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Changelog

Source: NEWS.md

curatedBreastData 2.40.2

SIGNIFICANT USER-VISIBLE CHANGES

  • Package data has been successfully offloaded to Zenodo (https://zenodo.org/records/21415886) and is no longer directly embedded in the package. The data is now dynamically retrieved and cached via BiocFileCache.

NEW FEATURES

  • Added new retrieval functions getCuratedBreastDataExprSetList() and getClinicalData() to access the remote dataset from Zenodo.
  • Embedded a miniature test dataset archive in inst/extdata for rapid local testing and offline execution without remote dependencies.
  • Added curatedBreastData_pData (pre-concatenated phenotype metadata from all datasets) to the package reference index, manual vignette, and documentation.
  • Configured a new pkgdown documentation site to host the package reference manual and manual vignette.

BUG FIXES

  • Fixed operator precedence bugs and replaced deprecated 1:... loop sequence generators with type-safe seq_along() and seq_len().
  • Converted sapply calls to type-safe vapply() in collapseDupProbes().
  • Updated DESCRIPTION metadata to include the latest R dependency (>= 4.6.0), missing biocViews, URL, and BugReports fields.

INTERNAL CHANGES

  • Migrated all package documentation to roxygen2 and removed legacy .Rd manual pages.
  • Converted the package vignette from Sweave (.Rnw) to R Markdown (.Rmd) for improved readability and compilation performance.
  • Added README.md and _pkgdown.yml mirroring the design of MultiAssayExperiment.
  • Configured GitHub Actions CI workflows for automated R CMD check and Bioconductor compliance validation (BiocCheck).

curatedBreastData 0.99.0

  • Initial package release.