Fix GitHub Actions Ubuntu runner libssl.so.3.1 error#62
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Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>
- Update RSPM URLs from focal (20.04) to noble (24.04) - Explicitly install libssl-dev and libcurl4-openssl-dev - Update system_requirements() to target Ubuntu 24.04 - Fixes ubuntu-latest (release) check failure with libssl.so.3.1 Resolves #60
- Install libglpk-dev (required by igraph) - Install libgmp3-dev and libxml2-dev (additional dependencies) - Update local check script to include knitr - Fixes igraph.so loading error in GitHub Actions Related to #60
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Hey @gvegayon, I wanted to learn how to use Copilot, so I got some hands-on practice by working on PR #60. It seems the error came from missing dependencies ( Are these fixes enough for CRAN? Also, do you know how to run the CRAN checks locally? |
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Thank you, @aoliveram! The main issue I have is that the new approach is a bit overkill. @copilot, can you address my comments instead and try to use r-lib to setup the R environment? That's the modern way.
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Cool! But we need to ensure that scripts is in the .Rbuildignore. Can you check that?
.github/workflows/r.yml
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| - name: Install system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y \ | ||
| libssl-dev \ | ||
| libcurl4-openssl-dev \ | ||
| libglpk-dev \ | ||
| libgmp3-dev \ | ||
| libxml2-dev | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "24.04"))') |
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copilot was fixing this in #60. Just closed that in favor of this.
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Thanks for doing this! But I would switch to use r-lib's actions instead: https://github.com/UofUEpiBio/epiworldR/blob/ea75e6e0d6856a30efc8978129ecf5a43c986799/.github/workflows/r.yml#L25-L57
* Initial plan * Switch to modern r-lib actions and add scripts to .Rbuildignore Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: gvegayon <893619+gvegayon@users.noreply.github.com>
Problem
The ubuntu-latest (release) check was failing with:
Root Cause
ubuntu-latestnow uses Ubuntu 24.04 (Noble Numbat)focalinstead ofnobleSolution
nobleinstead offocallibssl-devandlibcurl4-openssl-devbefore R package installationsystem_requirements()call to target Ubuntu 24.04Testing
This PR is based on #60 (arma::is_finite fix) and should:
Related Issues