[R] rJava Scientific Linux 6.5 - Can not install

[stephen sefick]

Included at the end of this message is the full compiler output. I have
installed jre-7 from Oracle; The java-1.7.0-jdk* packages and javacc are
installed. It looks like the archiver, header prep., and compiler are
missing. I can provide anything else that can help solve my problem. I
really appreciate all of the help. Kindest regards.

checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
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    : ''
compiler    : ''
header prep.: ''
cpp flags   : '-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/lib/amd64/server
-ljvm'configure: error: Java Development Kit (JDK) is missing or not
registered in R
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.



On Mon, Feb 2, 2015 at 12:54 PM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

> Don't know anything about SL but have you installed a Java run time
> independent of R?
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
> Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On February 2, 2015 10:39:14 AM PST, stephen sefick <ssefick at gmail.com>
> wrote:
> >Hello all,
> >
> >I am having a problem with installing rJava on SL 6.5. I am having
> >compile
> >errors when I try to from CRAN using install.packages("XLConnect",
> >repos="
> >http://cran.rstudio.com/"). I can provide anything necessary, but I am
> >unsure what to provide. Thank you for your help in advance.
> >
> >output of sessionInfo():
> >R version 3.1.0 Patched (2014-06-15 r65949)
> >Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> >locale:
> > [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
> > [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
> > [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
> > [7] LC_PAPER=en_US.utf8       LC_NAME=C
> > [9] LC_ADDRESS=C              LC_TELEPHONE=C
> >[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> >
> >attached base packages:
> >[1] graphics  grDevices utils     datasets  stats     methods   base
> >
> >other attached packages:
> >[1] devtools_1.7.0 ggplot2_1.0.0
> >
> >loaded via a namespace (and not attached):
> > [1] colorspace_1.2-4 digest_0.6.8     grid_3.1.0       gtable_0.1.2
> > [5] MASS_7.3-37      munsell_0.4.2    plyr_1.8.1       proto_0.3-10
> > [9] Rcpp_0.11.4      reshape2_1.4.1   scales_0.2.4     stringr_0.6.2
> >[13] tools_3.1.0
>
>


-- 
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**************************************************
sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
**************************************************

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