NEWS

ChIPQC 1.49.3

Add package anchors to \link{...} cross-references that target topics in other packages (GenomicRanges, DiffBind, BiocParallel), eliminating the “Found Rd file(s) with Rd \link{} targets missing package anchors” R CMD check NOTE. 9 man/*.Rd files updated. No code change.

Formally deprecate ChIPQCreport() per Bioconductor deprecation guidelines: the function now emits a .Deprecated() warning and returns invisibly. The Nozzle.R1 CRAN package it depended on is no longer available, so HTML report generation is no longer possible. Per Bioconductor policy the function will be made defunct in the next release cycle. The original source is preserved in inst/legacy/report.r for reference. See ?'ChIPQC-deprecated' for replacements (QC accessor methods; deeptools for visual reports).
Remove Nozzle.R1 from Imports: (no longer reachable from any executed code path).
Add zzz.R to the Collate: field (R 4.6 strict Collate enforcement).
Reduce R CMD check NOTE noise: import is from methods, geom_point from ggplot2, and multicoreWorkers/snowWorkers from BiocParallel; register the data-frame column names used in ggplot2::aes() calls (Sample, FRIP, FRIBL, etc.) via utils::globalVariables(). No behaviour change.
Fix \itemize \to \describe in man/ChIPQC.Rd and man/ChIPQCsample-class.Rd: items used \item{label}{description} (a \describe semantic) inside an \itemize wrapper, producing roughly 40 “Lost braces” NOTEs. The rendered output also improves (proper definition list rather than malformed bullets).