[R] rJava Scientific Linux 6.5 - Can not install
stephen sefick
ssefick at gmail.com
Tue Feb 3 14:58:08 CET 2015
I have solved the problem. Here are the steps in case this will help
anyone.
1) I downloaded, compiled, and installed latest R sources.
2) made sure I had all of the R development libraries install through
packages manager
3) update java jkd 1.6* to java jkd 1.7*
4) ran sudo R CMD javareconf
JAVA_HOME="/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.75.x86_64/"
5) Ensured all of the fields in the output of 4 were populated
6) in a sudo R session, I ran install.packages("rJava",
library=personal_library)
Stephen
On Mon, Feb 2, 2015 at 2:39 PM, stephen sefick <ssefick at gmail.com> wrote:
> 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
> **************************************************
>
> Let's not spend our time and resources thinking about things that are so
> little or so large that all they really do for us is puff us up and make us
> feel like gods. We are mammals, and have not exhausted the annoying little
> problems of being mammals.
>
> -K. Mullis
>
> "A big computer, a complex algorithm and a long time does not equal
> science."
>
> -Robert Gentleman
>
>
--
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**************************************************
sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
**************************************************
Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods. We are mammals, and have not exhausted the annoying little
problems of being mammals.
-K. Mullis
"A big computer, a complex algorithm and a long time does not equal
science."
-Robert Gentleman
[[alternative HTML version deleted]]
More information about the R-help
mailing list