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quantrr 1.3.2 - #30
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jabenninghoff
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Aug 18, 2026
jabenninghoff
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- 2026-08 Upkeep
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Pull request overview
This PR performs the August 2026 upkeep for the quantrr R package, updating dependency snapshots (renv), refreshing generated pkgdown/Quarto example site assets, and updating documentation/release notes for the intended 1.3.2 release.
Changes:
- Updated dependency management: renv version bump, lockfile refresh, and Bioconductor enablement.
- Refreshed generated example site assets (Quarto/pkgdown JS/CSS/search index) and workflows pinned to specific action SHAs.
- Updated documentation/release notes (NEWS) and various project config/ignore/lint settings.
Reviewed changes
Copilot reviewed 21 out of 41 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/quantrr.Rmd | Updates CRAN download link for macOS install instructions. |
| standalone/analysis/mfa.Rmd | Updates IRIS report link target. |
| renv/settings.json | Enables Bioconductor in renv settings. |
| renv/activate.R | Bumps renv autoloader version to 1.2.4. |
| renv.lock | Refreshes R version, repository URL, and many package records. |
| pkgdown/assets/example/site_libs/quarto-search/quarto-search.js | Updates search param handling and introduces new in-page highlight/tab activation behavior. |
| pkgdown/assets/example/site_libs/quarto-nav/quarto-nav.js | Narrows index.html stripping regex to avoid unintended replacements. |
| pkgdown/assets/example/site_libs/quarto-html/quarto.js | Removes axe checker initialization. |
| pkgdown/assets/example/site_libs/quarto-html/quarto-syntax-highlighting-*.css | Updates sourcemap references for regenerated syntax highlighting CSS. |
| pkgdown/assets/example/site_libs/quarto-html/axe/axe-check.js | Removes the axe checker module. |
| pkgdown/assets/example/site_libs/plotly-htmlwidgets-css-2.25.2/plotly-htmlwidgets.css | Adds css shim for plotly + ioslides behavior. |
| pkgdown/assets/example/site_libs/plotly-binding-4.12.1/plotly.js | Adds/updates plotly HTMLWidgets binding JS. |
| pkgdown/assets/example/search.json | Updates generated search index content. |
| pkgdown/assets/example/index.html | Updates Quarto generator version and regenerated HTML markup/assets. |
| NEWS.md | Adds release notes section for 1.3.2. |
| DESCRIPTION | Updates package metadata (but version is inconsistent with 1.3.2). |
| .Rprofile | Adds commented renv workaround note. |
| .Rbuildignore | Ignores new tool-related directories. |
| .lintr | Updates lintr configuration. |
| .gitignore | Ignores .positai directory. |
| .github/workflows/test-coverage.yaml | Pins GitHub Actions to specific SHAs and updates header date. |
| .github/workflows/R-CMD-check.yaml | Pins GitHub Actions to specific SHAs and updates header date/comment. |
| .github/workflows/missing-deps.yaml | Pins GitHub Actions to specific SHAs. |
| .github/workflows/lint.yaml | Pins GitHub Actions to specific SHAs and updates header date. |
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