Changes in version 2.46.0                        

SIGNIFICANT USER-VISIBLE CHANGES

  - The 34 datasets are no longer stored inside the package: they are
    hosted on Zenodo and downloaded individually on first use, then
    cached locally with BiocFileCache. This shrinks the installed
    package from ~400 MB to a few MB.
  - New exported function curatedCRCData(): call it with no arguments to
    list available datasets, with one dataset name to get an
    ExpressionSet, or with several names to get a named list. test =
    TRUE loads small offline subsets bundled with the package (used by
    examples, tests, and the vignette).
  - Legacy data(GSE39582_eset) access still works (it downloads through
    the same cache, deferred until the object is first used) but is
    deprecated and will be removed in a future release.
  - inst/extdata/createEsetList.R now loads datasets through the getter;
    a new test.mode option in the patientselection config files selects
    the offline subsets.
  - The cache is package-specific (tools::R_user_dir("curatedCRCData",
    "cache")); delete that directory to reclaim disk space. Downloads
    are verified against md5 checksums recorded in
    inst/extdata/zenodo-manifest.csv.

INTERNAL

  - inst/scripts/data-integrity-report.Rmd now verifies size_bytes as
    well as md5. R/getData.R compares size_bytes against the cached file
    on every cache hit, so a wrong size in the manifest would have
    silently evicted and re-downloaded a valid file on every call.
    Caught by Copilot review on lima1/curatedBladderData#3.

  - Replaced the never-executed RUnit scaffolding with testthat tests.

  - CI restored to R CMD check + BiocCheck + pkgdown via the waldronlab
    reusable workflow (previously reduced to pkgdown-only because
    checking 400 MB of data exhausted runner memory).

  - Removed external_data_store.txt and Namespace: auto; explicit
    NAMESPACE exporting only curatedCRCData().

DOCUMENTATION AND METADATA

  - Repaired UTF-8 transcoding damage ("??" artifacts) in 32 dataset man
    pages: author names, journal references, and statistical symbols
    restored (ASCII equivalents).
  - biocViews extended to ColonCancerData, MicroarrayData, RNASeqData,
    and GEO for better discoverability.
  - Removed the empty FULLVcuratedCRCData_counts.csv placeholder.

                       Changes in version 2.43.1                        

  - Updated package maintainer to Levi Waldron
    (lwaldron.research@gmail.com).
  - Refactored DESCRIPTION to use standard Authors@R fields, including
    maintainer ORCID and funding info (NCI 5U24CA180996).
  - Fixed invalid biocViews categories to strictly use acceptable
    ExperimentData terms.
  - Replaced the unnecessary affy dependency with Biobase in the package
    Suggests and the vignette.
  - Added a new CITATION file pointing to the 2018 Genome Biology
    meta-analysis paper (PMID: 30253799).
  - Initialized Git LFS to properly track .rda and .RData files.
  - Removed deprecated zzz.R warning.
  - Converted the vignette to RMarkdown (.Rmd).

                        Changes in version 1.0.0                        

  - Initial release of curatedCRCData, a comprehensive resource for
    clinically-oriented investigation of the colorectal cancer
    transcriptome.
  - It provides clinically-annotated expression data including The
    Cancer Genome Atlas (TCGA) RNASeqV2 and Agilent mRNA microarray
    datasets.
  - Probesets are mapped to official gene symbols using up-to-date maps.
  - All clinical annotations are hand-curated and machine-checked to
    ensure consistent syntax and maximum retention of available clinical
    variables.
  - ExpressionSet slots are populated with numerous metadata including
    PubMed IDs, citations, abstracts, study-specific warnings for
    retractions and duplicated samples, and probeset <--> gene maps.
  - The package vignette provides examples for selecting patients and
    datasets based on flexible rules, performing meta-analysis of
    potential biomarkers, creating publication-ready tables from
    ExpressionSet metadata, and simple exporting of data tables for non
    R-users.