Richard Vickery richard.vickeryrv at gmail.com
Tue Oct 23 01:39:05 UTC 2012

sorry I mistakenly deleted the R discussion from my inbox. Here is what I
get back:

> install.packages("rJava")Installing package(s) into ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15’
(as ‘lib’ is unspecified)trying URL
'http://cran.stat.sfu.ca/src/contrib/rJava_0.9-3.tar.gz'Content type
'application/x-gzip' length 537153 bytes (524 Kb)opened
URL==================================================downloaded 524 Kb
* installing *source* package ‘rJava’ ...** package ‘rJava’
successfully unpacked and MD5 sums checkedchecking for gcc... gcc -m32
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 -m32 -std=gnu99 accepts -g... yes
checking for gcc -m32 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -m32 -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 -m32 -std=gnu99 supports static inline...
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 : '/bin/java'
archiver    : '/bin/jar'
compiler    : '/bin/javac'
header prep.: '/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.7.0-openjdk-
java libs   : '-L/usr/lib/jvm/java-1.7.0-openjdk-
-L/usr/lib/jvm/java-1.7.0-openjdk- -ljvm'
checking whether JNI programs can be compiled... configure: error:
Cannot compile a simple JNI program. See config.log for details.

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’* removing
‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’* restoring
previous ‘/home/richard/R/i686-redhat-linux-gnu-library/2.15/rJava’Warning
in install.packages :
  installation of package ‘rJava’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmpz86WUb/downloaded_packages’> library(JGR)Loading required
package: rJavaError : .onLoad failed in loadNamespace() for 'rJava',
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object
  libjvm.so: cannot open shared object file: No such file or
directoryError: package ‘rJava’ could not be loaded
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