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
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 <ff809@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.html<http://www.r-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. >-- Joseph C. Magagnoli [[alternative HTML version deleted]]
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