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Fix R-CMD-check: update deprecated actions and retired ubuntu-20.04 runner - #795

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clairblacketer merged 1 commit into
OHDSI:mainfrom
PouyanJay:fix/github-actions-deprecations
Aug 4, 2026
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Fix R-CMD-check: update deprecated actions and retired ubuntu-20.04 runner#795
clairblacketer merged 1 commit into
OHDSI:mainfrom
PouyanJay:fix/github-actions-deprecations

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@PouyanJay

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Summary

Every R-CMD-check run currently fails during job setup, before any R code executes, because GitHub now automatically rejects deprecated action versions and has retired the ubuntu-20.04 hosted runner:

This request has been automatically failed because it uses a deprecated version of actions/cache: v3.3.1 … a deprecated version of actions/upload-artifact: v2

(actions/cache notice, artifact actions notice, ubuntu-20.04 retirement)

Changes

  • actions/cache v3.3.1 → v4
  • actions/upload-artifact v2 → v4 (both uses; artifact names were already unique per job, which v4 requires)
  • ubuntu-20.04 runner → ubuntu-22.04, with the RSPM repository (focal → jammy) and remotes::system_requirements() lookup updated to match

Verification

Run on my fork with these changes: https://github.com/PouyanJay/CommonDataModel/actions/runs/29622329863 — jobs now provision and execute (macOS completed successfully) instead of failing in ~4 seconds during setup.

Note: this also affects PR checks — currently every PR to this repo gets a red X from these setup failures regardless of its content (e.g. #794).

…nner

GitHub now automatically fails any job using actions/cache < v3 latest or
upload-artifact v2, and the ubuntu-20.04 hosted runner has been retired,
so every R-CMD-check run currently fails during setup before R starts.

- actions/cache v3.3.1 -> v4
- actions/upload-artifact v2 -> v4 (artifact names are already unique per job)
- ubuntu-20.04 runner -> ubuntu-22.04, with matching RSPM repo (focal -> jammy)
  and remotes::system_requirements lookup

@clairblacketer clairblacketer left a comment

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Thanks for this - I recently fixed the actions version but I did not fix the ubuntu issue. There were some other issues in the code that were causing errors after I got the actions working but ubuntu still failed.

@clairblacketer
clairblacketer merged commit bf81778 into OHDSI:main Aug 4, 2026
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codecov Bot commented Aug 4, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 44.15%. Comparing base (032e842) to head (a0b0fa3).
⚠️ Report is 114 commits behind head on main.

❗ There is a different number of reports uploaded between BASE (032e842) and HEAD (a0b0fa3). Click for more details.

HEAD has 2 uploads less than BASE
Flag BASE (032e842) HEAD (a0b0fa3)
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Additional details and impacted files
@@            Coverage Diff             @@
##             main     #795      +/-   ##
==========================================
- Coverage   51.51%   44.15%   -7.36%     
==========================================
  Files           8        8              
  Lines         231      231              
==========================================
- Hits          119      102      -17     
- Misses        112      129      +17     

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2 participants