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

Michael Rutter mar36 at psu.edu
Tue Jun 8 22:22:14 CEST 2010

On 06/08/2010 04:02 PM, Peter Muhlberger wrote:
> Hi Dirk:  Thanks for the reply!
> I'm sorry, but I think I tried openjdk, without success.  I'm
> currently using the "http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu"
> source, which appears to contain the Debian r-core.  If so, you seem
> to be suggesting I try to use openjdk-6-jdk.  Telling from my run of
> "sudo update-alternatives --config java", I gather that openjdk-6 was
> my default Java installation.  I then installed the openjdk jdk, my
> cpp flags pointed to '-I/usr/lib/jvm/java-6-openjdk/jre/../include'.
> But, when I try to compile rJava, I get:  "One or more JNI types
> differ from the corresponding native type."  rJava won't compile.
> Should I be doing this differently?
> Thanks again,
> Peter


On a relatively stock 64-bit Ububtu box running lucid, I was able to 
successfully compile rJava with:

sudo apt-get install openjdk-6-jdk
sudo sudo R CMD javareconf
sudo R
 > install.packages("RJava")

Here are the jdk and java packages I have installed:

mrutter at yorick ~> dpkg --get-selections | grep jdk
openjdk-6-jdk					install
openjdk-6-jre					install
openjdk-6-jre-headless				install
openjdk-6-jre-lib				install

mrutter at yorick ~> dpkg --get-selections | grep java
ca-certificates-java				install
java-common					install
libaccess-bridge-java				install
libaccess-bridge-java-jni			install
libbcmail-java					install
libbcmail-java-gcj				install
libbcprov-java					install
libgnuinet-java					install
libgnujaf-java					install
libgnumail-java					install
libitext-java					install
libitext-java-gcj				install
tzdata-java					install

My suggestion would be to remove the other jdk packages and match the 
jdk packages that I have installed and see if that works.


Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563

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