Startup {base}R Documentation

Initialization at Start of an R Session

Description

In R, the startup mechanism is as follows.

Unless --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 R_ENVIRON; if this is unset, ‘R_HOME/etc/Renviron.site’ is used (if it exists, which it does not in a ‘factory-fresh’ installation). The name of the user file can be specified by the R_ENVIRON_USER environment variable; if this is unset, the 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.

Then R searches for the site-wide startup profile file of R code unless the command line option --no-site-file was given. The path of this file is taken from the value of the R_PROFILE environment variable (after tilde expansion). If this variable is unset, the default is ‘R_HOME/etc/Rprofile.site’, which is used if it exists (which it does not in a ‘factory-fresh’ installation). This code is sourced into the base package. Users need to be careful not to unintentionally overwrite objects in base, and it is normally advisable to use local if code needs to be executed: see the examples.

Then, unless --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 R_PROFILE_USER environment variable (and tilde expansion will be performed). If this is unset, a file called ‘.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 base package is loaded, so objects in other packages need to be referred to by e.g. utils::dump.frames or after explicitly loading the package concerned.

R then loads a saved image of the user workspace from ‘.RData’ in the current directory if there is one (unless --no-restore-data or --no-restore was specified on the command line).

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

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

On front-ends which support it, the commands history is read from the file specified by the environment variable R_HISTFILE (default ‘.Rhistory’ in the current directory) unless --no-restore-history or --no-restore was specified.

The command-line option --vanilla implies --no-site-file, --no-init-file, --no-environ and (except for R CMD) --no-restore

Details

Note that there are two sorts of files used in startup: environment files which contain lists of environment variables to be set, and profile files which contain R code.

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 contains an expression 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. (If it is of the form ${foo}, the default is "".) This construction can be nested, so bar can be of the same form (as in ${foo-${bar-blah}}). Note that the braces are essential: for example $HOME will not be interpreted.

Leading and trailing white space in value are stripped. 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 ‘Renviron.site’ and ‘Rprofile.site’ are looked for first in architecture-specific directories, e.g. ‘R_HOME/etc/i386/Renviron.site’. And e.g. ‘.Renviron.i386’ will be used in preference to ‘.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.

On Unix versions of R here is also a file ‘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 ‘R_HOME/etc/Renviron’ itself. Note that this is distinct from ‘R_HOME/etc/Renviron.site’.

Command-line options may well not apply to alternative front-ends: they do not apply to R.app on OS X.

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

If you want ‘~/.Renviron’ or ‘~/.Rprofile’ to be ignored by child R processes (such as those run by R CMD check and R CMD build), set the appropriate environment variable R_ENVIRON_USER or R_PROFILE_USER to (if possible, which it is not on Windows) "" or to the name of a non-existent file.

See Also

For the definition of the ‘home’ directory on Windows see the ‘rw-FAQ’ Q2.14. It can be found from a running R by Sys.getenv("R_USER").

.Last for final actions at the close of an R session. commandArgs for accessing the command line arguments.

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

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

readRenviron to read ‘.Renviron’ files.

For profiling code, see Rprof.

Examples

## 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)
  ## (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'

## End(Not run)

[Package base version 3.2.0 Index]