Error with `lib/actions/setup-r-dependencies`: Package 'pandoc-citeproc' has no installation candidate

[isaactpetersen]

Describe the bug
In a GitHub Action workflow, the workflow often (but not always) fails during a lib/actions/setup-r-dependencies@v2 step with the following error:

Reading package lists...
  Building dependency tree...
  Reading state information...
  Package pandoc-citeproc is not available, but is referred to by another package.
  This may mean that the package is missing, has been obsoleted, or
  is only available from another source
  E: Package 'pandoc-citeproc' has no installation candidate
  Error: 
  ! error in pak subprocess
  Caused by error in `processx::run(sh, cmdline, stdout_callback = callback, stderr_to_stdout = TRUE)`:
  ! System command 'sudo' failed
  ---
  Backtrace:
  1. pak::lockfile_install(".github/pkg.lock")
  2. pak:::remote(function(...) { …
  3. err$throw(res$error)
  ---
  Subprocess backtrace:
   1. base::withCallingHandlers(cli_message = function(msg) { …
   2. get("lockfile_install_internal", asNamespace("pak"))(...)
   3. plan$install_sysreqs()
   4. pkgdepends:::sysreqs_install(cmds, config)
   5. base::lapply(cmds, function(cmd) { …
   6. local FUN(X[[i]], ...)
   7. processx::run(sh, cmdline, stdout_callback = callback, stderr_to_stdout = …
   8. base::throw(new_process_error(res, call = sys.call(), echo = echo, …
   9. | base::signalCondition(cond)
  10. global (function (e) …
  Execution halted
  Error: Process completed with exit code 1.

However, the workflow sometimes succeeds. I have observed no particular pattern to when it succeeds versus fails. This bug was also identified by Paul Bürkner:
https://forum.posit.co/t/github-action-e-package-pandoc-citeproc-has-no-installation-candidate/197536/2

It was noted that the problem can be resolved by reverting from ubuntu-latest (which is currently version 24.04.2) to ubuntu-22.04.

To Reproduce
Here is a link to a failed build:
https://github.com/isaactpetersen/Fantasy-Football-Analytics-Textbook/actions/runs/13927168427/job/38974622392

Here is my workflow file:

on:
  workflow_dispatch:
  push:
    branches: main

name: Quarto Publish to HTML

jobs:
  build-deploy:
    runs-on: ubuntu-latest
    permissions:
      contents: write
    steps:
      - name: Check out repository
        uses: actions/checkout@v4
        with:
          lfs: true
        
      - name: Checkout LFS objects
        run: git lfs checkout
        
      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        
      - name: Session info
        run: Rscript -e 'sessionInfo()'
        
      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2
        
      - name: Install libcurl on Linux
        if: runner.os == 'Linux'
        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
        
      - name: Install tinytex
        uses: r-lib/actions/setup-tinytex@v2
        
      - name: Install package dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        
      - name: Install cmdstan
        run: |
          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
          cmdstanr::install_cmdstan(cores = 2)
        shell: Rscript {0}
        
      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        
      - name: Render Quarto Project
        uses: quarto-dev/quarto-actions/render@v2
        env:
          QUARTO_PROFILE: html
        with:
          to: html
        
      - name: Render and Publish
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
          render: false
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        
      - name: Archive production artifacts
        uses: actions/upload-artifact@v4
        with:
          name: _book
          path: |
            _book/
            *.tex
            *.md

Expected behavior
I expect the workflow to be able to make use of pandoc-citeproc and to succeed.

[gaborcsardi]

This is the same as r-lib/pak#755.

For a workaround, you'd need to set the option for a longer update timeout, or turn off system dependency installation.