Installation of rJava

user1945827 picture user1945827 · Dec 10, 2015 · Viewed 33.8k times · Source

I've tried to solve this using the previous questions/answers on SO but without any success. So, here's my problem.

I'm using RStudio on and Ubuntu box (14.04) and I tried to upgrade rJava from sources and in the process I managed to lose it.

I tried to install it again using,

install.packages("rJava")

which returned the following error message,

configure: error: One or more Java configuration variables are not set.
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/darren/R/x86_64-pc-linux-gnu-library/3.2/rJava’
Warning in install.packages :
  installation of package ‘rJava’ had non-zero exit status

So, I went to the terminal and typed,

sudo R CMD javareconf

which also gave the following error,

trying to compile and link a JNI program 
detected JNI cpp flags    : 
detected JNI linker flags : -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
 #include <jni.h>
                 ^
compilation terminated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /usr/lib/R
Done.

I tried to follow these links, one and two but they didn't seem to resolve my issue; there are more links on SO but I'm not sure which one to follow. I've also un-installed and re-installed RStudio via the Ubuntu Software Centre but this didn't make any difference.

Can anyone else help?

In short, I want to be able to use RStudio with rJava again without it destroying any other uses of Java (such as jmol).

Answer

Simon Urbanek picture Simon Urbanek · Dec 19, 2015

You don't seem to have JDK installed. You will need at least

sudo apt-get install openjdk-7-jdk

then re-run

sudo R CMD javareconf

Make sure you do NOT set JAVA_HOME by hand - it will be detected automatically. You should then see something like this:

$ sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.7.0_91
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

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-7-openjdk-amd64/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/../include
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm