R SIG Debian - Jun 2010 - R Java compile problem

Hi folks:  I'm trying to update my JGR and related packages, but run
into a compile problem, that I suspect must be affecting others.  I
get this output when compiling rJava, JavaGD, etc.:

##
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags   : ''
java libs   : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64
-L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
##

When I run R CMD javareconf as root, I get:

##
# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version     : 1.6.0_0
Java home path   : /usr/lib/jvm/java-6-openjdk/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
JNI cpp flags    :

Updating Java configuration in /etc/R
Done.
##

When I investigate JAVA_HOME, I get:

##
# echo $JAVA_HOME
/usr/lib/jvm/java-6-sun
# ls /usr/lib/jvm/java-6-sun
bin        docs  include  lib      man          THIRDPARTYLICENSEREADME.txt
COPYRIGHT  ext   jre      LICENSE  README.html
##

So, JAVA_HOME does point to a proper installation of Sun's Java, so
far as I can tell.  The cpp flag seems to be the big problem, but I
don't know enough about this setup to figure out how to fix it.

I get R from the software source:
http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu.  Just installed R
version 2.11.1 (2010-05-31)

My operating system is 9.10 Karmic, kernel 2.6.31-22-generic.

I'm guessing that either there's a bug in javareconf or in the Sun
Java installation on my version of Ubuntu.  Not sure if there's a
workaround or whether there is some bug bboard to which I should
report this.

Suggestions welcome!

Ok, flag me for the annoying category of people who start to answer
their own questions (though still no solution).

I just noticed that while JAVA_HOME is pointing to the Sun version of
Java, the variables javareconf fills in are for openjdk, the open
source version of Java that I believe is auto-installed with Ubuntu.
(Does anyone know for sure?)

I also noticed that while the jre for openjdk is installed in my
system, the jdk, which presumably has the compiler info, is not
installed.  I installed it, ran javareconf again and, eureka!, my cpp
flags according to javareconf seem to be good.  I see:

##
cpp flags   : '-I/usr/lib/jvm/java-6-openjdk/jre/../include'
##

Triumphantly, I rerun the package update in R, but now get this error
(and something nearly identical for JGR itself):

##
checking JNI data types... configure: error: One or more JNI types
differ from the corresponding native type. You may need to use
non-standard compiler flags or a different compiler in order to fix
this.
ERROR: configuration failed for package ?rJava?
##

I'm guessing that rJava was compiled w/ Sun's Java and is balking at
openjdk.  From where I sit, it looks like there's a possible problem
with javareconf because it doesn't take JAVA_HOME, which points to
Sun's Java.

So, I'm guessing I need to get javareconf to use Sun's Java.  I used
this to reset my default Java:

##
sudo update-alternatives --config java
##

On resetting to Sun's Java, it still shows openjdk as 'auto', but
the
Sun Java gets starred.  I run javareconf, which now points the Java
home path to:  /usr/lib/jvm/java-6-sun-1.6.0.20/jre.  However, it
continues to tell me that JAVA_HOME is not a valid path even though
JAVA_HOME continues to reference Sun's jvm directory.  (cpp flags also
now correctly point to Sun's Java, according to the compiler.)

When I run package update, compiling seems to work for JavaGD at
least, but after the compile I get:

##
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/usr/local/lib/R/site-library/JavaGD/libs/JavaGD.so':
  libjvm.so: cannot open shared object file: No such file or directory
ERROR: loading failed
* removing ?/usr/local/lib/R/site-library/JavaGD?
* restoring previous ?/usr/local/lib/R/site-library/JavaGD?
##

JavaGD.so appears to be in the proper directory, but I'm looking at
the restored version.  And, yes, I'm running everything as root.

In the same run, when it gets to rJava, I have the same error as for
rJava running with openjdk: JNI types differ from the native type.

So, now I'm really stumped.  Again, perhaps this needs to be mentioned
to the tech people who put javareconf or perhaps Ubuntu's handling of
Java together, but I'm not sure where to do so.