[R] Installing rJava fails

From: jcheng liu <jcheng.liu_at_gmail.com>
Date: Fri, 18 Mar 2011 10:39:25 -0400

Dear all,
Installing rJava fails. The message was listed below. I wonder why cpp flag could not be detected, although I had installed. Thanks!!!

R CMD INSTALL rJava_0.9-0.tar.gz
* installing to library
‘/data1/mri_researchers/wexler_data/jiacheng/R-2.12.0/library’ * 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/java/jre1.6.0_24/lib/amd64/server

-L/usr/java/jre1.6.0_24/lib/amd64 -L/usr/java/jre1.6.0_24/../lib/amd64
-L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib

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 ‘/R-2.12.0/library/rJava’

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