareconf, ignoring the message that JAVA_HOME was not
a valid path.  And then I installed the Java packages, without a
hitch.  Ubuntu / Debian probably should be able to handle this w/o
user intervention, but don't.

Thanks for all the suggestions!