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

[Dirk Eddelbuettel]

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.