Trouble compiling Java-based R packages

Peter,

On 8 June 2010 at 13:51, Peter Muhlberger wrote:
| Hi folks: ?I guess my earlier posting was too involved, so let me try
| to get to the essence of my problem.
|
| I recently tried to compile JGR, rJava, etc. into my updated R.
| 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.

Quick caveat: I am not a Java user or programmer.

That said, I had wanted to get this work for years because several
interesting packages build on-top of rjava. ?And as of a few years ago it
started to work so I since then I am

?a) instrumenting Debian's r-base-core package to be Java-aware

?b) packaging /maintaining rjava for Debian as well

but all of that only with the non-Sun packages. E.g. rjava has a
build-depends on openjdk-6-jdk, and that seems to work. ?So start by
installing that.

I have also built JGR and other packages, and have the cran2deb robot build
quite a few more. ?But never with the Sun java, and certainly never when
mixing.

Beyond that, maybe the Java lists can be of more help than we can here.

--
?Regards, Dirk