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

[Stefan Th. Gries]

Hi

(Thx for the first responses and sorry for delay, been travelling ...)

Ok, when I copied some parts of my attempt to install rJava, I left
out the stuff that DID work so let me try again more comprehensively:

### R version
> R.version
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
> java -version
java version "1.6.0_0"
IcedTea6 1.3.1 (6b12-0ubuntu6.1) 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:~$


So, I start R with

> sudo R

Then, within R:

> install.packages("rJava") # choosing Austria

and I get:

############
downloaded 231 Kb

* Installing *source* package 'rJava' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : ''
compiler    : ''
header prep.: ''
cpp flags   : ''
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.

If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.

ERROR: configuration failed for package 'rJava'
** Removing '/usr/local/lib/R/site-library/rJava'

The downloaded packages are in
	/tmp/RtmpFN4dvI/downloaded_packages
Warning message:
In install.packages("rJava") :
  installation of package 'rJava' had non-zero exit status
############

So, I enter:

> sudo R CMD javareconf

and get

############
Java interpreter : /usr/bin/java
Java version     : 1.6.0_0
Java home path   : /usr/lib/jvm/java-6-openjdk/jre
Java compiler    : not present
Java headers gen.:
Java archive tool:
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    :

Updating Java configuration in /etc/R
Done.
############

But then, when I run

> sudo R
> install.packages("rJava") # choosing Austria

I get the same stuff as before although JDK is installed and I did the
reconf ...

Any pointers,
STG