Misc simplification, May 2026 edition

R/combine.R

@@ -25,7 +25,7 @@ NULL
 setMethod("combine", c("SpatialData", "SpatialData"), \(x, y, ...) {
     # ensure element names are unique across objects
     old <- list(unlist(colnames(x)), unlist(colnames(y)))
-    idx <- rep.int(c(1, 2), vapply(old, length, integer(1)))
+    idx <- rep.int(c(1, 2), lengths(old))
     new <- split(make.unique(unlist(old)), idx)
     for (i in c(1, 2)) {
         # get input element names

R/crop.R

@@ -201,7 +201,7 @@ setMethod("crop", "SpatialDataArray", \(x, y, j=1, ...) {
 
 #' @export
 #' @rdname crop
-#' @importFrom dplyr pull
+#' @importFrom dplyr pull .data
 #' @importFrom duckspatial ddbs_intersects
 #' @importFrom sf st_sf st_sfc st_as_sfc st_bbox st_polygon st_geometry<-
 setMethod("crop", "SpatialDataFrame", \(x, y, j=1, ...) {
@@ -225,8 +225,7 @@ setMethod("crop", "SpatialDataFrame", \(x, y, j=1, ...) {
     df <- data(transform(x, j))
     fd <- data(SpatialDataShape(fd))
     ok <- ddbs_intersects(df, fd, sparse=TRUE)
-    id_x <- NULL # R CMD check
-    x[pull(ok, id_x), ]
+    x[pull(ok, .data$id_x), ]
 })
 
 #' @export

R/extent.R

@@ -29,8 +29,8 @@ NULL
 setMethod("extent", "SpatialData", \(x, i=1) {
     ex <- .lapplyLayer(x, extent, i=i)
     ex <- unlist(ex, recursive=FALSE)
-    xy <- do.call(rbind, lapply(ex, do.call, what=cbind))
-    list(x=range(xy[, 1]), y=range(xy[, 2]))
+    xy <- dplyr::bind_rows(ex)
+    list(x=range(xy$x), y=range(xy$y))
 })
 
 #' @export

R/mask.R

@@ -180,9 +180,8 @@ setMethod("mask_i_by_j",
     if (nrow(collect(head(ij, 1))) == 0)
         stop("found no intersections",
             " between shapes 'i' and 'j'")
-    id_x <- id_y <- NULL # R CMD check
-    is <- pull(ij, id_y) # elements in i
-    js <- pull(ij, id_x) # masks in j
+    is <- pull(ij, .data$id_y) # elements in i
+    js <- pull(ij, .data$id_x) # masks in j
     na <- setdiff(seq_along(i), is)
     # aggregation
     mx <- assay(table, assay)

R/read.R

@@ -143,8 +143,8 @@ readSpatialData <- function(x,
                 stop("couldn't find ", l, " of name", .)
             j <- j[opt]
         }
-        f <- get(paste0("read", toupper(substr(l, 1, 1)), substr(l, 2, nchar(l)-1)))
-        lapply(j, \(.) do.call(f, list(.)))
+        f <- paste0("read", toupper(substr(l, 1, 1)), substr(l, 2, nchar(l)-1))
+        lapply(j, f)
     }
 
     names(ls) <- ls <- .LAYERS[!skip]

R/sdAttrs.R

@@ -133,7 +133,7 @@ setMethod("$", "SpatialDataAttrs", \(x, name) x[[name]])
         x$ome$version
     if (!length(v)) stop("couldn't find 'version' in 'spatialdata_attrs'")
     ok <- length(v) == 1 && is.character(v) && (v <- gsub("-.*", "", v)) %in% sprintf("0.%d", seq_len(6))
-    if (!ok) stop("invalid OME 'version'; expected '0.x' where x is 1-5")
+    if (!ok) stop("invalid OME 'version'; expected '0.x' where x is 1-6")
     return(v)
 }
 

R/sdFrame.R

@@ -168,8 +168,7 @@ SpatialDataShape <- \(data=NULL, meta=SpatialDataAttrs(type="frame"), metadata=l
 #' @rdname SpatialDataFrame
 #' @importFrom dplyr tally pull
 setMethod("length", "SpatialDataFrame", \(x) { 
-    n <- NULL # R CMD check
-    suppressWarnings(dplyr::pull(dplyr::tally(data(x)), n))
+    suppressWarnings(dplyr::pull(dplyr::tally(data(x)), .data$n))
 })
 
 #' @export

R/validity.R

@@ -48,11 +48,10 @@
 
 .validateImage <- \(object) {
     msg <- c()
-    res <- length(object)
     axs <- axes(object)
     typ <- vapply(axs, \(.) .$type, character(1))
     d <- sum(typ != "time")
-    for (k in seq_len(res)) {
+    for (k in seq_along(object)) {
         x <- data(object, k)
         if (length(dim(x)) != d) msg <- c(msg, paste(
             "'SpatialDataImage' resolution", k, "is not ", d, "D"))
@@ -67,11 +66,10 @@ setValidity2("SpatialDataImage", .validateImage)
 #' @importFrom ZarrArray type
 .validateLabel <- \(object) {
     msg <- c()
-    res <- length(object)
     axs <- axes(object)
     typ <- vapply(axs, \(.) .$type, character(1))
     d <- sum(typ == "space")
-    for (k in seq_len(res)) {
+    for (k in seq_along(object)) {
         x <- data(object, k)
         if (length(dim(x)) != d) msg <- c(msg, paste(
             "'SpatialDataLabel' resolution", k, "is not ", d, "D"))
@@ -85,22 +83,20 @@ setValidity2("SpatialDataLabel", .validateLabel)
 
 #' @importFrom dplyr count pull
 .validatePoint <- \(object) {
-    msg <- c()
     cnt <- tryCatch(error=\(.) 0, as.integer(
         pull(count(spatialdataR::data(object)), "n")))
-    if (!cnt) return(msg)
+    if (!cnt) return(NULL)
     if (!"geometry" %in% names(object)) 
-        msg <- c(msg, "'SpatialDataPoint' missing 'geometry'.")
-    return(msg)
+        return("'SpatialDataPoint' missing 'geometry'.")
+    return(NULL)
 }
 #' @importFrom S4Vectors setValidity2
 setValidity2("SpatialDataPoint", .validatePoint)
 
 .validateShape <- \(object) {
-    msg <- c()
     if (!"geometry" %in% names(object)) 
-        msg <- c(msg, "'SpatialDataShape' missing 'geometry'.")
-    return(msg)
+        return("'SpatialDataShape' missing 'geometry'.")
+    return(NULL)
 }
 #' @importFrom S4Vectors setValidity2
 setValidity2("SpatialDataShape", .validateShape)