setup-r-dependencies@v2 intermittently failing on ubuntu-latest

[aschmidt-amplify]

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Describe the bug When running a package check on mac-os latest, windows latest, and ubuntu latest, the setup-r-dependencies@v2 will fail with the message below. This does not always occur, but when it does, it is related to nloptr:

 Error: 
  ! error in pak subprocess
  Caused by error in `verify_extracted_package(filename, pkg_cache)`:
  ! 
  '/tmp/RtmpfVFPCA/file12c92330f168/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/nloptr_2.0.3.tar.gz'
  is not a valid binary, it is missing nloptr/Meta/package.rds.
  ---
  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$install()
   4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
   5. base::withCallingHandlers({ …
   6. pkgdepends:::handle_events(state, events)
   7. pkgdepends:::handle_event(state, i)
   8. proc$get_result()
   9. processx:::process_get_result(self, private)
  10. private$post_process()
  11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
  12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
  13. base::throw(pkg_error("{.path {filename}} is not a valid binary, it is missing {…
  14. | base::signalCondition(cond)
  15. global (function (e) …
  Execution halted

To Reproduce You MUST include a link to the full logs of the failed build. Bug reports which do not contain a link, or only contain a screenshot of the failed build will be closed.

Link to logs

My package is on a private github account so I cannot share a link to the code itself. However, this is the R-CMD-check.yaml in my github workflows folder:

on:
  pull_request:
    branches: [main]
    paths:
      - '.github/workflows/test_package.yml'
      - 'tests/testthat/*'
      - 'R/*'

name: R-CMD-check

permissions: read-all

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macos-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,   r: 'release'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check

      - uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

Expected behavior Non-failure. Here is a log to a successful install with nloptr

Additional context If I edit my workflow to use extra-packages: any::rcmdcheck, nloptr=?ignore, all checks will fail. And when I restore to just extra-packages: any::rcmdcheck, all checks (including ubuntu) will pass

[gaborcsardi]

I cannot read the logs at that URL.

[aschmidt-amplify]

Sorry about that. Not sure what happened. Here is the meat of the error:

Error: 
  ! error in pak subprocess
  Caused by error in `verify_extracted_package(filename, pkg_cache)`:
  ! 
  '/tmp/RtmptLVX0v/file129d102dad9e/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.4/nloptr_2.0.3.tar.gz'
  is not a valid binary, it is missing nloptr/Meta/package.rds.
  ---
  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$install()
   4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
   5. base::withCallingHandlers({ …
   6. pkgdepends:::handle_events(state, events)
   7. pkgdepends:::handle_event(state, i)
   8. proc$get_result()
   9. processx:::process_get_result(self, private)
  10. private$post_process()
  11. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, …
  12. pkgdepends:::verify_extracted_package(filename, pkg_cache)
  13. base::throw(pkg_error("{.path {filename}} is not a valid binary, it is missing {…
  14. | base::signalCondition(cond)
  15. global (function (e) …
  Execution halted
  Error: Process completed with exit code 1.

[aschmidt-amplify]

Here is a gist with the logs: https://gist.github.com/aschmidt-amplify/7138aa31f0e4c87fc16618f4c07f6b80

[gaborcsardi]

That's probably a failed download from PPPM, hopefully temporary.

[github-actions[bot]]

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