Installation of rJava

Question

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 1

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 

Answer 2

What is wrong with sudo apt-get install r-cran-rjava ?

See for example this earlier answer and the question / thread around it.

For an installation from scratch, you could still much worse than starting from sudo apt-get build-dep r-cran-rjava. It will get you the JDK corresponding to your Ubuntu version.