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@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
______________________________________________
R-help@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.
