I am relatively new to Ubuntu so I wont know a lot of commands that probably became standard to a lot of you guys.
I am trying to set up R and with it the necessary java dependencies to install e.g. JGR, rjava, etc. I read through quite a few instructions to do that but somehow I must have done sth wrong. Here is the state of R and java:

R --version



R version 2.14.1 (2011-12-22)

Copyright (C) 2011 The R Foundation for Statistical Computing

ISBN 3-900051-07-0

Platform: x86_64-pc-linux-gnu (64-bit)



java -version



java version "1.6.0_23"

OpenJDK Runtime Environment (IcedTea6 1.11pre) (6b23~pre11-0ubuntu1.11.10.1)

OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)



R CMD javareconf



Java interpreter : /usr/bin/java

Java version     : 1.6.0_23

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: /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib

JNI linker flags : -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/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm

JNI cpp flags    : 

But when I try to install 'JavaGD' in R, which is a dependency for JGR I get:

...

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/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.

...

Any help would be greatly appreciated. Thanks!