correct Installation and configuration of openJDK and R

Question

I am relatively new to Ubuntu so I wont know a lot of commands that probably became standard to a lot of you guys. I am trying to set up R and with it the necessary java dependencies to install e.g. JGR, rjava, etc. I read through quite a few instructions to do that but somehow I must have done sth wrong. Here is the state of R and java:

R --version

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

java -version

java version "1.6.0_23"
OpenJDK Runtime Environment (IcedTea6 1.11pre) (6b23~pre11-0ubuntu1.11.10.1)
OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)

R CMD javareconf

Java interpreter : /usr/bin/java
Java version     : 1.6.0_23
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
Java library path: /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
JNI cpp flags    : 

But when I try to install 'JavaGD' in R, which is a dependency for JGR I get:

...
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags   : ''
java libs   : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
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.
...

Any help would be greatly appreciated. Thanks!

Answer 1

I'm not familiar with R but based on your console it seems like R is requiring a JDK while you have a JRE as you default JAVA home variable. I would suggest you to make sure you have the JDK installed or install it (sudo apt-get install openjdk-6-jdk).
Also make sure that your JAVA_HOME environment variable is pointing to the JDK and not to the JRE (you can see in your output that currently the java home path is set to /usr/lib/jvm/java-6-openjdk/jre.

Answer 2

One shouldn't blindly install openjdk-6-jdk. What helped me, was to change the version of Java. Fortunately there is a nice Ubuntu tool for doing that:

sudo update-alternatives --config java

There you can see, what Javas are already available on system, and set the desired one. And then install either openjdk-7-jdk or openjdk-6-jdk (or both)

and only then run

sudo R CMD javareconf

More details about Java choices are on Ubuntu's Community Wiki

P.S. For people coming here from Google: Among other things, this post helps solving issues with rj instalation in R, with error message: R is not configured with full Java support. Please make sure an JDK is installed and run R CMD javareconf. When I did that, it said: NOTE: Your JVM has a bogus java.library.path system property!. So: no need messing with Java's library paths!.

Answer 3

R CMD javareconf as root

means, you have to use sudo, to issue your command:

sudo R CMD javareconf

You will get asked for your password (your normal userpassword).

Answer 4

Yossiles answer helped me on the way, but here is the newbie-friendly version, which also draws on the answer to this question.

What worked for me was was this:-

1) open /etc/environment in your favorite txteditor:

sudo gedit /etc/environment

2) add a new line with "JAVA_HOME" and the path to correct jr-directory, in the case of java 8, it is:

JAVA_HOME="/usr/lib/jvm/java-8-oracle/jre"

3) source the updated environment and check the variable:

source /etc/environment
echo $JAVA_HOME

4) update the java-R configuration like this:

sudo R CMD javareconf

5) install RJava, XLConnect or whatever java-dependent R-package you are looking for.

Answer 5

Yes, update-alternatives is the most convenient linking mechanism to maintain different JVM versions - even from different providers like Oracle / OpenJDK. I am open to correction but I would say one needs a JDK and not only a JVM for R setup.

The outline to prepare for R JAVA configuration are:

1. ensure that the required JVM is correctly located in /usr/lib/jvm
2. setup the linking using update-alternatives --install for each JAVA command required by R
3. use update-alternatives --configure to select a default JVM
4. refresh the R configuration

To ensure that the JDK is already in the correct location, query the list of installed JVMs with the command

ls /usr/lib/jvm

If the folder does not include a JDK then relocate the entire JVM folder from the extracted tar.gz (download) to /usr/lib/jvm with the command:

sudo mv <JDK folder> /usr/lib/jvm

separate terminal entries for update-alternatives is required by R for the following JAVA commands:

• interpreter : '/usr/bin/java'
• archiver : '/usr/bin/jar'
• compiler : '/usr/bin/javac'
• header prep.: '/usr/bin/javah'

the entries for jdk1.8.0_51 are as follows:

sudo update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk1.8.0_51/bin/java" 2

sudo update-alternatives --install "/usr/bin/jar" "jar"  "/usr/lib/jvm/jdk1.8.0_51/bin/jar" 2

sudo update-alternatives --install "/usr/bin/javac" "javac"  "/usr/lib/jvm/jdk1.8.0_51/bin/javac" 2

sudo update-alternatives --install "/usr/bin/javah" "javah"  "/usr/lib/jvm/jdk1.8.0_51/bin/javah" 2

NB. the output after execution of update-alternatives --install for JVM jdk1.8.0_51 should be similar output to:

update-alternatives: using /usr/lib/jvm/jdk1.8.0_51/bin/java to provide /usr/bin/java (java) in auto mode

to select the required JVM as default

sudo update-alternatives --config java

If only a single JVM is setup then the following output is presented in the terminal

There is only one alternative in link group java (providing /usr/bin/java): /usr/lib/jvm/jdk1.8.0_51/bin/java Nothing to configure.

alternatively the relevant entry# for the required JVM must be selected

to check that the correct JVM is linked

java --version

finally, update the R setup with:

sudo R CMD javareconf

Note that this setup could not seem to be working if you have attempted other ways to "hardwire" configure your JVM