[R] can't get rJava to install on Linux

[Godmar Back]

This is just a guess: looks like you have GNU's Java version in your
path (aka "gcj").
Perhaps rJava relies on Sun's Java version.

If so, install Sun's Java first. apt-get install sun-java6-jdk might do it.

 - Godmar


On Tue, Jul 7, 2009 at 9:28 PM, Mark Kimpel<mwkimpel at gmail.com> wrote:
> Having difficulties getting rJava to install on my Debian Squeeze box.
> Perused the R-help list and tried some things that have worked for
> others but not for me. Below is the output of my attempted build, R
> CMD javareconf -e, and sessionInfo(). Note I tried the R CMD
> javareconf also as root, restarted R after each of these, all no help.
>
>
> * 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/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javac'
> header prep.: '/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javah'
> cpp flags   : ''
> java libs   : '-L/usr/lib/../lib/gcj-4.3-90 -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 ‘/home/mkimpel/R_HOME/site-library-2.9.0/rJava’
>
> The downloaded packages are in
>        ‘/tmp/Rtmpfp9kiG/downloaded_packages’
> Warning message:
> In install.packages("rJava") :
>  installation of package 'rJava' had non-zero exit status
>
>  ./R CMD javareconf -e
> Java interpreter : /usr/bin/java
> Java version     : 1.5.0
> Java home path   : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre
> Java compiler    : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javac
> Java headers gen.: /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../bin/javah
> Java archive tool: /usr/bin/jar
> Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni
> JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm
> JNI cpp flags    :
>
> The following Java variables have been exported:
> JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
>
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.9.1 tools_2.9.1
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
>
> "The real problem is not whether machines think but whether men do."
> -- B. F. Skinner
>
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