Re: [R] Problem loading rJava...
Brian, I believe I had a similar problem. Make sure you have JDK (*sun-java6-jdk) * installed as well. Here is a link to a JDK install guide http://www.cyberciti.biz/faq/howto-ubuntu-linux-install-configure-jdk-jre/ On Mon, Aug 15, 2011 at 10:18 AM, Brian Lunergan ff...@ncf.ca wrote: Morning All: Having problems installing this one into my R setup and wondered if anyone on the list had the same problem and found a workable solution. First to the system particulars: OS is the Hardy Heron edition of Ubuntu Linux R version is 2.13.1 Java installation is sun-java6 Next up is the result of javareconf: R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.5.0 Java home path : /usr/lib/jvm/java-1.5.0-gcj-4.2-1.5.0.0/jre Java compiler: /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: /usr/lib/../lib/gcj-4.2-81:/usr/lib/jni JNI linker flags : -L/usr/lib/../lib/gcj-4.2-81 -L/usr/lib/jni -ljvm JNI cpp flags: Updating Java configuration in /etc/R Done. What little I've been able to find on this problem suggests that the blank space beside the cpp flags variable is the key point, but all the notes I found suggest programming solutions outside of my abilities. Are there any simple and to the point solutions that correct this issue, or am I SOL for using the package? Any help would be greatly appreciated as install of other packages and R commander plugins depend on solving it. Oh, yes. Here's the result when I try to pull in rJava. install.packages() Loading Tcl/Tk interface ... done --- Please select a CRAN mirror for use in this session --- Installing package(s) into /usr/local/lib/R/site-library (as lib is unspecified) trying URL 'http://cran.skazkaforyou.com/src/contrib/rJava_0.9-1.tar.gz' Content type 'application/x-gzip' length 527197 bytes (514 Kb) opened URL == downloaded 514 Kb * installing *source* package rJava ... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -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 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/bin/java' archiver: '/usr/bin/jar' compiler: '/usr/bin/javac' header prep.: '/usr/bin/javah' cpp flags : '' java libs : '-L/usr/lib/../lib/gcj-4.2-81 -L/usr/lib/jni -ljvm' 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 /usr/local/lib/R/site-library/rJava The downloaded packages are in /tmp/Rtmph5lTVR/downloaded_packages Warning message: In install.packages() : installation of package 'rJava' had non-zero exit status -- Brian Lunergan Nepean, Ontario Canada __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joseph C. Magagnoli [[alternative HTML version deleted]] __ 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
Re: [R] Problem loading rJava... (apparently solved)
On Mon, 2011-08-15 at 10:41 -0500, Joseph Magagnoli wrote: Brian, I believe I had a similar problem. Make sure you have JDK (*sun-java6-jdk) * installed as well. Here is a link to a JDK install guide http://www.cyberciti.biz/faq/howto-ubuntu-linux-install-configure-jdk-jre/ content trimmed somewhat for brevity Joseph: Thanks VERY much for the link. Worked through the steps and ran javareconf again. The cpp flags variable was no longer empty. Opened a root terminal window, fired up R, and (with a few warning shots by the system on compilation) rJava is now settled into place. Now to try pulling in the R commander plugin I was after that depended on rJava. I will say it again. Your help was much appreciated. I may be using an older edition of Ubuntu, but I sincerely believe the answers are out there in the collective memory of those on the list who used the Heron and R. Sorry, Dirk, but if a problem comes up I will still ask help of the list. If there is an answer (and so far all problems have been laid to rest with the help of Joseph and others) then great. Otherwise, I will simply accept that the particular functionality is unavailable either because it just will not work on the Heron, or the answer has faded from view. Regards... -- Brian Lunergan Nepean, Ontario Canada __ 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.
Re: [R] Problem loading rJava
Josef.Kardos at phila.gov writes: I finally realized I didn't have Java installed on my computer, so I downloaded Java and tested that it works. I then attempted to reinstall rJava and load the package, but got this; utils:::menuInstallLocal() package 'rJava' successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package 'rJava' updating HTML package descriptions This sound like you did not leave RGui when installing Java. Try again after a restart. Dieter __ 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.
