Skip to contents

Installing R, Rtools and RStudio

Source: vignettes/install_r.Rmd
install_r.Rmd

Introduction

This vignette explains how to install and configure R, Rtools, and RStudio.

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.

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

Making R stricter

R can be configured by changing environment variables and various options, see help("environment variables"), help("options"), help("install.packages"), and help(".libPaths"). Although options for startup can also be changed (see help("Startup") and the chapter R Startup from the book What They Forgot to Teach You About R), that should be done cautiously because those options likely make code behave differently on PCs where those options are not set, for example when changing which packages are automatically loaded at startup.

Various options can be changed to make R a bit stricter:

  • Warn in case of partial matching when extracting using $ (e.g., list(mean = 3)$me), when matching function arguments, and when getting object attributes:
    options(warnPartialMatchDollar = TRUE, warnPartialMatchArgs = TRUE, warnPartialMatchAttr = TRUE), with default FALSE for each of these. These options were introduced in R 2.6.0. Details: help("pmatch"), help("Extract"), and help("attr").
  • Error instead of warn when calling a:b when numeric a or b is longer than one, such as 3:c(5, 7):
    Sys.setenv("_R_CHECK_LENGTH_COLON_" = "TRUE"). This option was introduced in R 4.3.0. Details: help("colon", package = "base").
  • Error instead of silently using only the first element in logical operations such as c(TRUE, TRUE) && TRUE):
    Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "TRUE"). Details: help("Logic", package = "base"). This option was introduced in R 3.6.0 and is no longer used since R 4.3.0 because there calling && or || with length larger than one always gives an error.
  • Error instead of warn if a condition has length larger than one, such as if(3 < c(5, 7)):
    Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "TRUE"). Details: help("Control", package = "base"). This option was introduced in R 3.4.0 and is no longer used since R 4.2.0 because there conditions with length larger than one always give an error.
  • Error instead of warn in case of conflicts (i.e., if objects with the same name exist in two or more places on the search path):
    options(conflicts.policy = "strict"). This option was introduced in R 3.6.0. Details: help("conflicts", package = "base") and the section Conflicts in help("conflictRules", package = "base") for further options to tune conflict resolution, and conflicted::conflicts_prefer(<pkg>::<func>) from package conflicted to declare preferences (<pkg> and <func> should be replaced by the actual names of the package and function to get working code).
  • Print warnings immediately as they occur (options(warn = 1)) or make them an error (options(warn = 2)). The latter should only be used for debugging because it may trigger bugs and resource leaks. To suppress warnings altogether, use options(warn = -1) or wrap function calls in suppressWarnings() to suppress particular warnings. The default is options(warn = 0) to warn after the top-level function returns. Details: help("stop") and help("warning").
  • Enter the environment browser upon error:
    options(error = browser), with default options(error = NULL) to not enter the environment browser. Press Q or Escape to quit the browser mode and press c to continue code. Details: help("browser").

In addition, package strict makes R stricter by warning about various unsafe practices, such as the behaviour of sample() and diag() if called with an argument of length one, and type-unsafe sapply().

Information about R

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

  • capabilities() and extSoftVersion() provide details about external software that can be used with R.
  • Environment variables affect an R session. Its help page (help("environment variables")) lists some of these environment variables.
  • getRversion() provides the version of the running R.
  • .Machine (see help(".Machine")) and Sys.info() provide information about the machine and platform R is running on. Operating systems might identify themselves and their versions in surprising ways, and Windows might report older versions than the versions that are actually installed (see the section osVersion in help("sessionInfo", package = "utils") and the Note in help("win.version", package = "utils").
  • .Platform (see help(".Platform")) and R.Version() provide information about the platform R was built on.
  • Sys.getlocale() and l10n_info() provide details about the locale (i.e., settings that depend on the user’s language or region).
  • utils::sessionInfo() extracts parts of the information mentioned above about the operating system and R, and lists attached and loaded packages. Its printing method can be used to print additional information about the used locale (i.e., settings that depend on the user’s language or region) and random number generation: print(sessionInfo(), locale = TRUE, RNG = TRUE). sessioninfo::session_info() provides more details about the origin of loaded or installed packages, and has the option to show only information about selected packages and their dependencies.

Rtools

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

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, use pkgbuild::check_build_tools(debug = TRUE) to check and install Rtools.

If you have installed Rtools, you might get the question Do you want to install from sources the packages which need compilation? when updating packages. You can choose Yes to install the latest package versions by building them from source, or choose No to get slightly less up-to-date package versions but a faster installation. See the section Troubleshooting in the vignette R packages for details: vignette("r_pkgs", package = "checkrpkgs").

RStudio

RStudio is an integrated development environment for R developed by Posit that can be downloaded here.

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 (i.e., make sure that R does not use information or data that is not present on another PC). A more disrupting change to enhance portability is to deselect the options Show diagnostics for R and Prompt to install missing R packages discovered in R source files at Tools > Options > Code > Diagnostics. Deselecting these options ensures namespaces are not automatically loaded when RStudio loads a project.

In the same tab General, you can also specify the version of R that should be used and the default working directory (see help("getwd")) to be used when not in a project.

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. Nice editor themes are the light Xcode and the dark Tomorrow Night Bright, Idle Fingers, and Pastel On Dark. Nice editor fonts are Consolas, Cacadia Mono Light, and Lucida Console.

Choosing a good editor font deserves some attention: using a font with clearly distinct characters prevents confusing similar characters when reading or debugging code. The following strings group together characters that in some fonts are similar in appearance. Letters are indicated with their names in the same case as used in the string:

  • B8 S5 y4 Z2: BEE, eight; ESS, five; wye, four; ZED, two
  • gq ijy rnm uvvw UVVW: gee, cue; eye, jay, wye; ar, en, em; u, repeated vee, double-u; U, repeated VEE, double-U
  • ., :; "'' __: dot, comma; colon, semicolon; double quotes, repeated single quotes; repeated underscores
  • cldcIdc|dc1: cee, el, dee, cee, EYE, dee, cee, vertical bar, dee, cee, one
  • 71lI|i/: seven, one, el, EYE, vertical bar, eye, slash
  • oQO0D: oh, CUE, OH, zero, DEE

Combining these strings gives B8 S5 y4 Z2 gq ijy rnm uvvw UVVW ., :; "'' __ cldcIdc|dc1 71lI|i/ oQO0D which can be used to compare fonts, for example using Adobe Fonts, Font Squirrel, Google Fonts, or MyFonts.

Documentation and help

Resources with more details than this vignette: