My additions to my sitewide Rprofile file.

r-my-rprofile.R

# Use the special "Cloud repo" for CRAN
options(repos = structure(c(CRAN="https://cloud.r-project.org/")))

if (interactive()) suppressMessages({
    # The packages I always want present by default at the prompt.
    require(devtools)
    require(magrittr)

    # Display menu selection prompts in the terminal instead of an 
    # annoying popup GUI window.
    options(menu.graphics = FALSE)
    
    # Use my alternate pager script to make searches case-insensitive, and
    # leave the screen uncleared when you close it (so that you can see the
    # R help page content at the same time as the R prompt.)
    options("pager" = file.path(Sys.getenv("HOME"), "programs/R-pager.sh"))
    
    # Simpler quitting. Most of the time I don't want to save when I quit,
    # so this saves me the time of having to type q("no") every time, or
    # do that interactive prompt.
    #
    # Potentially there might be projects where I would prefer to autosave
    # on quit. For those, I can set the option "saveOnQuit" to "yes".
    quit = function(
        save = getOption("saveOnQuit", default="no")
        , ...
    ){
      base::quit(save, ...)
    }
    q = quit
})

R-pager.sh

#!/bin/bash
# My customized pager script. Everything below this comment block is identical to
# the R pager script installed by the R debian package at /usr/lib/R/bin/pager,
# except that I've replaced ${PAGER} with /bin/less explicitly, and added
# the -I and -X flags.
#
# The "-I" flag makes searches in the pager case-insensitive by default.
# The "-X" flag tells the pager not to clear the screen when it closes. That
# allows me to continue to see the help content at the same time as having
# the prompt available; which is helpful because I have the memory of a
# fruitfly and tend to mis-type commands unless I have the documentation
# right there in front of me.
#
# Inconveniently, a shell script is necessary for this, because R seems to
# try to verify that the "pager" option string is the path and name of an
# executable file, so doing.e.g option(pager="/bin/less -IX") will give an
# error along the lines of "No file named 'less -IX' found".

## For the curious: "pager $1" doesn't work in batch, because "more" will
## eat the rest of stdin.  The no-argument version is intended for use at
## the end of a pipeline.
##
## PAGER is determined at configure time and recorded in `etc/Renviron'.
## This is documented to be a 'command line' so we do not quote it.
if test -n "${1}"; then
  exec /bin/less -IX < ${1}
else
  exec /bin/less -IX
fi

### Local Variables: ***
### mode: sh ***
### sh-indentation: 2 ***
### End: ***

One annoying note: Although R supports a system-wide Rprofile (/etc/R/Rprofile.site), a user-level Rprofile (~/.Rprofile), and a directory-level Rprofile (/path/to/project/.Rprofile) it doesn't load all three. The system-wide Rprofile is always loaded, but the user-level one is ignored if there is a directory-level Rprofile in the current directory. (This is different from how must other systems behave, which have a similar three-level config hierarchy.)

Since I use Packrat, I am often working in a directory with a .Rprofile file in it. So to make sure my customizations get loaded every time, I added a line to my system-wide /etc/R/Rprofile.site that loads this up.

### R startup customizations
source("/etc/R/aaronw-profile.R")