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Checking your setup

Source: vignettes/checking-your-setup.qmd

Lifecycle: experimental

Lifecycle: experimental

These helpers are experimental. Output formatting and the set of programs that are checked may change between releases.

Installed programs

check_installed_programs() reports the installed version of R, RStudio, Quarto, Rtools, and related tools, and — when the machine is online — the newest version available:

Official installation and release information is available from the R Project, RStudio IDE User Guide, Quarto installation guide, and Rtools documentation.

type selects which group of programs to report on, and skip_online_check = TRUE makes the call purely local:

bio::check_installed_programs(type = "main", skip_online_check = TRUE)

Behaviour without a network

Looking up “the newest available version” needs three things to work: a reachable network, a reachable endpoint, and a response in the expected shape. bio treats a failure in any of them as “the available version is unknown” rather than as an error:

  • no connectivity → a message that the computer is offline;
  • the endpoint refuses or times out → a warning naming the tool;
  • the page or API answers in an unexpected format → a warning naming the tool.

In every case the installed versions are still reported. A broken or blocked download never prevents you from seeing what you actually have installed.

RStudio Desktop specifics

RStudio can be installed for one user or for all users, and bio looks in both kinds of location:

install_dir <- bio:::find_rstudio_install_dir()
bio::get_rstudio_install_scope(install_dir)

The scope only describes where the application lives. RStudio’s preferences, keybindings, and internal state are always per operating-system user. Posit’s guide documents the supported RStudio configuration directories.

Your session

check_user_info() collects the details worth pasting into a bug report:

Smaller helpers answer one question each:

bio::get_os_type()
bio::is_64bit_os()
bio::is_32bit_os()

Packages

Check whether specific packages are installed, list everything that is, or find out which packages a directory of scripts actually uses:

bio::is_pkg_installed(c("dplyr", "ggplot2", "notapackage"))

bio::get_pkgs_installed()

bio::list_pkgs_used_in_dir(path = ".")
bio::list_pkgs_used_in_files("analysis.R")

list_pkgs_used_in_dir() scans .R, .Rmd, and .qmd files, so it is a quick way to build the install list for a course folder. For reproducible project libraries rather than discovery alone, see renv.

Versions

Compare two versions, or list the archived versions of a CRAN package:

bio::compare_version(v_installed = "4.5.0", v_required = "4.6.0")

bio::pkg_list_archived_versions("ggplot2")

compare_version() returns a comparison of two version strings; it is the helper behind the “is available online” annotations in check_installed_programs().