R: Initialization at Start of an R Session

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 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)

[Package base version 2.6.2 Index]