Running R on JASMIN
On the JASMIN `sci` servers and LOTUS, we support the use of R through the "jasr" environment(s), as listed on the Jaspy page.
module load jasr
$ Rscript --help Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args] --options accepted are --help Print usage and exit --version Print version and exit --verbose Print information on progress --default-packages=list Where 'list' is a comma-separated set of package names, or 'NULL' or options to R, in addition to --no-echo --no-restore, such as --save Do save workspace at the end of the session --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 user R profile --restore Do restore previously saved objects at startup --vanilla Combine --no-save, --no-restore, --no-site-file --no-init-file and --no-environ 'file' may contain spaces but not shell metacharacters Expressions (one or more '-e <expr>') may be used *instead* of 'file' See also ?Rscript from within R <br>
The version number (currently 4.0.5) is reported when you start R, or if you type:
Here are commands to do a simple plot to a file, which you can use to test running R either interactively or with "Rscript" as described above.
png("myplot.png") x <- c(1,2,3,4) y <- x*x plot(x,y) dev.off()
(You could use the "display" command on JASMIN to view the output file.)
Here is a minimal example of using the "library" command to load one of the many add-on libraries that have been installed to supplement the core R distribution. It uses the "prettyunits" package to convert a number of bytes to human-readable format.
[firstname.lastname@example.org ~]$ module load jasr [email@example.com ~]$ R --quiet > library(prettyunits) > pretty_bytes(12345678)  "12.35 MB" >