I remember JGR installation on SuSE 10.3 as a nightmare that eventually I overcame with JGR designers' help. I have installed SuSE 11.1, latest R version and am trying to install JGR again. It is still a nightmare. I have followed the guidelines on http://jgr.markushelbig.org/JGR_on_Linux.html I have made sure I have the so R libraries. I have installed java-1.6.0-sun and its development environment. Following the on-line guidelines for JGR installation, the process fails on trying to install "rJava" ... please see all the messages in the following. I get the same error if I try to install "rJava" in advance of JGR. Thank you very much, Maura As root: linux-326k:/home/mauede # sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm JNI cpp flags : Updating Java configuration in /usr/lib64/R Done. linux-326k:/home/mauede # sudo R> install.packages('JGR')--- Please select a CRAN mirror for use in this session --- CRAN mirror Selection: 24 also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ trying URL 'http://cran.stat.unipd.it/src/contrib/rJava_0.6-3.tar.gz' Content type 'application/octet-stream' length 240527 bytes (234 Kb) opened URL ================================================== downloaded 234 Kb trying URL 'http://cran.stat.unipd.it/src/contrib/JavaGD_0.5-2.tar.gz' Content type 'application/octet-stream' length 87076 bytes (85 Kb) opened URL ================================================== downloaded 85 Kb trying URL 'http://cran.stat.unipd.it/src/contrib/iplots_1.1-3.tar.gz' Content type 'application/octet-stream' length 331100 bytes (323 Kb) opened URL ================================================== downloaded 323 Kb trying URL 'http://cran.stat.unipd.it/src/contrib/JGR_1.6-7.tar.gz' Content type 'application/octet-stream' length 506759 bytes (494 Kb) opened URL ================================================== downloaded 494 Kb * Installing *source* package ‘rJava’ ... 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 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/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64/server -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64 -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -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/lib64/R/library/rJava’ * Installing *source* package ‘JavaGD’ ... 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 checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking return type of signal handlers... void checking for memset... yes checking for mkdir... yes checking for rmdir... yes checking for select... yes checking for socket... yes checking Java support in R... present: interpreter : '/usr/bin/java' cpp flags : '' java libs : '-L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64/server -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/amd64 -L/usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -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 ‘JavaGD’ * Removing ‘/usr/lib64/R/library/JavaGD’ * Installing *source* package ‘iplots’ ... ** R ** inst ** preparing package for lazy loading Error : package 'rJava' required by 'iplots' could not be found ERROR: lazy loading failed for package ‘iplots’ * Removing ‘/usr/lib64/R/library/iplots’ * Installing *source* package ‘JGR’ ... ** R ** inst ** preparing package for lazy loading Error : package 'rJava' required by 'JGR' could not be found ERROR: lazy loading failed for package ‘JGR’ * Removing ‘/usr/lib64/R/library/JGR’ The downloaded packages are in ‘/tmp/Rtmpf6sSE6/downloaded_packages’ Updating HTML index of packages in '.Library' Warning messages: 1: In install.packages("JGR") : installation of package 'rJava' had non-zero exit status 2: In install.packages("JGR") : installation of package 'JavaGD' had non-zero exit status 3: In install.packages("JGR") : installation of package 'iplots' had non-zero exit status 4: In install.packages("JGR") : installation of package 'JGR' had non-zero exit status>tutti i telefonini TIM! 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MAura, On Jun 19, 2009, at 7:36 , <mauede at alice.it> <mauede at alice.it> wrote:> I remember JGR installation on SuSE 10.3 as a nightmare that > eventually I overcame with JGR designers' help. > I have installed SuSE 11.1, latest R version and am trying to > install JGR again. > It is still a nightmare. >Well, good Linux distros offer JGR as binaries so it's one-liner to install it ;). All other distros I use are easy to install even from sources - SuSE seems is notoriously struggling ...> I have followed the guidelines on http://jgr.markushelbig.org/JGR_on_Linux.html > I have made sure I have the so R libraries. > I have installed java-1.6.0-sun and its development environment. > Following the on-line guidelines for JGR installation, > the process fails on trying to install "rJava" ... please see all > the messages in the following. > I get the same error if I try to install "rJava" in advance of JGR. > > Thank you very much, > Maura > > > As root: > > linux-326k:/home/mauede # sudo R CMD javareconf > Java interpreter : /usr/bin/java > Java version : 1.6.0_0 > Java home path : /usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre > Java compiler : /usr/bin/javac > Java headers gen.: /usr/bin/javah > Java archive tool: /usr/bin/jar > Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/ > amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/ > lib64:/lib64:/lib:/usr/lib > JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/ > lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/ > amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm > JNI cpp flags : >^^^ - it appears that you don't have full JDK installed properly or it's non-standard location - R cannot find flags needed to compile JNI. You don't have either of ${JAVA_HOME}/include, ${JAVA_HOME}/../ include, ${JAVA_HOME}/jre/include so you'll need to figure out whether a) you just didn't install them or b) they are installed in a non- standard location. The fix for a) is to install them, the fix for b) is set set them using JAVA_CPPFLAGS when calling javareconf (and report back to us to see if that's something we can add to R). Cheers, Simon> Updating Java configuration in /usr/lib64/R > Done. >