| Startup {base} | R Documentation |
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 or empty, ‘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 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.
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’, 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 file. The name of this file can be specified by the R_PROFILE_USER environment variable. If this is unset, a file called ‘.Rprofile’ in the current directory or in the user's home directory (in that order) is searched for. The user profile is sourced into the user 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.
It then loads a saved image of the user workspace from ‘.RData’ 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 name space 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’) unless --no-restore-history was specified (or --no-restore).
The command-line flag --vanilla implies --no-site-file, --no-init-file, --no-restore and --no-environ.
.First <- function() { ...... }
.Rprofile <startup file>
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: $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.
The file ‘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 ‘R_HOME/etc/Renviron’ itself. Note that this is distinct from ‘R_HOME/etc/Renviron.site’.
.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.
For profiling code, see Rprof.
## 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)