\HeaderA{Startup}{Initialization at Start of an R Session}{Startup}
\aliasA{.First}{Startup}{.First}
\methaliasA{.First.sys}{Startup}{.First.sys}
\aliasA{.OptRequireMethods}{Startup}{.OptRequireMethods}
\aliasA{.Renviron}{Startup}{.Renviron}
\aliasA{.Rprofile}{Startup}{.Rprofile}
\aliasA{Renviron}{Startup}{Renviron}
\methaliasA{Renviron.site}{Startup}{Renviron.site}
\aliasA{Rprofile}{Startup}{Rprofile}
\methaliasA{Rprofile.site}{Startup}{Rprofile.site}
\keyword{environment}{Startup}
\begin{Description}\relax
In \R, the startup mechanism is as follows.

Unless \option{--no-environ} was given on the command line, \R{}
searches for site and user files to process for setting environment
variables.  The name of the site file is the one pointed to by the
environment variable \env{R\_ENVIRON}; if this is unset or empty,
\file{\var{R\_HOME}/etc/Renviron.site} is used (if it exists, which it
does not in a \sQuote{factory-fresh} installation).
The user files searched for are \file{.Renviron} in the current or in
the user's home directory (in that order).
See \sQuote{Details} for how the files are read.

Then \R{} searches for the site-wide startup profile unless the command
line option \option{--no-site-file} was given.  The name of this file
is taken from the value of the \env{R\_PROFILE} environment variable.
If this variable is unset, the default is
\file{\var{R\_HOME}/etc/Rprofile.site}, which is used if it exists
(which it does not in a \sQuote{factory-fresh} installation).
This code is sourced into the \pkg{base} package.  Users need to be
careful not to unintentionally overwrite objects in \pkg{base}, and it
is normally advisable to use \code{\LinkA{local}{local}} if code needs to be
executed: see the examples.

Then, unless \option{--no-init-file} was given, \R{} searches for a file
called \file{.Rprofile} in the current directory or in the user's
home directory (in that order) and sources it into the user
workspace.

Note that when the site and user profile files are sourced only the
\pkg{base} package is loaded, so objects in other packages need to be
referred to by e.g. \code{utils::dump.frames} or after explicitly
loading the package concerned.

It then loads a saved image of the user workspace from \file{.RData}
if there is one (unless \option{--no-restore-data} or
\option{--no-restore} was specified on the command line).

Next, if a function \code{.First} is found on the search path,
it is executed as \code{.First()}.  Finally, function
\code{.First.sys()} in the \pkg{base} package is run. This calls
\code{\LinkA{require}{require}} to attach the default packages specified by
\code{\LinkA{options}{options}("defaultPackages")}.  If the \pkg{methods}
package is included, this will have been attached earlier (by function
\code{.OptRequireMethods()}) so that name space initializations such
as those from the user workspace will proceed correctly.

A function \code{.First} (and \code{\LinkA{.Last}{.Last}}) can be defined in
appropriate \file{.Rprofile} or \file{Rprofile.site} files or have
been saved in \file{.RData}.  If you want a different set of packages
than the default ones when you start, insert a call to
\code{\LinkA{options}{options}} in the \file{.Rprofile} or \file{Rprofile.site}
file.  For example, \code{options(defaultPackages = character())} will
attach no extra packages on startup (only the \code{base} package) (or
set \code{R\_DEFAULT\_PACKAGES=NULL} as an environment variable before
running \R).  Using \code{options(defaultPackages = "")} or
\code{R\_DEFAULT\_PACKAGES=""} enforces the R \emph{system} default.

On front-ends which support it, the commands history is read from the
file specified by the environment variable \env{R\_HISTFILE} (default
\file{.Rhistory}) unless \option{--no-restore-history} was specified
(or \option{--no-restore}).

The command-line flag \option{--vanilla} implies
\option{--no-site-file}, \option{--no-init-file},
\option{--no-restore} and \option{--no-environ}.
\end{Description}
\begin{Usage}
\begin{verbatim}
.First <- function() { ...... }

.Rprofile <startup file>
\end{verbatim}
\end{Usage}
\begin{Details}\relax
Note that there are two sorts of files used in startup:
\emph{environment files} which contain lists of environment variables
to be set, and \emph{profile files} which contain \R{} code.

Lines in a site or user environment file should be either comment
lines starting with \code{\#}, or lines of the form
\code{\var{name}=\var{value}}. The latter sets the environmental
variable \code{\var{name}} to \code{\var{value}}, overriding an
existing value.  If \code{\var{value}} contains an expression of the
form \code{\$\{foo-bar\}}, the value is that of the environmental
variable \code{foo} if that exists and is set to a non-empty value,
otherwise \code{bar}.  (If it is of the form \code{\$\{foo\}}, the
default is \code{""}.)  This construction can be nested, so \code{bar}
can be of the same form (as in \code{\$\{foo-\$\{bar-blah\}\}}).  Note that
the braces are essential: \code{\$HOME} will not be interpreted.

Leading and trailing white space in \code{\var{value}} are stripped.
\code{\var{value}} is then processed in a similar way to a Unix shell:
in particular the outermost level of (single or double) quotes is
stripped, and backslashes are removed except inside quotes.
\end{Details}
\begin{Note}\relax
The file \file{\var{R\_HOME}/etc/Renviron} is always read very early in
the start-up processing.  It contains environment variables set by \R{}
in the configure process.  Values in that file can be overridden in
site or user environment files: do not change
\file{\var{R\_HOME}/etc/Renviron} itself.  Note that this is distinct from
\file{\var{R\_HOME}/etc/Renviron.site}.
\end{Note}
\begin{SeeAlso}\relax
\code{\LinkA{.Last}{.Last}} for final actions at the close of an \R{} session.
\code{\LinkA{commandArgs}{commandArgs}} for accessing the command line arguments.

There are examples of using startup files to set defaults for graphics
devices in the help for
\code{\LinkA{X11}{X11}} and \code{\LinkA{quartz}{quartz}}.

\emph{An Introduction to R} for more command-line options: those
affecting memory management are covered in the help file for
\LinkA{Memory}{Memory}.

For profiling code, see \code{\LinkA{Rprof}{Rprof}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
## Example ~/.Renviron on Unix
R_LIBS=~/R/library
PAGER=/usr/local/bin/less

## Example .Renviron on Windows
R_LIBS=C:/R/library
MY_TCLTK="c:/Program Files/Tcl/bin"

## Example of setting R_DEFAULT_PACKAGES (from R CMD check)
R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'
# this loads the packages in the order given, so they appear on
# the search path in reverse order.

## Example of .Rprofile
options(width=65, digits=5)
options(show.signif.stars=FALSE)
setHook(packageEvent("grDevices", "onLoad"),
        function(...) grDevices::ps.options(horizontal=FALSE))
set.seed(1234)
.First <- function() cat("\n   Welcome to R!\n\n")
.Last <- function()  cat("\n   Goodbye!\n\n")

## Example of Rprofile.site
local({
  # add MASS to the default packages, set a CRAN mirror
  old <- getOption("defaultPackages"); r <- getOption("repos")
  r["CRAN"] <- "http://my.local.cran"
  options(defaultPackages = c(old, "MASS"), repos = r)
})

## if .Renviron contains
FOOBAR="coo\bar"doh\ex"abc\"def'"

## then we get
> cat(Sys.getenv("FOOBAR"), "\n")
coo\bardoh\exabc"def'
## End(Not run)\end{ExampleCode}
\end{Examples}

