Startup                 package: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 or empty,
     '$R_HOME/etc/Renviron.site' is used (if it exists, which it does
     not in a 'factory-fresh' installation). 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 file
     called '.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 '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'.

Usage:

     .First <- function() { ...... }

     .Rprofile <startup file>

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: '$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.

Note:

     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'.

See Also:

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

     _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'.

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=yes
     TCL_LIBRARY=c:/packages/Tcl/lib/tcl8.4

     ## 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)

