[R] help updating package rJava (on ubuntu)

[Karl Brand]

Simon,

Thanks for yout fast response. Thing is - i managed to get Version 0.9-1 
installed and fully functional. And

$ locate jdk

returns too many entries to post here, so i'm pretty sure its on the 
machine.

So i'd like to know how i can ensure it's "registered in R". This i have 
no idea how to do. I simply don't have enough R and linux experience. 
Also the thread i mentioned 
http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing

seems to be about pointing R at the right location of certain aspects of 
Java. But lacks enough explicit details for myself to be able use.

Thanks again, also for any further suggestions,

Karl



On 02/18/2012 07:45 PM, Simon Urbanek wrote:
>
> 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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>

-- 
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