On Jun 19, 2009, at 10:08 , <mau...@alice.it> <mau...@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.urba...@r-project.org]
Inviato: ven 19/06/2009 15.43
A: mau...@alice.it
Cc: stats-rosuda-de...@listserv.uni-augsburg.de; r-h...@stat.math.ethz.ch
Oggetto: Re: JGR installation errors
MAura,
On Jun 19, 2009, at 7:36 , <mau...@alice.it> <mau...@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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