rjava jdk not found

Error

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root

So means that R is not able to detect Java properly

So lets fix this

Found following pages useful so want to give credits

http://r.789695.n4.nabble.com/rjava-JDK-not-found-td889163.html
http://svn.r-project.org/R/trunk/src/scripts/javareconf

Run command once with sudo

$ sudo R CMD javareconf

Note its output

For me following things were present

jj@jj-VirtualBox:~$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_38
Java home path   : /usr/lib/jvm/jdk1.6.0_38/jre
Java compiler    : /usr/bin/javac
Java headers gen.:
Java archive tool:
Java library path: $(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux

Updating Java configuration in /etc/R
Done.

Now rerun the same command without sudo

jj@jj-VirtualBox:~$ R CMD javareconf
Java interpreter : /usr/lib/jvm/jdk1.6.0_38/jre/bin/java
Java version     : 1.6.0_38
Java home path   : /usr/lib/jvm/jdk1.6.0_38
Java compiler    : /usr/lib/jvm/jdk1.6.0_38/bin/javac
Java headers gen.: /usr/lib/jvm/jdk1.6.0_38/bin/javah
Java archive tool: /usr/lib/jvm/jdk1.6.0_38/bin/jar
Java library path: /usr/lib/jvm/jdk1.6.0_38/jre/lib/i386/client:/usr/lib/jvm/jdk1.6.0_38/jre/lib/i386:/usr/lib/jvm/jdk1.6.0_38/jre/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
JNI linker flags : -L/usr/lib/jvm/jdk1.6.0_38/jre/lib/i386/client -L/usr/lib/jvm/jdk1.6.0_38/jre/lib/i386 -L/usr/lib/jvm/jdk1.6.0_38/jre/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I/usr/lib/jvm/jdk1.6.0_38/include -I/usr/lib/jvm/jdk1.6.0_38/include/linux

Updating Java configuration in /etc/R
/usr/lib/R/bin/javareconf: 370: /usr/lib/R/bin/javareconf: cannot create /etc/R/Makeconf.new: Permission denied
*** cannot create /etc/R/Makeconf.new
*** Please run as root if required.

So we can see that JAVAH and JAR paths are not detected in sudo command execution.

So if we read the R page

http://svn.r-project.org/R/trunk/src/scripts/javareconf

We can re run the command using sudo giving paths required

sudo R CMD javareconf JAVA=/usr/lib/jvm/jdk1.6.0_38/jre/bin/java JAVA_HOME=/usr/lib/jvm/jdk1.6.0_38 JAVAC=/usr/lib/jvm/jdk1.6.0_38/bin/javac JAR=/usr/lib/jvm/jdk1.6.0_38/bin/jar JAVAH=/usr/lib/jvm/jdk1.6.0_38/bin/javah

This should tell where to find what and it should be able to do what it wants