Run
R CMD javareconf -e
as the being suggest by the output. That will try to guess where is Java. Or
you can install the JDK_HOME and JAVA_HOME variables.
Good luck.
Caveman
On Fri, Mar 18, 2011 at 4:39 PM, jcheng liu <jcheng.liu@gmail.com> wrote:
> Dear all,
> Installing rJava fails. The message was listed below. I wonder why cpp flag
> could not be detected, although I had installed. Thanks!!!
> -Jiacheng
>
> 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
> -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 ‘/R-2.12.0/library/rJava’
>
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>
>
> ______________________________________________
> 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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