[R] Startup on Windows 2000

ripley@stats.ox.ac.uk ripley at stats.ox.ac.uk
Fri Oct 18 08:49:18 CEST 2002

Unfortunately the Startup.Rd file was written for Unix, and in 1.6.0 is
not accurate for other platforms.  It has been altered in R-patched.

On Thu, 17 Oct 2002, Cliff Lunneborg wrote:

> I am having difficulty coming to grips with Appendix B.2 of the
> otherwise very useful "An Introduction to R" and the related help file
> for Startup. I am running RGui 1.6.0 on a Windows 2000 machine from the
> default installation. How the concepts discussed in B.2 and the Startup
> help file relate to what I see on my machine is something of a mystery.
> I quote from the Startup file:
> "In R, the startup mechanism is as follows.
> Unless --no-environ was given, R searches for user and site files to
> process for setting environment variables. The name of the site file is
> the one pointed to by the environment variable R\_ENVIRON; if this is
> unset, `$R_HOME/etc/Renviron.site' is used. The user files searched for
> are `.Renviron' in the current or in the user's home directory (in that
> order). See Details for how the files are read."
> How can I tell if "--no-environ" was given? I cannot find either
> Renviron.site or .Renviron on my system.

The files need not exist, and are only used if they do exist.  *You* gave
the command line so you specified --no-environ or not.

$R_HOME/etc/Renviron.site is only used on Unix: that was a documentation

> Then, Startup continues:
> "Then R searches for the site-wide startup profile unless the command
> line option --no-site-file was given. The name of this file is taken
> from the value of the R\_PROFILE environment variable. If this variable
> is unset, the default is `$R_HOME/etc/Rprofile.site'. This code is
> loaded into package base."
> Can I tell if "--no-site-file" was given? I don't find any object named
> Rprofile.site on my machine.

Same answer.  Rprofile.site is intended for R code to be run initially for
all users and all usages of that R installation, e.g. to load local

> Returning to Startup:
> "Then, unless --no-init-file was given, R searches for a file called
> `.Rprofile' in the current directory or in the user's home directory (in
> that order) and sources it into the user workspace."
> Was "--no.init.file" given in the default startup? I cannot find a file
> .Rprofile anywhere.

Same answer.

> Back to Startup:
> "It then loads a saved image of the user workspace from `.RData' if
> there
> is one (unless --no-restore-data was specified, or --no-restore)."
> Since R opens with a saved workspace, I'd guess "--no-restore-data" was
> not specified.

Same answer.

> "Finally, if a function .First exists, it is executed as .First()."
> I located such a function in a Rprofile file. It appears to load the
> ctest package.

Yes, but you can put such an object earlier in the search path and so
override that one.

> "The functions .First and .Last can be defined in the appropriate
> startup
> profiles or reside in `.RData'."
> What or where are these appropriate startup profiles?

Rprofile.site, .Rprofile.

> I located a
> second Rprofile file in the \etc folder, but when I added a .First
> function there it seemed to override the other .First function. Is that
> intentional?

Yes.  Most things in R are intentional!

> Later in the Startup help:
> "Lines in a site or user environment file should be either comment lines
> starting with #, or lines of the form name=value. The latter sets the
> environmental variable name to value, overriding an existing value. If
> value is of the form ${foo-bar}, the value is that of the environmental
> variable foo if that exists and is set to a non-empty value, otherwise
> bar. This construction can be nested, so bar can be of the same form (as
> in ${foo-${bar-blah}})."
> Are environment files the same as profile files?

No, that's why the names are different (and the examples given are
different).  An environment file is like .Renviron, and is described in
the Details section (as the help file says).  A profile file contains R

> Finally, towards the bottom of the Startup help:
> "Examples
> ## Some examples with a Unix flavour
> # ~/.Renviron
> R_LIBS=~/R/library
> PAGER=/usr/local/bin/less
> # .Rprofile
> options(width=65, digits=5)
> options(show.signif.stars=FALSE)
> ps.options(horizontal=FALSE)
> set.seed(1234)
> .First <- function() cat("\n   Welcome to R!\n\n")
> .Last <- function()  cat("\n   Goodbye!\n\n")
> ## if .Renviron contains
> FOOBAR="coo\bar"doh\ex"abc\"def'"
> ## then we get
> > cat(Sys.getenv("FOOBAR"), "\n")
> coo\bardoh\exabc"def' "
> What would some Windows examples look like?

.Rprofile the same.


> I love R, and I would really like to learn something more about how it
> is being customized for me and how I can (if I should) try to customize
> it myself.

Some of this is in the rw-FAQ, including the use of .Renviron.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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