Spontaneous repository issues with setup-r using ubuntu-latest runner

[mdneuzerling]

I can no longer set up R on Ubuntu through the setup-r action. This happened spontaneously about 3 hours ago. The setup-r step "succeeds" with the below error, but subsequent steps fail because Rscript cannot be found.

Run r-lib/actions/setup-r@master
Added matchers: 'rcmdcheck'. Problem matchers scan action output for known warning or error strings and report these inline.
Added matchers: 'testthat'. Problem matchers scan action output for known warning or error strings and report these inline.
Added matchers: 'r'. Problem matchers scan action output for known warning or error strings and report these inline.
sudo DEBIAN_FRONTEND=noninteractive apt-get update -qq
W: Conflicting distribution: https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease (expected bionic but got stable)
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Origin' value from 'microsoft-ubuntu-bionic-prod bionic' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Label' value from 'microsoft-ubuntu-bionic-prod bionic' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Suite' value from 'bionic' to 'stable'
E: Repository 'https://packages.microsoft.com/repos/microsoft-ubuntu-bionic-prod bionic InRelease' changed its 'Codename' value from 'bionic' to 'stable'
W: Conflicting distribution: https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease (expected xenial but got stable)
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Origin' value from 'microsoft-ubuntu-xenial-prod xenial' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Label' value from 'microsoft-ubuntu-xenial-prod xenial' to 'vscode stable'
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Suite' value from 'xenial' to 'stable'
E: Repository 'https://packages.microsoft.com/ubuntu/16.04/prod xenial InRelease' changed its 'Codename' value from 'xenial' to 'stable'
(node:4886) UnhandledPromiseRejectionWarning: Failed to install R: Error: The process 'sudo' failed with exit code 100
(node:4886) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1)
(node:4886) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.

I've set up an empty R package with a basic workflow to reproduce the error. I've used the yaml file as generated by usethis::use_github_actions(), but I've changed the runner to ubuntu-latest. You can find the failed workflow here.

R-CMD-check.yaml contents:

on: [push, pull_request]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v1
      - uses: r-lib/actions/setup-r@master
      - name: Install dependencies
        run: Rscript -e "install.packages(c('remotes', 'rcmdcheck'))" -e "remotes::install_deps(dependencies = TRUE)"
      - name: Check
        run: Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')"

[jimhester]

There seems to be an issue with the microsoft apt repositories, these are part of the base VM, so this is not specific to r-lib/actions.

See this thread for others having the same issues.

https://github.community/t5/GitHub-Actions/ubuntu-latest-Apt-repository-list-issues/td-p/41122

[mdneuzerling]

Thank you so much, @jimhester !

[github-actions]

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