[R] help updating package rJava (on ubuntu)

[Simon Urbanek]

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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