Wrap as_forecast_sample example in \donttest{}

[seabbs-bot]

Description

This PR closes #1383.

The example for as_forecast_sample() (added in #1367) calls estimate_infections() directly, which fits a Stan model. R CMD check reports it taking ~37s of CPU/elapsed time:

Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
as_forecast_sample 37.01  0.179  37.424

Other Stan-fitting examples in the package (estimate_infections, epinow, forecast_secondary, estimate_truncation) wrap the fit in \donttest{}. This PR matches that convention.

Initial submission checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have tested my changes locally (using devtools::test() and devtools::check()).
• I have added or updated unit tests where necessary.
• I have updated the documentation if required and rebuilt docs if yes (using devtools::document()).
• I have followed the established coding standards (and checked using lintr::lint_package()).
• I have added a news item linked to this PR.

This was opened by a bot. Please ping @seabbs for any questions.

Summary by CodeRabbit

• Bug Fixes

  • Corrected date-extraction logic in forecast trajectory extension to resolve dimension mismatches that occurred when projecting beyond the original observation window.

• Documentation

  • Updated documentation examples and improved build efficiency by optimising how example code is handled during automated verification processes.

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Walkthrough

This PR wraps the long-running as_forecast_sample() example in \donttest{} to exclude it from R CMD check execution, preventing Stan MCMC fitting from inflating test runtime. The changelog and source documentation are updated accordingly, with the generated .Rd file reflecting the corrected example wrapping structure.

Changes

Documentation Example Wrapping

Layer / File(s)	Summary
Changelog entries NEWS.md	Added forecast_infections() bug fix note and documented that as_forecast_sample() example is now wrapped in \donttest{} to avoid Stan runtime during R CMD check.
Example wrapping implementation R/as_forecast_sample.R, man/as_forecast_sample.Rd	Roxygen example in R/as_forecast_sample.R is wrapped with \donttest{ ... } block; generated .Rd file updates the example guard structure accordingly.

Possibly related PRs

• epiforecasts/EpiNow2#1367: Added the as_forecast_sample() S3 methods and example that is now wrapped in \donttest{} by this PR.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main change: wrapping the as_forecast_sample example in \donttest{} to prevent long-running checks.
Linked Issues check	✅ Passed	All objectives from issue #1383 are met: the example is wrapped in \donttest{}, the @examplesIf guard is preserved, the convention matches other Stan-fitting examples, and R CMD check runtime is reduced.
Out of Scope Changes check	✅ Passed	All changes are scoped to the stated objective: wrapping the as_forecast_sample example in \donttest{}, with supporting documentation updates and a NEWS.md entry.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch long-running-scoringutils-example

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[seabbs]

We changed this in review but I think it actually breaks package convention and leads to a long running example. Note we likely need an issue for storing a few fits as epinowcast does so our examples can all be running (or a shared script that pkgdown runs or something if that is now possible)