It is really strange what I see on this output. Your machine is 64 bit
(i386) and the libjvm is being compiled to 32 bit (I do not know what could
elicit such behavior).
Can you try and JDK 6 version?
I am on a ubuntu 12.04 64 bit and I have rJava:
orvaquim@orvaquimcism:~$ R CMD javareconf -e
Java interpreter : /usr/bin/java
Java version : 1.6.0_27
Java home path : /usr/lib/jvm/java-6-openjdk-amd64/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$(JAVA_HOME)/../include
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I/usr/lib/jvm/java-6-openjdk-amd64/jre/../include -fpic -O3 -pipe
-g -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -o conftest.so conftest.o
-L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -ljvm
-L/usr/lib/R/lib -lR
The following Java variables have been exported:
JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
Running: /bin/bash
Hope it helps
Caveman
On Wed, Jul 31, 2013 at 6:28 AM, Erin Hodgess <erinm.hodg...@gmail.com>wrote:
> 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]]
>
>
> ______________________________________________
> 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.
>
>
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