[R] problems installing rJava

From: Juan Pablo Romero Méndez <jpablo.romero_at_gmail.com>
Date: Sun, 11 May 2008 12:27:26 -0500


I'm having trouble installing rJava on R-2.6.1 / Suse10.3.

What could be wrong?


  Juan Pablo

This is the output of

> install.packages("rJava", dependencies=T)

* 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... /usr/bin/grep checking for egrep... /usr/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/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/../include
-I/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/../include/linux' java libs : '-L/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/lib/i386/server -L/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/lib/i386 -L/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/../lib/i386 -ljvm' checking whether JNI programs can be compiled... yes checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package 'rJava' ** Removing '/usr/lib/R/library/rJava'

The downloaded packages are in

        /tmp/RtmpNOU9fz/downloaded_packages Updating HTML index of packages in '.Library' Warning message:
In install.packages("rJava", dependencies = T) :   installation of package 'rJava' had non-zero exit status >

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