R SIG Debian - Mar 2011 - JGR compile problem: JNI type error with a twist

Hi folks:  Updated my system again and am stuck on a JGR compile
problem.  What I've seen in discussion of the problem doesn't seem to
be helping.

As others have encountered, it can't compile rJava (for one), getting
this error:

checking JNI data types... configure: error: One or more JNI types
differ from the corresponding native type.

Also, consistently with what others report, when I run javareconf, I get:

JAVA_HOME is not a valid path, ignoring

It seems that some people have fixed this problem by pointing
JAVA_HOME to the valid jdk directory.  My problem is that it is
already pointing to /usr/lib/jvm/java-6-sun-1.6.0.24, my installed sun
jdk directory according to Synaptic.  I've also pointed to sun java
using update-alternatives on both java and javac.

It's true that JAVA_HOME points to java-6-sun-1.6.0.24 via a symbolic
link named java-6-sun.  Can't see how that would be a problem.

Any thoughts / suggestions?

If it's any help, a list of JAVA_HOME gives:

# ls $JAVA_HOME
bin        db    ext      jre  LICENSE  README.html  THIRDPARTYLICENSEREADME.txt
COPYRIGHT  demo  include  lib  man      sample

bin has an executable javac.

Cheers, Peter