Upgrading R without losing all your packages

upgrading
package management
Author

Aaron Braver

Published

June 30, 2023

If you upgrade R to a new major or minor release (e.g. 4.0 or 4.1, but not 4.1.1), your library of installed packages doesn’t come along for the ride.

Before you upgrade

Before you upgrade, you should make a list of all of your installed packages—this is easy with sessioninfo::package_info("installed"). If you’ve got packages installed from multiple sources (like CRAN and also Github), it’s best to save these as separate lists to facilitate automated reinstallation of these grouped by source:

library(tidyverse)

# Figure out what's installed
installed_packages <- sessioninfo::package_info("installed") |> 
  mutate("where_from" = dplyr::case_when(
    str_detect(source, "CRAN") ~ "CRAN",
    str_detect(source, "Github") ~ "Github",
    .default = "other" # catch any packages from other sources;
                       # not automatically installed below
    )
  ) |> 
  nest(.by = where_from)

# Where to write the lists of packages.  Change as needed
file_location <- fs::path("~/Desktop/tmp/")

# Write these lists to disk
installed_packages %>% 
  pwalk(function(where_from, data) {
    write_csv(data,
              file = fs::path(file_location,
                              paste0(where_from, "_packages"),
                              ext = "csv"))
  })

After you upgrade

Then, after you upgrade R, you can re-install the packages from these lists:

# Install manually some things we'll need since they won't be installed anymore
install.packages(c("remotes", "dplyr", "stringr"))

file_location <- "~/Desktop/tmp/" # Change as needed

# Install CRAN packages
CRAN_packages <- read.csv(paste0(file_location, "CRAN_packages", ".csv"))
remotes::install_cran(CRAN_packages$package)

# Install Github packages
github_packages <- read.csv(paste0(file_location, "Github_packages", ".csv")) |>
  dplyr::mutate(github_source = stringr::str_extract(source,
      "(?<=Github \\().*(?=@)")) # Get the username and repo name
remotes::install_github(github_packages$github_source)

NB: If you have locally installed packages, or packages from another source, these aren’t automatically reinstalled with the code above, but are listed in other_packages.csv.