Done !
>
> > install.packages("rJava")
> Warning in install.packages("rJava") :
> argument 'lib' is missing: using
> '/home/martial/R/x86_64-unknown-linux-gnu-library/2.9'
> trying URL 'http://cran.fr.r-project.org/src/contrib/rJava_0.6-2.tar.gz'
> Content type 'application/x-tar' length 237115 bytes (231 Kb)
> opened URL
> ==================================================
> downloaded 231 Kb
>
> * Installing *source* package rJava ...
>
>
>
> checking Java support in R... present:
> interpreter : '/usr/bin/java'
> archiver : ''
> compiler : ''
> header prep.: ''
> cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include'
> 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.
>
>
The fact is that some the path for the archiver, the compiler and the header
are missing.
Thus, when doing the javareconf, just add the path for the missing variables.
~$ sudo R CMD javareconf JAVAC=/usr/lib/jvm/java-6-openjdk/jre/../bin/javac
JAR=/usr/bin/jar JAVAH=/usr/bin/javah
Java interpreter : /usr/bin/java
Java version : 1.6.0_0
Java home path : /usr/lib/jvm/java-6-openjdk/jre
Java compiler : /usr/lib/jvm/java-6-openjdk/jre/../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$(JAVA_HOME)/../include
Updating Java configuration in /usr/local/lib64/R
Done.
Then launch the R and install the package:
~$ sudo R
install.packages("rJava")
(...)
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/lib/jvm/java-6-openjdk/jre/../bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include'
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'
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... no
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether JRI is requested... no
(...)
** building package indices ...
* DONE (rJava)
That's all ! ^^
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