renv::restore() failing inside GitHub Action: curl Connection timed out/URL returned error

[martin-raisely]

I am trying to use renv inside a GitHub Action. renv::restore() works on my local machine and also on a GitHub codespace but when I run it inside a GitHub Action I keep getting curl errors.

Here's an example of what I see - the packages that this error occurs on seems to change each time - though it does seem to always include [email protected] and it seems to have already successfully downloaded it earlier..

[TRUNCATED]
- Downloading DT from CRAN ...                  OK [1.4 Mb in 0.99s]
[TRUNCATED]
- Downloading memoise from CRAN ...             OK [17.4 Kb in 0.48s]
- Downloading mime from CRAN ...                OK [12.3 Kb in 0.3s]
- Downloading sass from CRAN ...                	ERROR [curl: (56) Recv failure: Connection timed out]
- Downloading sass from CRAN ...                	ERROR [curl: (22) The requested URL returned error: 404]
- Downloading bslib from CRAN ...               	ERROR [curl: (22) The requested URL returned error: 404]
- Downloading rmarkdown from CRAN ...           	ERROR [curl: (22) The requested URL returned error: 404]
- Downloading htmlwidgets from CRAN ...         	ERROR [curl: (22) The requested URL returned error: 404]
- Downloading DT from CRAN ...                  	ERROR [curl: (22) The requested URL returned error: 404]
Warning: Warning: failed to find source for 'htmltools 0.5.6' in package repositories
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/sass_0.4.7.tar.gz' [curl: (56) Recv failure: Connection timed out]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/Archive/sass/sass_0.4.7.tar.gz' [curl: (22) The requested URL returned error: 404]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/Archive/bslib/bslib_0.5.1.tar.gz' [curl: (22) The requested URL returned error: 404]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/Archive/rmarkdown/rmarkdown_2.25.tar.gz' [curl: (22) The requested URL returned error: 404]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/Archive/htmlwidgets/htmlwidgets_1.6.2.tar.gz' [curl: (22) The requested URL returned error: 404]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/sass_0.4.7.tar.gz' [curl: (56) Recv failure: Connection timed out]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/Archive/DT/DT_0.30.tar.gz' [curl: (22) The requested URL returned error: 404]
Error: Error: failed to retrieve package '[email protected]'
Execution halted
Traceback (most recent calls last):
8: renv::restore()
7: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
6: retrieve(packages)
5: handler(package, renv_retrieve_impl(package))
4: renv_retrieve_impl(package)
3: renv_retrieve_repos(record)
2: stopf("failed to retrieve package '%s'", renv_record_format_remote(record))
1: stop(sprintf(fmt, ...), call. = call.)
Error: Process completed with exit code 1.

Here's my github workflow .yml

name: render-project

on:
  push:
    branches:
    - 'main'
  workflow_dispatch:

jobs:
  render_project:
    runs-on: raisely_data_actions (Ubuntu 22.04.3 LTS-R version 4.3.1)
    env:
      RENV_PATHS_ROOT: ~/.local/share/renv
    steps:
      - uses: quarto-dev/quarto-actions/setup@v2
        with:
          version: 1.3.450
      - name: Install dependencies
        run: |
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libsodium-dev
          sudo apt-get install libglpk-dev
          sudo apt-get install libharfbuzz-dev  libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
      - name: Checkout repo
        uses: actions/checkout@v3
      - name: Install R
        uses: r-lib/actions/setup-r@v2
      - name: Restore packages
        uses: r-lib/actions/setup-renv@v2
      - name: Run render
        run: |
          source("driver.R")
        shell: Rscript {0}
      - uses: stefanzweifel/git-auto-commit-action@v4
        with:
          commit_message: gh action update results

Here's my renv.lock (converted to .txt so I could upload to github) renv.lock.

I have tried including the following config settings in my .RProfile file which I'm confident is running before renv to increase the number of retries and timeout.

options(renv.config.connect.retry = 20L)
options(renv.config.connect.timeout = 60L)

Any thoughts helpful! Sorry not quite sure how to do a reprex for this.

[kevinushey]

Based on the reported error, it seems most likely that CRAN was inaccessible for a short period of time: I don't think there's any explicit action required here?

[martin-raisely]

It happens every time I try and run restore::renv() inside a codespace.

Looking at other recent issues it seems like there may be a common problem with downloading packages:

• renv::restore() fails to download private GitHub Repositories #1722
• renv::restore() failing to download packages - potentially due to differences in R versions #1714

Not sure if this has something to do with #1711

[martin-raisely]

I think I have managed to get around/solve this issues by adding the following settings to my .Rprofile before source("renv/activate.R").

options(renv.config.connect.retry = 20L)
options(renv.config.connect.timeout = 60L)
options(renv.download.trace = TRUE)
source("renv/activate.R")

It still might be worth investigate why if a URL that should work fails we go to an Archive/ URL that won't work (there's nothing there), e.g.:

Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/sass_0.4.7.tar.gz' [curl: (56) Recv failure: Connection timed out]
Warning: Warning: error downloading 'http://cran.r-project.org/src/contrib/Archive/sass/sass_0.4.7.tar.gz' [curl: (22) The requested URL returned error: 404]

[kevinushey]

For what it's worth, I'd recommend using the Cloud repository, https://cloud.r-project.org -- it should be more reliable than the main CRAN server.