[R] JGR installation errors

[Simon Urbanek]

MAura,

On Jun 19, 2009, at 7:36 , <mauede at alice.it> <mauede at alice.it> wrote:

> I remember JGR installation on SuSE 10.3 as a nightmare that  
> eventually I overcame with JGR designers' help.
> I have installed SuSE  11.1, latest R version and am trying to  
> install JGR again.
> It is still a nightmare.
>

Well, good Linux distros offer JGR as binaries so it's one-liner to  
install it ;). All other distros I use are easy to install even from  
sources - SuSE seems is notoriously struggling ...

>  I have followed the guidelines on    http://jgr.markushelbig.org/JGR_on_Linux.html
> I have made sure I have the so R libraries.
> I have installed java-1.6.0-sun and its development environment.  
> Following the on-line guidelines for JGR installation,
> the process fails on trying to install "rJava"   ... please see all  
> the messages in the following.
> I get the same error if I try to install "rJava" in advance of JGR.
>
> Thank you very much,
> Maura
>
>
> As root:
>
> linux-326k:/home/mauede # sudo R CMD javareconf
> Java interpreter : /usr/bin/java
> Java version     : 1.6.0_0
> Java home path   : /usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/ 
> lib64:/lib64:/lib:/usr/lib
> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/ 
> lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/ 
> amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm
> JNI cpp flags    :
>

^^^ - it appears that you don't have full JDK installed properly or  
it's non-standard location - R cannot find flags needed to compile  
JNI. You don't have either of ${JAVA_HOME}/include, ${JAVA_HOME}/../ 
include, ${JAVA_HOME}/jre/include so you'll need to figure out whether  
a) you just didn't install them or b) they are installed in a non- 
standard location. The fix for a) is to install them, the fix for b)  
is set set them using JAVA_CPPFLAGS when calling javareconf (and  
report back to us to see if that's something we can add to R).

Cheers,
Simon


> Updating Java configuration in /usr/lib64/R
> Done.
>