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

[Mark Kimpel]

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