On Feb 18, 2012, at 10:44 AM, Karl Brand wrote:
> Esteemed useRs and Devs,
>
> Attempts to update package:rJava to the latest version have failed. See my
code and output below.
>
> Notably, as suggested here
http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing
>
> $ sudo apt-get install r-cran-rjava
>
> ran successfully without error or warning, but my rJava package is not
updated, and remains un-updatable...
>
> Greatly appreciate any suggestions getting my rJava updated,
>
> Karl
>
>
>
> > update.packages(lib.loc = "/usr/lib/R/site-library")
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> rJava :
> Version 0.9-1 installed in /usr/lib/R/site-library
> Version 0.9-3 available at http://cran.xl-mirror.nl
> Update (y/N/c)? y
>
> <snip>
>
> 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/usr/java/packages/lib/amd64
-L/usr/lib/jni -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.
>
> ...so i do as suggested:
>
> $ sudo R CMD javareconf
> Java interpreter : /usr/bin/java
> Java version : 1.6.0_23
> 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:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib
-L/usr/lib -ljvm
> JNI cpp flags :
>
> Updating Java configuration in /etc/R
> Done.
>
> But i still get the same error when trying to update rJava!
>
Obviously - your'e lacking JDK on your machine - see the output above (you
have only JRE, not JDK). If you want to compile rJava form sources you need to
install JDK first, then add Java support to R (via javareconf) and then build
rJava.
Cheers,
Simon
> > sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_AU.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> --
> Karl Brand
> Department of Genetics
> Erasmus MC
> Dr Molewaterplein 50
> 3015 GE Rotterdam
> T +31 (0)10 704 3455 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
>
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