docs: add \value sections to DuckDBGRanges man pages; bump to 0.99.1

Document return values (roxygen @return) for the DuckDBGRanges and
DuckDBGRangesList class and utility man pages, covering constructors, accessors,
replacement, coercion, and range-operation methods. Clears the R CMD BiocCheck
missing-\value WARNING.

Author: aboyounp-gne

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DuckDBGRanges
-Version: 0.99.00
-Date: 2026-07-18
+Version: 0.99.1
+Date: 2026-07-22
 Title: DuckDB-Backed GenomicRanges Implementation
 Description:
     Provides DuckDB-backed implementations of GenomicRanges data structures

NEWS.md

@@ -1,3 +1,13 @@
+# DuckDBGRanges 0.99.1
+
+## Documentation
+
+- Added `\value` sections (roxygen `@return`) to the `DuckDBGRanges` and
+  `DuckDBGRangesList` class and utility man pages, documenting the values
+  returned by the constructors, accessors, replacement, coercion, and
+  range-operation methods. Resolves the `R CMD BiocCheck` "missing \value"
+  WARNING.
+
 # DuckDBGRanges 0.9.8
 
 ## Testing and diagnostics

R/DuckDBGRanges-class.R

@@ -190,6 +190,18 @@
 #'                     keycol = "id")
 #' gr
 #'
+#' @return
+#' The \code{DuckDBGRanges()} constructor returns a DuckDBGRanges object.
+#' Accessors return the requested component of the ranges (for example
+#' \code{seqnames()}, \code{start()}, \code{end()}, \code{width()},
+#' \code{strand()}, \code{ranges()}, \code{seqinfo()}, \code{length()},
+#' \code{names()}, and \code{elementMetadata()}); \code{dbconn()} and
+#' \code{tblconn()} return the backing DuckDB connection. Replacement methods
+#' (such as \code{seqlengths<-}, \code{genome<-}, and \code{dimtbls<-}) return
+#' the updated DuckDBGRanges. Coercion methods return the corresponding
+#' in-memory object (for example a \link[GenomicRanges]{GRanges}), subsetting
+#' returns a DuckDBGRanges, and the show method returns \code{NULL} invisibly.
+#'
 #' @aliases DuckDBGRanges-class
 #'
 #' @aliases dbconn,DuckDBGRanges-method

R/DuckDBGRanges-utils.R

@@ -337,6 +337,19 @@
 #' # Subset by overlaps (uses overlapsAny internally)
 #' subset <- subsetByOverlaps(query, subject)
 #'
+#' @return
+#' Overlap methods return a \link[S4Vectors]{Hits} object
+#' (\code{findOverlaps()}), an integer vector (\code{countOverlaps()}), a
+#' logical vector (\code{overlapsAny()}), or a DuckDBGRanges
+#' (\code{subsetByOverlaps()}). Intra-range methods (\code{shift()},
+#' \code{narrow()}, \code{resize()}, \code{flank()}, \code{promoters()},
+#' \code{terminators()}) return a \link[GenomicRanges]{GRanges}. Inter-range,
+#' set-operation, range-restriction, and tiling methods (such as \code{range()}
+#' and \code{reduce()}) return a DuckDBGRanges (or DuckDBGRangesList where the
+#' result is grouped). Nearest-neighbor, distance, comparison, and ordering
+#' methods return the corresponding integer or logical vectors (or a
+#' \link[S4Vectors]{Hits}).
+#'
 #' @aliases findOverlaps,GRanges,DuckDBGRanges-method
 #' @aliases findOverlaps,DuckDBGRanges,DuckDBGRanges-method
 #' @aliases findOverlaps,DuckDBGRanges,GRanges-method

R/DuckDBGRangesList-class.R

@@ -174,6 +174,18 @@
 #'                             keycol = list(group = c("gr1", "gr2", "gr3", "gr4")))
 #' grlist
 #'
+#' @return
+#' The \code{DuckDBGRangesList()} constructor returns a DuckDBGRangesList object.
+#' Accessors return the requested component (for example \code{seqnames()},
+#' \code{start()}, \code{end()}, \code{width()}, \code{strand()},
+#' \code{length()}, \code{names()}, and \code{seqinfo()}); \code{dbconn()} and
+#' \code{tblconn()} return the backing DuckDB connection. Replacement methods
+#' (such as \code{names<-}, \code{seqlengths<-}, \code{genome<-}, and
+#' \code{dimtbls<-}) return the updated DuckDBGRangesList. Coercion methods
+#' return the corresponding in-memory object (for example a
+#' \link[GenomicRanges]{GRangesList}), and subsetting returns a
+#' DuckDBGRangesList.
+#'
 #' @aliases DuckDBGRangesList-class
 #'
 #' @aliases updateObject,DuckDBGRangesList-method

R/DuckDBGRangesList-utils.R

@@ -68,6 +68,10 @@
 #' # Get range per list element
 #' range(grlist)
 #'
+#' @return
+#' \code{range()} returns a DuckDBGRangesList giving the range (minimum start to
+#' maximum end) spanned within each list element, per seqname/strand.
+#'
 #' @aliases
 #' range,DuckDBGRangesList-method
 #'