Software at OSC |
RIntroductionR is a language and environment for statistical computing and graphics. It is similar to the S language and environment developed at Bell Laboratories (formerly AT&T, now Lucent Technologies). R provides a wide variety of statistical and graphical techniques, and is highly extensible. VersionVersions 2.5.1 and 2.8.0 are currently available at OSC. R 2.8.0 is the default: module load R AvailabilityR is available on the Glenn Cluster. Usagemodule load R Starting an R session, interactively, requires running the command: R A review of the command options for 'R' is available online: [opt-login01] ~ :: R --help Usage: R [options] [< infile] [> outfile] or: R CMD command [arguments] Start R, a system for statistical computation and graphics, with the specified options, or invoke an R tool via the 'R CMD' interface. Options: -h, --help Print short help message and exit --version Print version info and exit --encoding=ENC Specify encoding to be used for stdin RHOME Print path to R home directory and exit --save Do save workspace at the end of the session --no-save Don't save it --no-environ Don't read the site and user environment files --no-site-file Don't read the site-wide Rprofile --no-init-file Don't read the .Rprofile or ~/.Rprofile files --restore Do restore previously saved objects at startup --no-restore-data Don't restore previously saved objects --no-restore-history Don't restore the R history file --no-restore Don't restore anything --vanilla Combine --no-save, --no-restore, --no-site-file, --no-init-file and --no-environ --no-readline Don't use readline for command-line editing --min-vsize=N Set vector heap min to N bytes; '4M' = 4 MegaB --max-vsize=N Set vector heap max to N bytes; --min-nsize=N Set min number of cons cells to N --max-nsize=N Set max number of cons cells to N --max-ppsize=N Set max size of protect stack to N -q, --quiet Don't print startup message --silent Same as --quiet --slave Make R run as quietly as possible --verbose Print more information about progress -d, --debugger=NAME Run R through debugger NAME --debugger-args=ARGS Pass ARGS as arguments to the debugger -g, --gui=TYPE Use TYPE as GUI; possible values are 'X11' (default), 'Tk' and (with package gnomeGUI) 'gnome' --arch=NAME Specify a sub-architecture --args Skip the rest of the command line -f, --file=FILE Take input from 'FILE' Commands: BATCH Run R in batch mode COMPILE Compile files for use with R SHLIB Build shared library for dynamic loading INSTALL Install add-on packages REMOVE Remove add-on packages build Build add-on packages check Check add-on packages LINK Front-end for creating executable programs Rprof Post-process R profiling files Rdconv Convert Rd format to various other formats Rd2dvi Convert Rd format to DVI/PDF Rd2txt Convert Rd format to pretty text Sd2Rd Convert S documentation to Rd format Stangle Extract S/R code from Sweave documentation Sweave Process Sweave documentation config Obtain configuration information about R Please use 'R CMD command --help' to obtain further information about the usage of 'command'. Running 'R' interactively is not appropriate for OSC's batch scheduling, on any of the clusters. In a batch script use the command: R CMD BATCH infile outfile More information about running 'R' in batch is available online, as well: [opt-login01] ~ :: R CMD BATCH --help
Usage: R CMD BATCH [options] infile [outfile]
Run R non-interactively with input from infile and place output (stdout
and stderr) to another file. If not given, the name of the output file
is the one of the input file, with a possible '.R' extension stripped,
and '.Rout' appended.
Options:
-h, --help print short help message and exit
-v, --version print version info and exit
-- end processing of options
Further arguments starting with a '-' are considered as options as long
as '--' was not encountered, and are passed on to the R process, which
by default is started with '--restore --save --no-readline'.
See also help('BATCH') inside R.
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