R SIG Debian - Jun 2010 - Trouble compiling Java-based R packages

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.

Cheers, Peter

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