title: rJava installation in R on debian
body: <p>After updating to R 3.0.1 on a Debian 64-bit machine, the rJava package does not want to install. </p>
  
  <p>configuration failed, so sudo R CMD javareconf [this worked on another debian machine]. however it does not work here, has anybody else had this problem? [see terminal output below] </p>
  
  <pre><code>henk@crunchbang:~$ sudo R CMD javareconf
  Java interpreter : /usr/bin/java
  Java version     : 1.6.0_18
  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
  
  trying to compile and link a JNI progam 
  detected JNI cpp flags    : 
  detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
  gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic  -O3 -pipe  -g  -c conftest.c -o conftest.o
  conftest.c:1:17: error: jni.h: No such file or directory
  conftest.c: In function ‘main’:
  conftest.c:4: warning: implicit declaration of function ‘JNI_CreateJavaVM’
  make: *** [conftest.o] Error 1
  Unable to compile a JNI program
  
  
  Java library path: 
  JNI cpp flags    : 
  JNI linker flags : 
  Updating Java configuration in /usr/lib64/R
  Done.
  
  # check java
  henk@crunchbang:~$ java -version
  java version "1.6.0_18"
  OpenJDK Runtime Environment (IcedTea6 1.8.13) (6b18-1.8.13-0+squeeze2)
  OpenJDK 64-Bit Server VM (build 14.0-b16, mixed mode)
  </code></pre>
  
  <p>java environment:</p>
  
  <pre><code>henk@crunchbang:~$ aptitude search "?provides(java-runtime)"
  i A default-jre                            - Standard Java or Java compatible Runtime        
  i A default-jre-headless                   - Standard Java or Java compatible Runtime (headle
  p   gcj-4.4-jre                            - Java runtime environment using GIJ/classpath    
  p   gcj-4.4-jre-headless                   - Java runtime environment using GIJ/classpath (he
  p   gcj-jre                                - Java runtime environment using GIJ/classpath    
  p   gcj-jre-headless                       - Java runtime environment using GIJ/classpath (he
  i A openjdk-6-jre                          - OpenJDK Java runtime, using Hotspot JIT         
  i A openjdk-6-jre-headless                 - OpenJDK Java runtime, using Hotspot JIT (headles
  i   sun-java6-jre                          - Sun Java(TM) Runtime Environment (JRE) 6 (archit
  </code></pre>