title: Can't install rJava on ubuntu system
body: <p>I've seen a few posts related to this...but all the suggested solutions ive seen dont seem to work....I am running R in an EC2 instance and ran the following commands to try and install rJava but to no avail...any help would be greatly appreciated.</p>
  
  <pre><code> &gt; install.packages("rJava")
   Installing package(s) into ‘/home/ubuntu/R/library’
   (as ‘lib’ is unspecified)
   trying URL 'http://cran.stat.nus.edu.sg/src/contrib/rJava_0.9-3.tar.gz'
   Content type 'application/x-gzip' length 537153 bytes (524 Kb)
   opened URL
   ==================================================
   downloaded 524 Kb
  
  * installing *source* package ‘rJava’ ...
  ** package ‘rJava’ successfully unpacked and MD5 sums checked
  checking for gcc... gcc -std=gnu99
  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 -std=gnu99 accepts -g... yes
  checking for gcc -std=gnu99 option to accept ISO C89... none needed
  checking how to run the C preprocessor... gcc -std=gnu99 -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 -std=gnu99 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    : ''
  compiler    : ''
  header prep.: ''
  cpp flags   : ''
  java libs   : '-L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk-amd64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni -L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
  configure: error: Java Development Kit (JDK) is missing or not registered in R
  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 ‘/home/ubuntu/R/library/rJava’
  Warning in install.packages :
    installation of package ‘rJava’ had non-zero exit status
  
  The downloaded source packages are in
      ‘/tmp/RtmpaEiskU/downloaded_packages’
  &gt; system("sudo R CMD javareconf")
  Java interpreter : /usr/bin/java
  Java version     : 1.6.0_24
  Java home path   : /usr/lib/jvm/java-6-openjdk-amd64/jre
  Java compiler    : not present
  Java headers gen.: 
  Java archive tool: 
  Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
  JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni -L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
  JNI cpp flags    : 
  
  Updating Java configuration in /etc/R
  Done.
  
  &gt; install.packages("rJava")
  [same as before, just skipping to the error parts...]
   java libs   : '-L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk-amd64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni -L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
  configure: error: Java Development Kit (JDK) is missing or not registered in R
  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 ‘/home/ubuntu/R/library/rJava’
  Warning in install.packages :
    installation of package ‘rJava’ had non-zero exit status
  
  The downloaded source packages are in
      ‘/tmp/RtmpaEiskU/downloaded_packages’
  &gt; sessionInfo()
  R version 2.15.1 (2012-06-22)
  Platform: x86_64-pc-linux-gnu (64-bit)
  
  locale:
   [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C        
   [5] LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C           
   [9] LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  loaded via a namespace (and not attached):
  [1] tools_2.15.1
  </code></pre>