NEWS

curatedBreastData 2.40.2

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.

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.

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.

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).