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Fix GitHub Actions Ubuntu runner libssl.so.3.1 error#62

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gvegayon merged 5 commits intomasterfrom
fix-github-actions-libssl-from-d43
Dec 4, 2025
Merged

Fix GitHub Actions Ubuntu runner libssl.so.3.1 error#62
gvegayon merged 5 commits intomasterfrom
fix-github-actions-libssl-from-d43

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@aoliveram
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@aoliveram aoliveram commented Nov 12, 2025

Problem

The ubuntu-latest (release) check was failing with:

unable to load shared object 'curl.so': libssl.so.3.1: cannot open shared object file

Root Cause

  • GitHub Actions ubuntu-latest now uses Ubuntu 24.04 (Noble Numbat)
  • Ubuntu 24.04 uses OpenSSL 3.1.x
  • Workflow was configured for Ubuntu 20.04 (Focal) which uses OpenSSL 1.x
  • Package manager URLs pointed to focal instead of noble

Solution

  1. Updated RSPM URLs to use noble instead of focal
  2. Explicitly install libssl-dev and libcurl4-openssl-dev before R package installation
  3. Updated system_requirements() call to target Ubuntu 24.04

Testing

This PR is based on #60 (arma::is_finite fix) and should:

  • ✅ Pass all 5 CI checks (including ubuntu-latest release)
  • ✅ Not affect existing functionality

Related Issues

Copilot AI and others added 4 commits September 29, 2025 15:46
Initial plan
50bfa13
@gvegayon
Replace deprecated arma::is_finite with std::isfinite
81b2df8 
Co-authored-by: gvegayon <[email protected]>
@aoliveram
Fix GitHub Actions Ubuntu runner libssl issue
098211c 
- 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
@aoliveram
Add missing system dependencies for igraph
ca30971 
- 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
@aoliveram
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aoliveram commented Nov 13, 2025

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 (libssl.so.3.1, libglpk.so.40), so I updated the system requirement calls ("20.04" → "24.04") and everything is working now.

Are these fixes enough for CRAN? Also, do you know how to run the CRAN checks locally?

@aoliveram aoliveram requested a review from gvegayon November 13, 2025 01:10
@gvegayon gvegayon mentioned this pull request Dec 3, 2025
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gvegayon
gvegayon requested changes Dec 3, 2025
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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.

scripts/check-github-actions-local.sh
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@gvegayon gvegayon Dec 3, 2025

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Cool! But we need to ensure that scripts is in the .Rbuildignore. Can you check that?

.github/workflows/r.yml Outdated
Comment on lines 60 to 73
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@gvegayon gvegayon Dec 3, 2025

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This sounds a bit overkill.

src/infection.cpp
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@gvegayon gvegayon Dec 3, 2025

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copilot was fixing this in #60. Just closed that in favor of this.

.github/workflows/r.yml
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@gvegayon gvegayon Dec 3, 2025

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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

Copilot AI mentioned this pull request Dec 3, 2025
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Copilot AI commented Dec 3, 2025

@gvegayon I've opened a new pull request, #63, to work on those changes. Once the pull request is ready, I'll request review from you.

@gvegayon
Switch GitHub Actions to modern r-lib actions (#63)
e8c746d 
* Initial plan

* Switch to modern r-lib actions and add scripts to .Rbuildignore

Co-authored-by: gvegayon <[email protected]>

---------

Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: gvegayon <[email protected]>
@gvegayon gvegayon self-requested a review December 4, 2025 07:55
@gvegayon gvegayon merged commit aeea532 into master Dec 4, 2025
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@gvegayon gvegayon deleted the fix-github-actions-libssl-from-d43 branch December 4, 2025 07:56
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@aoliveram @gvegayon

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