NEWS
curatedBladderData 1.50.0
SIGNIFICANT USER-VISIBLE CHANGES
- The 12 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 about
75 MB to a few MB.
- New exported function
curatedBladderData(): call it with no arguments
to list the 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(GSE89_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 selects the
offline subsets.
- The cache is package-specific, at
tools::R_user_dir("curatedBladderData", "cache"). Downloads are
verified against md5 checksums recorded in
inst/extdata/zenodo-manifest.csv.
BUG FIXES
biocViews listed OvarianCancerData; removed, and GEO added.
- The package-level help page described ovarian cancer, listed the
curatedOvarianData author list, and named a different maintainer than
DESCRIPTION. Corrected to match DESCRIPTION.
- Replaced the unused
affy dependency with Biobase, which is where
ExpressionSet, exprs() and pData() actually come from.
createEsetList.R no longer errors when the filters exclude every
dataset (which() on an empty list).
INTERNAL
- Added testthat tests and
inst/scripts/ documenting how the Zenodo
files, the offline fixtures and the data stubs are generated.