help updating package rJava (on ubuntu)

Hi Hasan,

Success. For myself and FWIW to other useR's here's how i spent the sunny half of my sunday to achieve it :/

Many thanks for your and Simon's input,

Karl

Since:

$ javac -version

returned nothing i believe you (and Simon) were right, i.e, it (and JDK) were missing on my system. Furthermore:

$ sudo 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    : not present
Java headers gen.:
Java archive tool:
Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
JNI cpp flags    :

Updating Java configuration in /etc/R
Done.

Some things are clearly absent i.e.,
Java compiler    : not present
Java headers gen.:
Java archive tool:

Now i have:

$ javac -version
javac 1.6.0_23

$ sudo 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: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
JNI cpp flags    : -I$(JAVA_HOME)/../include

Updating Java configuration in /etc/R
Done.

Certainly i don't know exactly what was needed to achieve this. BUT - for posterities sake, this is what i did:

## purge and reinstall openjdk-6-jdk which turned outwasn't installed!
## how this can be when i have a /usr/lib/jvm/java-6-openjdk full of
## files i don't understand. Moreover since i had the previosu version
## of rJava running fine!!!
$ sudo apt-get purge openjdk-6-jdk
<snip>
Package openjdk-6-jdk is not installed, so not removed
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

## install openjdk-6-jdk
$ sudo apt-get install openjdk-6-jdk

## Per- http://ubuntuforums.org/showthread.php?t=1491846
## added 2 entries to /etc/bash.bashrc file
$ gksudo gedit /etc/bash.bashrc

## entries were:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/jre
export PATH=$PATH:$JAVA_HOME/bin

## note the addition of /jre for JAVA_HOME per-
## http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing

<saved bash.bashrc file then reloaded>

$ source /etc/bash.bashrc

## confirmed
$ echo $JAVA_HOME
/usr/lib/jvm/java-6-openjdk/jre

## configured java
$ sudo R CMD javareconf

I was then able to update rJava in a new R-session.

Also note that per- http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing

$ apt-get install r-cran-rjava

did NOT enable me to update my rJava. Unless i buggered up something else along the way :/




On 02/18/2012 10:20 PM, Hasan Diwan wrote:

On 18 February 2012 13:13, Karl Brand<k.brand at erasmusmc.nl>  wrote:

Thanks for yout fast response. Thing is - i managed to get Version 0.9-1
installed and fully functional. And

$ locate jdk
returns too many entries to post here, so i'm pretty sure its on the
machine.

What you want to look for is javac, not jdk. On my ubuntu system, this
is to be found at /usr/lib/jvm/java-6-openjdk-i386/bin/javac

So i'd like to know how i can ensure it's "registered in R". This i have no
idea how to do. I simply don't have enough R and linux experience. Also the
thread i mentioned
http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing
seems to be about pointing R at the right location of certain aspects of
Java. But lacks enough explicit details for myself to be able use.

A previous response indicated R javareconf -- this is the only
configuration you should need. Let me know if you have further
problems.

-- 
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3455 |F +31 (0)10 704 4743 |M +31 (0)642 777 268