Download R and RStudio

R updates are installed differently on each operating system. RStudio is a separate application and is not updated by the R commands below.

1. Save your package list

   Run this in the R console before updating. It records only add-on packages, not the packages that come with R.

   ip <- installed.packages()
   packages_before <- rownames(ip)[is.na(ip[, "Priority"])]
   saveRDS(packages_before, "~/r-packages-before-update.rds")

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2. Check for and install a newer R version

   Windows — automatic option

   Open the standard R console as a user who can install software, then paste the complete command. It checks the latest available R version and opens the installer only when an update exists.

   if (!requireNamespace("installr", quietly = TRUE)) {
     install.packages("installr")
   }
   installr::updateR()

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   Complete the installer prompts. When asked, choose to copy packages, keep the old packages, and update packages.

   macOS

   There is no equivalent universal R self-updater. Download the newest signed installer from the official CRAN macOS page, close RStudio, and run the installer.

   Linux

   Update R with your distribution's package manager and the appropriate CRAN repository. Follow the instructions for your distribution on the official CRAN Linux page.

3. Tell RStudio which R version to use

   Windows: restart RStudio, then open Tools → Global Options → General → Basic → R Sessions. Select Change beside R version, choose the newest installation, confirm, and restart RStudio.

   macOS and Linux: close and reopen RStudio after updating R. It normally uses the system's current R installation.

   Verify the active installation in the RStudio console:

   R.version.string
   R.home()
   .libPaths()

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4. Restore and update packages

   On Windows, the updater can copy your packages automatically. Keep the old package library until you have confirmed that your projects work. For a manual installation or any packages still missing, run this in the new R version:

   packages_before <- readRDS("~/r-packages-before-update.rds")
   missing <- setdiff(packages_before, rownames(installed.packages()))
   if (length(missing)) install.packages(missing)
   update.packages(ask = FALSE, checkBuilt = TRUE)

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   Important: do not manually copy R's base or recommended packages. Compiled packages may need to be reinstalled for the new R version. Bioconductor, GitHub, local, and renv project packages may require their original installation method.

Guidance based on the CRAN installr manual, R Installation and Administration, and Posit's RStudio guide.

Updating RStudio Desktop: you only need to update RStudio when the application displays a notification that a newer version is available. Follow the instructions shown by RStudio; updating R and updating RStudio are separate processes.