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 [[alternative HTML version deleted]]
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