[R-sig-Debian] rJava in R 2.8.1 on Ubuntu 8.10

[Michael Rutter]

Just to confirm on my 64-bit AMD machine based on the amd64 ubuntu
binaries, I get the following:

mrutter at yorick ~> sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_0
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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L$(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    : -I$(JAVA_HOME)/../include

Updating Java configuration in /etc/R
Done.

Michael

On Mon, Jan 26, 2009 at 8:32 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> On 26 January 2009 at 17:24, Stefan Th. Gries wrote:
> | Hi all
> |
> | I have problems installing rJava on my system.
> |
> | ######## My system:
> |
> | > R.version # at R prompt
> | platform       x86_64-pc-linux-gnu
> | arch           x86_64
> | os             linux-gnu
> | system         x86_64, linux-gnu
> | status
> | major          2
> | minor          8.1
> | year           2008
> | month          12
> | day            22
> | svn rev        47281
> | language       R
> | version.string R version 2.8.1 (2008-12-22)
> |
> | > java -version # at terminal prompt
> | java version "1.6.0_0"
> | IcedTea6 1.3.1 (6b12-0ubuntu6) Runtime Environment (build 1.6.0_0-b12)
> | OpenJDK 64-Bit Server VM (build 1.6.0_0-b12, mixed mode)
> | stgries at stgries-acer:~$
> |
> | on Ubuntu 8.10 (Kernel 2.6.27-9)
> | on an AMD Phenom Triple-Core
> |
> |
> |
> | The problem arises here:
> |
> | java libs   : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server
> | -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64
> | -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L
> | -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib
> | -ljvm'
> | configure: error: Java Development Kit (JDK) is missing or not registered in R
> | Make sure R is configured with full Java support (including JDK). Run
> | R CMD javareconf
> | as root to add Java support to R.
> |
> | When I then do that
> |
> | > sudo R CMD javareconf # at terminal
> |
> | I get this:
> |
> | Updating Java configuration in /etc/R
> | Done.
>
> That's not right.  Did you build your own R, or did you use the Ubuntu 8.10
> binaries from CRAN?
>
> This should show something similar to (from my i386 Ubuntu system without
> rJava):
>
> edd at joe:~$ sudo R CMD javareconf
> Java interpreter : /usr/bin/java
> Java version     : 1.6.0_0
> 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: $(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib
> JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm
> JNI cpp flags    :
>
> Updating Java configuration in /etc/R
> Done.
>
> | However, it still doesn't work, returning the same crap as before.
> | Also, when I try
> |
> | > R CMD javareconf -e # at terminal
> |
> | I just get
> |
> | shift: 57: can't shift that many
> |
> | Any hints would be much appreciated
>
> What is /bin/sh for you?  On my system /bin/sh -> dash and it works.
>
> FWIW rJava entered Debian this weekend and should be part of the next Ubuntu
> release as well.
>
> Dirk
>
> --
> Three out of two people have difficulties with fractions.
>
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>



-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter