Unable to install rJava in R 3.0 in Ubuntu 13.04
JavaRUbuntuJava Native-InterfaceRjavaJava Problem Overview
I am not able to call rJava
package in R 3.0
. I got the following message
Error: package ‘rJava’ was built before R 3.0.0: please re-install it
I am getting error when I tried to re-install rJava
package. I have provided the output of R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.7.0_21
Java home path : /usr/lib/jvm/java-7-openjdk-i386/jre
Java compiler : /usr/lib/jvm/java-7-openjdk-i386/jre/../bin/javac
Java headers gen.: /usr/lib/jvm/java-7-openjdk-i386/jre/../bin/javah
Java archive tool: /usr/lib/jvm/java-7-openjdk-i386/jre/../bin/jar
trying to compile and link a JNI progam
detected JNI cpp flags :
detected JNI linker flags :
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
compilation terminated.
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/lib/R
Done.
I am using Ubuntu 13.04. I also tried apt-get install r-cran-rjava
which is not helping to solve the issue. Regarding jni.h there were some solution here. But, not sure how can I use the solution here.
Java Solutions
Solution 1 - Java
I ran into the exact same issue. My solution was to install the openjdk-7-* via
sudo apt-get install openjdk-7-*
Followed that with
sudo R CMD javareconf
and I was then able to install rJava in R via install.packages("rJava")
.
While perhaps not the most elegant solution it appears to have solved my problems with getting rJava to work.
Solution 2 - Java
For those getting the error:
error: unable to load shared object '/some/dir/rJava/libs/rJava.so': libjvm.so:
cannot open shared object file: No such file or directory
I solved the error locating the library in the system and linking them to /usr/lib
:
$sudo updatedb
$locate libjvm.so
/usr/lib/debug/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server/libjvm.so
/usr/lib/debug/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/zero/libjvm.so
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/jamvm/libjvm.so
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server/libjvm.so
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/zero/libjvm.so
$sudo ln -s /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib/
Solution 3 - Java
Installing rJava from the distribution packages as proposed in this askUbuntu answer also works:
sudo apt-get install r-cran-rjava
NOTE: tried from a Debian system.