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. > > ______________________________________________ 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.