rJava installation in R on debian - r

Question

After updating to R 3.0.1 on a Debian 64-bit machine, the rJava package does not want to install.
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]
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)
java environment:
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

Answer 1

I took these steps (on an EC2 with Ubuntu 14.04 and RStudio-Server) to install the R package qdap which requires rJava:
(I'm probably quoting other sources here and there and I don't remember from where, but thanks.)
Install these repositories from http://sites.psu.edu/theubunturblog/cran2deb4ubuntu/
(debian: http://r-forge.r-project.org/projects/cran2deb/)
sudo add-apt-repository ppa:marutter/rrutter
sudo add-apt-repository ppa:marutter/c2d4u
sudo apt-get update
Install Java:
sudo apt-get install openjdk-7-jdk
ls /usr/lib/jvm
Set a system-wide environment variable for Java:
sudo joe /etc/profile.d/javaenvvar.sh
which contains:
# JAVA environment variable
# for openjdk-7-jdk in order to use the R package `qdap`.
export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64/jre
export PATH=$PATH:$JAVA_HOME/bin
Then exit BASH and sign in again. Check your path changes:
echo $PATH
echo $JAVA_HOME
Then:
sudo R CMD javareconf
Should return:
Java interpreter : /usr/bin/java
Java version : 1.7.0_65
Java home path : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Create the file /etc/ld.so.conf.d/java.conf with the following entries:
/usr/lib/jvm//usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64
/usr/lib/jvm//usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server
Then install rJava from those new repositories:
sudo apt-get install r-cran-rjava
That just installed rJava to /usr/lib/R/site-library which is accessible to all users of RStudio-Server, hopefully.
sudo update-alternatives --config java
Hopefully, there's only one java installed.
Update R packages:
sudo R
> packageStatus()
> update.packages()
Install R packages system wide (still within sudo R):
> install.packages("qdap", lib="/usr/lib/R/site-library")
Reset RStudio-Server:
Sign out of RStudio-Server first.
sudo rstudio-server stop
sudo rstudio-server start
Sign back in to RStudio-Server.
If you get a memory error, try detaching some packages.
The EC2 t2-micro has only 1 GB of RAM.

Answer 2

I had the same problem, the solution was updating to openjdk-7-* and use update-alternatives --config java to set the java-7-openjdk path.