% File src/library/base/man/Startup.Rd
% Part of the R package, http://www.R-project.org
% Copyright 1995-2013 R Core Team
% Distributed under GPL 2 or later

\name{Startup}
\alias{Startup}
\alias{Rprofile}
\alias{.Rprofile}
\alias{Rprofile.site}
\alias{Renviron}
\alias{Renviron.site}
\alias{.Renviron}
\alias{.First}
\alias{.First.sys}
\alias{.OptRequireMethods}
\concept{environment variable}
\alias{R_DEFAULT_PACKAGES}
\alias{R_ENVIRON}
\alias{R_ENVIRON_USER}
\alias{R_PROFILE}
\alias{R_PROFILE_USER}

\title{Initialization at Start of an R Session}
\description{
  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,
  \file{\var{\link{R_HOME}}/etc/Renviron.site} is used (if it exists,
  which it does not in a \sQuote{factory-fresh} installation).  The name
  of the user file can be specified by the \env{R_ENVIRON_USER}
  environment variable; if this is unset, the 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 file of \R code
  unless the command line option \option{--no-site-file} was given.  The
  path of this file is taken from the value of the \env{R_PROFILE}
  environment variable (after \link{tilde expansion}).  If this variable
  is unset, the default is \file{\var{\link{R_HOME}}/etc/Rprofile.site},
  which is used if it exists
#ifdef unix
  (which it does not in a \sQuote{factory-fresh} installation).
#endif
#ifdef windows
  (it contains settings from the installer in a \sQuote{factory-fresh}
  installation).
#endif
  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{\link{local}} if code needs to be
  executed: see the examples.

  Then, unless \option{--no-init-file} was given, \R searches for a user
  profile, a file of \R code.  The path of this file can be specified by
  the \env{R_PROFILE_USER} environment variable (and
  \link{tilde expansion} will be performed).  If this is unset, a file
  called \file{.Rprofile} is searched for in the current directory or in
  the user's home directory (in that order).  The user profile file is
  sourced into the 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.

  \R then loads a saved image of the user workspace from \file{.RData}
  in the current directory 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{\link{require}} to attach the default packages specified by
  \code{\link{options}("defaultPackages")}.  If the \pkg{methods}
  package is included, this will have been attached earlier (by function
  \code{.OptRequireMethods()}) so that namespace initializations such
  as those from the user workspace will proceed correctly.

  A function \code{.First} (and \code{\link{.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{\link{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 \pkg{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} in the current directory) unless
  \option{--no-restore-history} or \option{--no-restore} was specified.

  The command-line option \option{--vanilla} implies
  \option{--no-site-file}, \option{--no-init-file},
  \option{--no-environ} and (except for \command{R CMD})
  \option{--no-restore}
#ifdef windows
  Under Windows, it also implies \option{--no-Rconsole}, which
  prevents loading the \file{\link{Rconsole}} file.
#endif
}
\details{
  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: for example \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.

  On systems with sub-architectures (mainly Windows), the
  files \file{Renviron.site} and \file{Rprofile.site} are looked for
  first in architecture-specific directories,
  e.g. \file{\var{\link{R_HOME}}/etc/i386/Renviron.site}.
  And e.g. \file{.Renviron.i386} will be used in preference
  to \file{.Renviron}.
}
\note{
  It is not intended that there be interaction with the user during
  startup code.  Attempting to do so can crash the \R process,
  especially so prior to \R 3.0.2.
  
#ifdef unix
  On Unix versions of \R here is also a  file
  \file{\var{\link{R_HOME}}/etc/Renviron} which is 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{\link{R_HOME}}/etc/Renviron} itself.  Note that this is
  distinct from \file{\var{\link{R_HOME}}/etc/Renviron.site}.

  Command-line options may well not apply to alternative front-ends:
  they do not apply to \command{R.app} on OS X.
#endif
#ifdef windows
  The startup options are for \command{Rgui}, \command{Rterm} and
  \code{R} but not for \command{Rcmd}: attempting to use
  e.g. \option{--vanilla} with the latter will give a warning or error.

  Unix versions of \R have a file \file{\var{\link{R_HOME}}/etc/Renviron}
  which is read very early in the start-up processing.  It contains
  environment variables set by \R in the configure process, and is not
  used on \R for Windows.
#endif

  \command{R CMD check} and \command{R CMD build} do not always read the
  standard startup files, but they do always read specific
  \samp{Renviron} files.  The location of these can be controlled by the
  environment variables \env{R_CHECK_ENVIRON} and \env{R_BUILD_ENVIRON}.
  If these are set their value is used as the path for the
  \samp{Renviron} file; otherwise, files \file{~/.R/check.Renviron} or
  \file{~/.R/build.Renviron} or sub-architecture-specific versions are
  employed.

  If you want \file{~/.Renviron} or \file{~/.Rprofile} to be ignored by
  child \R processes (such as those run by \command{R CMD check} and
  \command{R CMD build}), set the appropriate environment variable
  \env{R_ENVIRON_USER} or \env{R_PROFILE_USER} to (if possible, which it
  is not on Windows) \code{""} or to the name of a non-existent file.
}
%% R_PROFLE_USER is used in src/unix/sys-unix.c and src/gnuwin32/sys-win32.c
%% R_ENVIRON, R_ENVIRON_USER are used in src/main/Renviron.c
%% R_PROFILE is used in src/main/startup.c
\seealso{
  For the definition of the \sQuote{home} directory on Windows see the
  \file{rw-FAQ} Q2.14.  It can be found from a running \R by
  \code{Sys.getenv("R_USER")}.

  \code{\link{.Last}} for final actions at the close of an \R session.
  \code{\link{commandArgs}} for accessing the command line arguments.

  There are examples of using startup files to set defaults for graphics
  devices in the help for
#ifdef windows
  \code{\link{windows.options}}.
#endif
#ifdef unix
  \code{\link{X11}} and \code{\link{quartz}}.
#endif

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

  \code{\link{readRenviron}} to read \file{.Renviron} files.

  For profiling code, see \code{\link{Rprof}}.
}
\examples{
\dontrun{
## 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)
  ## (for Unix terminal users) set the width from COLUMNS if set
  cols <- Sys.getenv("COLUMNS")
  if(nzchar(cols)) options(width = as.integer(cols))
  # interactive sessions get a fortune cookie (needs fortunes package)
  if (interactive())
    fortunes::fortune()
})

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

## then we get
# > cat(Sys.getenv("FOOBAR"), "\n")
# coo\bardoh\exabc"def'
}}
\keyword{environment}