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
[[alternative HTML version deleted]]
On Mon, Feb 2, 2015 at 1:39 PM, 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.The actual error would be a good start. You can probably solve your problem by copying the error message into google, but if that doesn't help you can post it back here. Best, Ista 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.
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
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 [[alternative HTML version deleted]]