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Recent S4Vectors versions build the aggregate() evaluation environment from an object's mcols columns via makeFixedColumnEnv(), which requires a same-named accessor function for every column. Columns without one (e.g. rmsk's "swScore") abort with "object 'swScore' of mode 'function' was not found", breaking the vignette and any annot_from_gr()/annot_snps() call. Replace all aggregate(x, by, expr, drop=FALSE) calls with explicit grouped reductions that do not rely on S4Vectors' non-standard evaluation: - add internal collapse_hits_annotations() helper for the annotation-string collapses in annot_from_gr() and annot_snps() - use extractList() + mean()/sum() for the numeric mispriming reductions in utils.R Behavior is preserved, including empty groups collapsing to "" and annot_from_gr() converting those to NA. Bump version to 1.11.1. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Recent S4Vectors versions build the aggregate() evaluation environment from an object's mcols columns via makeFixedColumnEnv(), which requires a same-named accessor function for every column. Columns without one (e.g. rmsk's "swScore") abort with "object 'swScore' of mode 'function' was not found", breaking the vignette and any annot_from_gr()/annot_snps() call.
Replace all aggregate(x, by, expr, drop=FALSE) calls with explicit grouped reductions that do not rely on S4Vectors' non-standard evaluation:
Behavior is preserved, including empty groups collapsing to "" and annot_from_gr() converting those to NA. Bump version to 1.11.1.