[R] R: JGR installation errors

[Simon Urbanek]

On Jun 19, 2009, at 10:08 , <mauede at alice.it> <mauede at alice.it> wrote:

> It works now. Thank you.
> I even succeeded in starting R by clicking on JGR icon that I placed  
> on my desktop.
> I wonder whether some Java or system flag that unlocks Mutex (I  
> ignore what it is) has to be set somewhere ...
> maybe fron the .bashrc file.
> The first time I happened to get JGR running (as root) a warning  
> popped up (I haven't saved it)
> about a possible crash caused by Mutex being unlocked by anothe  
> thread ...
> I restarted JGR as regular user and that message is not printed out  
> any more.
> I do not know whether I can feel confident everything is fine with  
> this installation ... ?
>
>

That's fine - the way JGR works is that the first callback moves form  
the start thread to the R thread hence the message, but it's safe  
since it stays in the R thread afterwards. The message is a warning in  
general but in that one case it's ok. If it occurred later after JGR  
is started, that would be something to worry about.

Cheers,
Simon


> Regards,
> Maura
> -----Messaggio originale-----
> Da: Simon Urbanek [mailto:simon.urbanek at r-project.org]
> Inviato: ven 19/06/2009 15.43
> A: mauede at alice.it
> Cc: stats-rosuda-devel at listserv.uni-augsburg.de; r-help at stat.math.ethz.ch
> Oggetto: Re: JGR installation errors
>
> 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.
> >
>
>
>
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