Startup package:base R Documentation _I_n_i_t_i_a_l_i_z_a_t_i_o_n _a_t _S_t_a_r_t _o_f _a_n _R _S_e_s_s_i_o_n _D_e_s_c_r_i_p_t_i_o_n: 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'. _U_s_a_g_e: .First <- function() { ...... } .Rprofile _D_e_t_a_i_l_s: 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. _N_o_t_e: 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'. _S_e_e _A_l_s_o: '.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'. _E_x_a_m_p_l_e_s: ## 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)