Brian,
I believe I had a similar problem.  Make sure you have JDK (*sun-java6-jdk)
* installed as well.
Here is a link to a JDK install guide
 http://www.cyberciti.biz/faq/howto-ubuntu-linux-install-configure-jdk-jre/


On Mon, Aug 15, 2011 at 10:18 AM, Brian Lunergan <ff809@ncf.ca> wrote:

> Morning All:
>
> Having problems installing this one into my R setup and wondered if
> anyone on the list had the same problem and found a workable solution.
>
> First to the system particulars:
>
> OS is the Hardy Heron edition of Ubuntu Linux
> R version is 2.13.1
> Java installation is sun-java6
>
> Next up is the result of javareconf:
>
>  R CMD javareconf
> Java interpreter : /usr/bin/java
> Java version     : 1.5.0
> Java home path   : /usr/lib/jvm/java-1.5.0-gcj-4.2-1.5.0.0/jre
> Java compiler    : /usr/bin/javac
> Java headers gen.: /usr/bin/javah
> Java archive tool: /usr/bin/jar
> Java library path: /usr/lib/../lib/gcj-4.2-81:/usr/lib/jni
> JNI linker flags : -L/usr/lib/../lib/gcj-4.2-81 -L/usr/lib/jni -ljvm
> JNI cpp flags    :
>
> Updating Java configuration in /etc/R
> Done.
>
> What little I've been able to find on this problem suggests that the
> blank space beside the cpp flags variable is the key point, but all the
> notes I found suggest programming solutions outside of my abilities. Are
> there any simple and to the point solutions that correct this issue, or
> am I SOL for using the package? Any help would be greatly appreciated as
> install of other packages and R commander plugins depend on solving it.
> Oh, yes. Here's the result when I try to pull in rJava.
>
> > install.packages()
> Loading Tcl/Tk interface ... done
> --- Please select a CRAN mirror for use in this session ---
> Installing package(s) into ‘/usr/local/lib/R/site-library’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.skazkaforyou.com/src/contrib/rJava_0.9-1.tar.gz'
> Content type 'application/x-gzip' length 527197 bytes (514 Kb)
> opened URL
> ==================================================
> downloaded 514 Kb
>
> * installing *source* package ‘rJava’ ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/wait.h that is POSIX.1 compatible... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for string.h... (cached) yes
> checking sys/time.h usability... yes
> checking sys/time.h presence... yes
> checking for sys/time.h... yes
> checking for unistd.h... (cached) yes
> checking for an ANSI C-conforming const... yes
> checking whether time.h and sys/time.h may both be included... yes
> configure: checking whether gcc supports static inline...
> yes
> checking whether setjmp.h is POSIX.1 compatible... yes
> checking whether sigsetjmp is declared... yes
> checking whether siglongjmp is declared... yes
> checking Java support in R... present:
> interpreter : '/usr/bin/java'
> archiver    : '/usr/bin/jar'
> compiler    : '/usr/bin/javac'
> header prep.: '/usr/bin/javah'
> cpp flags   : ''
> java libs   : '-L/usr/lib/../lib/gcj-4.2-81 -L/usr/lib/jni -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.
>
> If you don't have root privileges, run
> R CMD javareconf -e
> to set all Java-related variables and then install rJava.
>
> ERROR: configuration failed for package ‘rJava’
> * removing ‘/usr/local/lib/R/site-library/rJava’
>
> The downloaded packages are in
>        ‘/tmp/Rtmph5lTVR/downloaded_packages’
> Warning message:
> In install.packages() :
>  installation of package 'rJava' had non-zero exit status
> >
>
>
> --
> Brian Lunergan
> Nepean, Ontario
> Canada
>
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> PLEASE do read the posting guide
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>



-- 
Joseph C. Magagnoli

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