On 03/16/2011 06:46 AM, Martin Morgan wrote: > On 03/16/2011 05:01 AM, MLSC MANIPAL wrote: >> *Dear Sir, >> I have successfully installed jdk and rJava using the following commands: >> >> sudo apt-get install r-cran-rjava >> >> sudo apt-get install sun-java6-jdk sun-java6-jre >> >> But when I try to install using : install.packages("rJava"), it is giving >> the follwinfg error: >> * >> Warning in install.packages("rJava") : >> argument 'lib' is missing: using '/usr/local/lib/R/site-library' >> --- Please select a CRAN mirror for use in this session --- >> Loading Tcl/Tk interface ... done >> trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/rJava_0.8-8.tar.gz' >> Content type 'application/x-gzip' length 522057 bytes (509 Kb) >> opened URL >> ================================================== >> downloaded 509 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 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/jvm/java-6-openjdk/jre/lib/i386/server >> -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386 >> -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 >> -L/usr/java/packages/lib/i386 >> -L/usr/lib/jni -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/local/lib/R/site-library/rJava? >> * restoring previous ?/usr/local/lib/R/site-library/rJava? >> >> The downloaded packages are in >> ?/tmp/Rtmpp8n1WE/downloaded_packages? >> Warning message: >> In install.packages("rJava") : >> installation of package 'rJava' had non-zero exit status >> >> *The same problem while installing Java related web packages such as >> RWebService,Sjava,JavaGD etc... >> * >> *I am using R version 2.11.1 (2010-05-31)* >> >> *I already run the following command in root and it was successful: R CMD >> javareconf >> >> *Java interpreter : /usr/bin/java >> Java version : 1.6.0_20 >> Java home path : /usr/lib/jvm/java-6-openjdk/jre >> Java compiler : /usr/bin/javac >> Java headers gen.: /usr/bin/javah >> Java archive tool: /usr/bin/jar >> Java library path: >> $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../ lib/i386:/usr/java/packages/lib/i386:/usr/lib/jni:/lib:/usr/lib >> >> JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386 >> -L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/usr/lib/jni >> -L/lib -L/usr/lib -ljvm >> JNI cpp flags : > > Both rJava and SJava have this in their configuration file > > if test -n "${JAVA}" && test -n "${JAVAC}" && test -n "${JAVAH}" && \ > test -n "${JAVA_CPPFLAGS}" && test -n "${JAVA_LIBS}" && test -n > "${JAR}"; then > have_all_flags=yes; > fi > > so I suspect they fail because JAVA_CPPFLAGS is '' (for me, this has the > value -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux). It seems > like R CMD javareconf should be determining this (javareconf is in > R_HOME/bin/). You might manually edit R_HOME/etc/ so that JAVA_CPPFLAGS meant R_HOME/etc/Makeconf > points to something appropriate (the location of the include files > requires for your java installation). > > It might help to install a newer version of R. > > Martin > >> Updating Java configuration in /etc/R >> Done.* >> >> * >> >> * >> * >> >> *Hence, Can you please suggest me a solution for this?* >> >> * * >> >> *Thanking you in anticipation.* >> >> * * >> >> *Regards,* >> >> *Rayan* >> >> [[alternative HTML version deleted]] >> >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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