[R] 2 "linux/R environment" questions

[Prof Brian Ripley]

On Wed, 11 Oct 2006, Stefan Grosse wrote:

> Joe Byers schrieb:
>> JGR, when I manually compiled it for my system by specifying my location
>> of java 1.5.0_06, worked fairly nicely.  The autoinstall does not find
>> my installation of this java version since Redhat EL4 does not support
>> it.  Redhat EL5 will in the near future.  Maybe JGR will autoinstall then.
>>
> Can you tell how you worked that out (the manual compilation)? I failed
> on Fedora Core 5 with JRE 1.5.0_08 with install.packages and dep=true. I
> tried a hint from the JGR mailing list but failed...

Which arch and how did you install R?  For me, it works with R compiled 
from the sources (but not installed from RPM) on FC5 i686, but not x86_64.
The issue is a run-time one:

> library(JGR)
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots
createObject.FindClass org/rosuda/iplots/Framework failed
Exception in thread "main" java.lang.InternalError

and that class of problem seems all too common on amd64 versions of Sun 
JRE.  (On FC3, I managed to make it work with a self-compiled gcc 4.1.1, 
and haven't yet tried that on FC5.)

The key is to use alternatives(8) to make sure the right jre is found, or 
to set JAVA_HOME.

If you install R from RPMs you will probably need to run R CMD javareconf 
to get the right environment variables set in R itself.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595