You can install it from Michael Rutter's PPA: sudo apt-add-repository -y ppa:marutter/c2d4u sudo apt-get update sudo apt-get install r-cran-rjava
The last time I tried the official Ubuntu repository, rJava still did not work under R 3.0.x (because R 3.0.x requires recompiling all R packages). I'm not sure if that has changed or not. Michael's repository has been working well for me (including many other R packages that have system dependencies). Regards, Yihui -- Yihui Xie <xieyi...@gmail.com> Phone: 206-667-4385 Web: http://yihui.name Fred Hutchinson Cancer Research Center, Seattle On Tue, Jul 30, 2013 at 9:28 PM, Erin Hodgess <erinm.hodg...@gmail.com> wrote: > Dear R People: > > I am trying to install rJava on an Ubuntu 13.04 64 bit system. But the > Java part is causing me fits. Here is the code: > >> install.packages("rJava",depen=TRUE) > Installing package into ‘/home/erin/R/x86_64-pc-linux-gnu-library/3.0’ > (as ‘lib’ is unspecified) > --- Please select a CRAN mirror for use in this session --- > trying URL 'http://cran.at.r-project.org/src/contrib/rJava_0.9-4.tar.gz' > Content type 'application/x-gzip' length 498108 bytes (486 Kb) > opened URL > ================================================== > downloaded 486 Kb > > * installing *source* package ‘rJava’ ... > ** package ‘rJava’ successfully unpacked and MD5 sums checked > checking for gcc... gcc -std=gnu99 > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/wait.h that is POSIX.1 compatible... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for string.h... (cached) yes > checking sys/time.h usability... yes > checking sys/time.h presence... yes > checking for sys/time.h... yes > checking for unistd.h... (cached) yes > checking for an ANSI C-conforming const... yes > checking whether time.h and sys/time.h may both be included... yes > configure: checking whether gcc -std=gnu99 supports static inline... > yes > checking whether setjmp.h is POSIX.1 compatible... yes > checking whether sigsetjmp is declared... yes > checking whether siglongjmp is declared... yes > checking Java support in R... present: > interpreter : '/usr/lib/jvm/jdk1.7.0_25/jre/bin/java' > archiver : '/usr/lib/jvm/jdk1.7.0_25/bin/jar' > compiler : '/usr/lib/jvm/jdk1.7.0_25/bin/javac' > header prep.: '/usr/lib/jvm/jdk1.7.0_25/bin/javah' > cpp flags : '' > java libs : '' > configure: error: One or more Java configuration variables are not set. > Make sure R is configured with full Java support (including JDK). Run > R CMD javareconf > as root to add Java support to R. > > If you don't have root privileges, run > R CMD javareconf -e > to set all Java-related variables and then install rJava. > > ERROR: configuration failed for package ‘rJava’ > * removing ‘/home/erin/R/x86_64-pc-linux-gnu-library/3.0/rJava’ > > The downloaded source packages are in > ‘/tmp/RtmpSzdy7i/downloaded_packages’ > Warning message: > In install.packages("rJava", depen = TRUE) : > installation of package ‘rJava’ had non-zero exit status >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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 > > loaded via a namespace (and not attached): > [1] tcltk_3.0.1 tools_3.0.1 >> q() > Save workspace image? [y/n/c]: y > > Now here is the command line: > > erin@erin-Lenovo-IdeaPad-Y480:~$ sudo R CMD javareconf > Java interpreter : /usr/bin/java > Java version : 1.7.0_25 > Java home path : /usr/lib/jvm/jdk1.7.0_25/jre > Java compiler : /usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > > trying to compile and link a JNI progam > detected JNI cpp flags : -I$(JAVA_HOME)/../include > -I$(JAVA_HOME)/../include/linux > detected JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG > -I/usr/lib/jvm/jdk1.7.0_25/jre/../include > -I/usr/lib/jvm/jdk1.7.0_25/jre/../include/linux -fpic -O2 -pipe -g -c > conftest.c -o conftest.o > gcc -std=gnu99 -shared -o conftest.so conftest.o > -L/usr/lib/jvm/jdk1.7.0_25/jre/lib/i386/client -ljvm -L/usr/lib/R/lib -lR > /usr/bin/ld: skipping incompatible > /usr/lib/jvm/jdk1.7.0_25/jre/lib/i386/client/libjvm.so when searching for > -ljvm > /usr/bin/ld: cannot find -ljvm > collect2: error: ld returned 1 exit status > make: *** [conftest.so] Error 1 > Unable to compile a JNI program > > > Java library path: > JNI cpp flags : > JNI linker flags : > Updating Java configuration in /usr/lib/R > Done. > > erin@erin-Lenovo-IdeaPad-Y480:~$ > > I'm thinking that there is a problem with shared/static libraries, > perhaps? > > > Has anyone else run into this, please? Any help much appreciated. > > Sincerely, > Erin > > > -- > Erin Hodgess > Associate Professor > Department of Computer and Mathematical Sciences > University of Houston - Downtown > mailto: erinm.hodg...@gmail.com ______________________________________________ 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.
