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Fix R oldrel-1 CI failure: replace ggpubr with patchwork + graceful internet error handling#508

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copilot/fix-errors-in-pr-506
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Fix R oldrel-1 CI failure: replace ggpubr with patchwork + graceful internet error handling#508
Copilot wants to merge 2 commits intomainfrom
copilot/fix-errors-in-pr-506

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Copilot AI commented Mar 6, 2026

PR #506 was failing on ubuntu-latest (oldrel-1) because ggpubrggrepel >= 0.9.2 → R >= 4.5.0, breaking dependency resolution on R 4.4.x. This PR applies the fix from PR #507 (drop ggpubr for patchwork) alongside the internet-resource error handling from PR #506.

Changes

Dependency fix (PR #507)

  • Replace ggpubr::ggarrange() with patchwork::wrap_plots() in autoplot.seroincidence.by.R and graph_seroresponse_model_1.R
  • Swap ggpubrpatchwork in DESCRIPTION Imports; removes transitive ggrepel dependency
  • Update vdiffr snapshot for new patchwork layout

Graceful internet resource errors (PR #506)

  • load_noise_params() and load_sr_params(): wrap URL loading in tryCatch + withCallingHandlers; emit cli::cli_abort() with class internet_resource_unavailable on failure; re-signal non-URL errors unchanged via rlang::cnd_signal()
  • Switch from readRDS() to readr::read_rds(); move readr from Suggests → Imports
  • Add tests for URL failure path, non-URL error re-throw, and deprecated load_curve_params()

Misc

  • Fix pre-existing stop()cli::cli_abort() in autoplot.seroincidence.by.R (linter flags modified files)

  • Add tests/vdiffr.Rout.fail to .gitignore

  • Bump version to 1.4.0.9004

  • The title of your PR should briefly describe the change.

  • The body of your PR should contain Fixes #issue-number (if relevant).

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…raceful internet error handling

Co-authored-by: kristinawlai <57973437+kristinawlai@users.noreply.github.com>
Copilot AI changed the title [WIP] Fix errors identified in PR #506 Fix R oldrel-1 CI failure: replace ggpubr with patchwork + graceful internet error handling Mar 6, 2026
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