Cran fix release 1.3.0

[kristinawlai]

Fixing CRAN errors from expect_snapshot_data()

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

Files with missing lines	Coverage Δ
R/check_strata.R	100.00% <ø> (ø)
R/expect_snapshot_data.R	100.00% <100.00%> (ø)
R/sim_pop_data.R	65.82% <ø> (ø)

... and 2 files with indirect coverage changes

[Copilot]

Pull request overview

This PR addresses CRAN errors by converting expect_snapshot_data() from an internal function accessed via ssdtools::: to a properly exported function within the package. The function was copied from the ssdtools package with permission and is now included in the package's public API.

Key Changes

• Added expect_snapshot_data() as an exported internal function with full implementation and documentation
• Updated all test files to use the local expect_snapshot_data() instead of ssdtools:::expect_snapshot_data()
• Updated auto-generated documentation files from roxygen2 7.3.3

Reviewed changes

Copilot reviewed 14 out of 23 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
R/expect_snapshot_data.R	New file implementing the snapshot testing function for data frames, copied from ssdtools
R/check_strata.R	Removed invalid @dev roxygen tag
tests/testthat/test-strata.R	Updated to use local expect_snapshot_data() instead of ssdtools:::
tests/testthat/test-sim_pop_data_multi.R	Updated to use local expect_snapshot_data() instead of ssdtools:::
tests/testthat/test-sim_pop_data.R	Updated to use local expect_snapshot_data() with explicit name parameter
tests/testthat/test-as_sr_params.R	Updated to use local expect_snapshot_data() instead of ssdtools:::
tests/testthat/test-analyze_sims.R	Updated to use local expect_snapshot_data() instead of ssdtools:::
tests/testthat/test-ab.R	Updated to use local expect_snapshot_data() and reformatted indentation
tests/testthat/_snaps/graph.curve.params/*.svg	Added white background rectangles to SVG snapshots
tests/testthat/_snaps/autoplot.pop_data/*.svg	Removed stroke-linejoin: miter attribute from legend rectangles
tests/testthat/_snaps/autoplot.curve_params/autoplot-curve-params.svg	Added white background rectangle to SVG snapshot
man/expect_snapshot_data.Rd	New documentation file for exported function
man/check_strata.Rd	Removed \keyword{internal} tag
man/plot_curve_params_one_ab.Rd	Auto-generated documentation updates from ggplot2 (includes typo fix)
NAMESPACE	Added export for expect_snapshot_data
DESCRIPTION	Version bump to 1.3.0.9060 and RoxygenNote update to 7.3.3
NEWS.md	Added entry documenting the change

---

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[kristinawlai]

@d-morrison Checks pass except for pkgdown. I asked Copilot to explain the error and this is the response. This is my first time using it, so I'm hesitant to make a change based on Copilot, but what do you think?

The failure occurred during the pkgdown site deployment job, specifically while running quarto::quarto_render() in R. The key error is:

Error running quarto CLI from R. 
Caused by error in `quarto::quarto_render()`: 
✖ Error returned by quarto CLI.
! System command 'quarto' failed

This indicates that the Quarto CLI is either not installed or not available in the system PATH during the workflow run.

Solution:
Add a step to install Quarto before any calls to quarto::quarto_render(). You can insert the following step before running your R scripts in the pkgdown-build job:

- name: Install Quarto
  run: |
    wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.550/quarto-1.4.550-linux-amd64.deb
    sudo dpkg -i quarto-1.4.550-linux-amd64.deb

Place this step after setting up R but before any rendering steps. This will ensure the quarto command line tool is present, resolving the "System command 'quarto' failed" error.

Relevant workflow file: .github/workflows/pkgdown.yaml (ref: 17cd0518e919390eee1e87a50eec4ab766414f6a).The failure occurred during the pkgdown site deployment job, specifically while running quarto::quarto_render() in R. The key error is:

Error running quarto CLI from R. 
Caused by error in `quarto::quarto_render()`: 
✖ Error returned by quarto CLI.
! System command 'quarto' failed

This indicates that the Quarto CLI is either not installed or not available in the system PATH during the workflow run.

Solution:
Add a step to install Quarto before any calls to quarto::quarto_render(). You can insert the following step before running your R scripts in the pkgdown-build job:

- name: Install Quarto
  run: |
    wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.550/quarto-1.4.550-linux-amd64.deb
    sudo dpkg -i quarto-1.4.550-linux-amd64.deb

Place this step after setting up R but before any rendering steps. This will ensure the quarto command line tool is present, resolving the "System command 'quarto' failed" error.

Relevant workflow file: .github/workflows/pkgdown.yaml (ref: 17cd0518e919390eee1e87a50eec4ab766414f6a).

[d-morrison]

@kristinawlai the key error message is:

if you run quarto::quarto_render(quiet = FALSE) on your local, you should get something like:

note that the file path begins with data-raw; quarto is trying to compile data-raw/test_sim_020425.qmd, which shouldn't be part of the pkgdown site. The solution is to ignore everything in data-raw:

https://github.com/UCD-SERG/serocalculator/pull/465/files#diff-469a07f57393912a9c17c3ea50ceebe991e32b008beb167a200b17e91fdac6d2R3-R4

[d-morrison]

looks good! see comments

[github-actions]

📕 Preview documentation for this PR has been cleaned up.

[kristinawlai]

@d-morrison This is ready to go and passes all checks + check_win_devel(). I'll update the version number to 1.3.1 for the CRAN release branch once this is merged into main.

[d-morrison]

Looks good - thanks!