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.

In order to activate the R environment, you will need to use:

module load jasr

Note that the Jaspy page lists all available environments. You can also list the R packages that are available in the environment by typing:

ls $CONDA_PREFIX/lib/R/library/

Once you have activated the environment, you can start R, using:

If you have an R script that you wish to run, you can use the "Rscript" command, such as:

Rscript <myscript>

The following shows the options available when using "Rscript":

$ 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:

R --version

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.

[username@sci3.jasmin.ac.uk ~]$ module load jasr
[username@sci3.jasmin.ac.uk ~]$ R --quiet
> library(prettyunits)
> pretty_bytes(12345678)
[1] "12.35 MB"
>