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Installing R, Rtools and RStudio

Source: vignettes/install_r.Rmd
install_r.Rmd

Introduction and notation

This vignette contains instructions on installing and configuring R, RStudio, and Rtools.

In this vignette, text between angled brackets (<...>) is used to refer to text that should be replaced with specific text to get working code. For example, <pkgname> is used as a place holder to refer to a package name and should be replaced with utils if you want to obtain information about package utils, and with methods if you want to obtain information about package methods. Similarly, <funcname> is used as a place holder to refer to a function name that should be filled in with a specific function name to get working code.

R

To install R, visit a nearby CRAN mirror (i.e., a website with the same content as the main CRAN page), download R via Download R for Windows > base > Download R-X.Y.Z for Windows and install it by opening the downloaded .exe-file.

Note that R is not required to read R-scripts: R-scripts are plain-text files that can be read by applications such as Microsoft NotePad.

Configuring R

R can be configured to be a bit stricter, described in the help files for general options (help("options")) and environment variables (help("environment variables")):

  • Warn in case of partial matching (help("pmatch")) such as list(mean = 3)$me: options(warnPartialMatchArgs = TRUE, warnPartialMatchAttr = TRUE, warnPartialMatchDollar = TRUE). The default is FALSE for each of these.
  • Error instead of warn when calling a:b when numeric a or b is longer than one, such as 3:c(5, 7) (introduced in R 4.3.0): Sys.setenv("_R_CHECK_LENGTH_COLON_" = "TRUE").
  • Error instead of silently using only the first element in logical operations (help("Logic", package = "base")) such as c(TRUE, TRUE) && TRUE) (introduced in R 3.6.0, no longer used since R 4.3.0 because there calling && or || with length larger than one always gives an error): Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "TRUE").
  • Error instead of warn if a condition (help("Control", package = "base")) has length larger than one, such as if(3 < c(5, 7)) {print("Not OK")} (introduced in R 3.y.z, no longer used since R 4.2.0 because there conditions with length larger than one always give an error): Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "TRUE").
  • Print warnings() immediately as they occur (options(warn = 1)) or make warnings an error (help("stop")): options(warn = 2). The latter should only be used for debugging because it may trigger bugs and resource leaks (per its help-page). The default is options(warn = 0) to warn after the top-level function returns.
  • Enter the [environment browser][browser()] upon error (default: options(error = NULL)): options(error = browser); press Q or Escape to quit the browser mode; press c to continue code.

In addition, various packages contain ways to make R stricter:

  • Package strict warns about various unsafe practices, such as the behaviour of sample() and diag() if called with an argument of length one and type-unsafe sapply(); additional ideas are in the GitHub issues.
  • Package conflicted avoids silent conflict resolution (i.e., choosing the latest attached package out of multiple packages to use a function from; see help("conflict")), and provides conflicts_prefer(<pkgname>::<funcname>) to declare preferences once.

Finally, options for startup (described in help("Startup")) and installing packages (see help("install.packages") and help(".libPaths")) can be used to configure R but can also lead to code that behaves different on PCs where these options are not set, such that they, for example, do not automatically load a package or add a path to the search path.

Information about R

Several variables and functions provide information about R and the current R session:

  • .Machine (see help(".Machine")) and Sys.info() provide information about the machine and platform R is running on. getRversion() provides the version of the running R.
  • .Platform (see help(".Platform")) and R.Version() provide information about the platform R was built on.
  • Sys.getlocale() provides details about the locale.
  • sessionInfo() extracts parts of the information provided by the functions mentioned above about the operating system and R. It also lists attached and loaded packages. Its printing method can be used to print additional information about the used locale, time zone, and random number generation: print(sessionInfo(), locale = TRUE, RNG = TRUE).
  • capabilities() and extSoftVersion() provide details about external software that can be used with R.
  • The help page on environment variables (help("environment variables")) lists some of the environment variables which affect an R session.

How operating systems identify themselves and their versions can be arcane, and specifically Windows versions might report older versions than the versions that are actually installed (see the section osVersion in help("sessionInfo") and the Note in help("win.version").

RStudio

RStudio is an integrated development environment for R that can be downloaded from Posit.

RStudio can also be used to read and modify plain-text files.

Configuring RStudio

After installing RStudio, start RStudio, go to Tools > Global Options > General to deselect the option Restore .RData into workspace at startup and set the option Save workspace to .RData on exit to Never to make work portable.

The version of RStudio to use can be selected at Tools > Global Options > General > R version.

Keyboard shortcuts can be modified at Tools > Modify Keyboard Shortcuts, e.g., to change the shortcut Run current line or selection from Ctrl+Enter to Ctrl+R so it can be used with one hand. Sometimes RStudio does not use the modified keyboard shortcuts. Going to Tools > Modify Keyboard Shortcuts usually fixes that without the need to actually reset the shortcuts.

The appearance of code can be changed at Tools > Global options > Appearance. The default Editor theme is the light Textmate, another nice light Editor theme is Xcode. Nice dark Editor themes are Tomorrow Night Bright, Idle Fingers, and Pastel On Dark, with Editor fonts Consolas, Cacadia Mono Light, or Lucida Console.

To check that characters in a typeface or font can be properly distinguished from each other when choosing a font, for example using Adobe Fonts or Google Fonts, the following string groups together characters that in some fonts are similar in appearance: 71lI|i/ oQO0D gq B8 S5 Z2 ijy4 ., :; "'' __ cldcIdc|dc1d rnm UVVWuvvw

The string consists of the following characters (using upper case letter that are easier to distinguish, with ‘lower’ and ‘upper’ indicating the case used in the string):

  • SEVEN, ONE, lower EL, upper I, vertical BAR, lower I, SLASH
  • lower O, upper CUE, upper O, ZERO, upper DEE
  • lower GEE, lower CUE
  • upper BEE, EIGHT
  • upper ESS, FIVE
  • upper ZED, TWO
  • lower I, lower JAY, lower WYE, FOUR
  • DOT, COMMA,
  • COLON, SEMICOLON
  • double QUOTES, single QUOTES, single QUOTES
  • UNDERSCORE, UNDERSCORE
  • lower CEE, lower EL, lower DEE, lower CEE, upper I, lower DEE, lower CEE,
    vertical BAR, lower DEE, lower CEE, ONE, lower DEE
  • lower AR, lower EN, lower EM
  • upper U, upper VEE, upper VEE, upper double-U,
    lower U, lower VEE, lower VEE, lower double-U

Rtools

Rtools is not an R package but software used to build R from source and to build R packages from source: packages from GitHub and older versions of packages from CRAN or Bioconductor (see the section ‘Installing packages’ in the vignette R packages for instructions: vignette("r_pkgs", package = "checkrpkgs")). Rtools is not needed to install current versions of packages from CRAN or Bioconductor on Windows.

To install Rtools, download the version appropriate for the installed version of R (see the output of getRversion()) from CRAN via Download R for Windows > Rtools > RTools X.Y and set it up using the instructions given there. See also the HowTo by Tomas Kalibera. Alternatively, pkgbuild::check_build_tools(debug = TRUE) can be used to check and install Rtools.

Documentation and help

For developers