address r-universe reports (v.99.40 -> .41) (#230)

* fix URL: and BugReports:
* fix R CMD check warnings
* in vignette, call spatialdataR::transform() explicitly
* v0.99.41

Author: HelenaLC

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: spatialdataR
 Title: Representation of Python's spatialdata in R
 Depends: R (>= 4.6)
-Version: 0.99.40
+Version: 0.99.41
 Description: R interface to Python/scverse's 'spatialdata' framework for 
     unified spatial omics data handling. Adheres to OME-NGFF standards, 
     providing lazy, on-disk representations for multiscale images and 
@@ -64,6 +64,6 @@ biocViews:
 License: Artistic-2.0
 Encoding: UTF-8
 VignetteBuilder: knitr
-URL: https://helenalc.github.io/SpatialData/, https://github.com/HelenaLC/SpatialData
-BugReports: https://github.com/HelenaLC/SpatialData/issues
+BugReports: https://github.com/HelenaLC/spatialdataR/issues
+URL: https://helenalc.github.io/spatialdataR, https://github.com/HelenaLC/spatialdataR
 Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -190,6 +190,7 @@ importFrom(graph,graph.par)
 importFrom(graph,graphAM)
 importFrom(graph,nodeData)
 importFrom(graph,nodes)
+importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,is)
@@ -199,6 +200,7 @@ importFrom(methods,setClassUnion)
 importFrom(methods,setMethod)
 importFrom(methods,setOldClass)
 importFrom(methods,setReplaceMethod)
+importFrom(methods,slot)
 importFrom(rlang,"!!")
 importFrom(rlang,.data)
 importFrom(rlang,call2)

R/SpatialData.R

@@ -29,6 +29,8 @@
 #' @param x,object \code{SpatialData} object.
 #' @param i,j character string, scalar or vector of indices
 #'   specifying the element to extract from a given layer.
+#' @param k scalar index specifying which scale to use; 
+#'   \code{Inf} to use lowest available resolution.
 #' @param drop ignored.
 #' @param name character string for extraction (see \code{?base::`$`}).
 #' @param value (list of) element(s) with layer-compliant object(s), 

R/methods.R

@@ -10,6 +10,7 @@
 
 #' @exportMethod $
 #' @rdname SpatialData
+#' @importFrom methods slot
 setMethod("$", "SpatialData", \(x, name) slot(x, name))
 
 #' @exportMethod $<-
@@ -24,8 +25,9 @@ setMethod("[[", c("SpatialData", "numeric"), \(x, i, ...) {
     callNextMethod(x, i)
 })
 
-#' @rdname SpatialData
 #' @export
+#' @rdname SpatialData
+#' @importFrom methods slot
 setMethod("[[", c("SpatialData", "character"), \(x, i, ...) slot(x, i))
 
 # data/meta ----
@@ -151,8 +153,9 @@ setMethod("layer", c("SpatialData", "ANY"), \(x, i) stop(.invalid_i))
 
 # element ----
 
-#' @rdname SpatialData
 #' @export
+#' @rdname SpatialData
+#' @importFrom methods slot
 setMethod("element", c("SpatialData", "character"), 
     \(x, i) slot(x, layer(x, i))[[i]])
 
@@ -260,6 +263,7 @@ for (e in one) eval(.set(e), parent.env(environment()))
 #' @exportMethod images<- labels<- points<- shapes<- tables<-
 NULL
 
+#' @importFrom methods slot slot<-
 f <- \(l) setReplaceMethod(l, 
     c("SpatialData", getSlots("SpatialData")[[l]]), 
     \(x, value) {
@@ -357,6 +361,7 @@ typ <- c(
     shape="SpatialDataShape", 
     table="SingleCellExperiment")
 
+#' @importFrom methods slot
 f <- \(e) setReplaceMethod(e, 
     c("SpatialData", "character", typ[[e]]), 
     \(x, i, value) {
@@ -406,6 +411,7 @@ for (e in one) eval(f(e), parent.env(environment()))
 #' @exportMethod image<- label<- point<- shape<- table<-
 NULL
 
+#' @importFrom methods slot
 f <- \(e) setReplaceMethod(e, 
     c("SpatialData", "ANY", "NULL"), 
     \(x, i, ..., value) {

R/utils.R

@@ -31,6 +31,7 @@
     return(x)
 }
 
+#' @importFrom methods slot<-
 .sync_tables_sdattrs <- \(x, old, new) {
     if (!length(ts <- tables(x))) return(x)
     for (i in seq_along(ts)) {
@@ -73,6 +74,7 @@
     return(x)
 }
 
+#' @importFrom methods slot<-
 .sync_tables_on_drop <- \(x) {
     if (!length(ts <- tables(x))) return(x)
     all_nms <- unlist(colnames(x)[.ls])

R/validity.R

@@ -192,7 +192,6 @@ setValidity2("SpatialData", .validateSpatialData)
     return(msg)
 }
 .validateAttrsLabel <- \(x) {
-    x <- label(sd)
     msg <- c()
     za <- meta(x)
     msg <- .validateAttrs_multiscales(za, msg)

inst/NEWS

@@ -1,3 +1,8 @@
+changes in version 0.99.41
+
+- fix vignette to call 'spatialdataR::transform()' explicitly
+- address R CMD check warnings re: undocumented arguments, undefined functions
+
 changes in version 0.99.40
 
 - validty & setters now assure that each layer is a completely named list
@@ -27,9 +32,12 @@ changes in version 0.99.36
 
 changes in version 0.99.35
 
-- class renaming
 - bug fix: 'centroids,shape' was previously 
   returning vertex coordinates for polygons
+- class renaming:
+  sdArray/Frame > SpatialDataArray/Frame,
+  Image/LabelArray > SpatialDataImage/Label,
+  Shape/PointFrame > SpatialDataShape/Point
 
 changes in version 0.99.34
 

man/SpatialData.Rd

@@ -8,7 +8,7 @@ output:
     toc_depth: 2
     toc_float: true
 vignette: |
-  %\VignetteIndexEntry{Introduction to spatialdataR}
+  %\VignetteIndexEntry{spatialdataR}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 bibliography: "refs.bib"
@@ -28,23 +28,25 @@ knitr::opts_chunk$set(cache=FALSE, message=FALSE, warning=FALSE)
 
 ## Introduction
 
-The `r BiocStyle::Biocpkg("spatialdataR")` package provides an R interface to the 
-[SpatialData](https://spatialdata.scverse.org) framework, a unified ecosystem 
-for handling spatial omics data. Developed as part of the 
-[scverse](https://scverse.org) project [@Virshup2023-scverse], `SpatialData` aims to solve the 
-challenges of integrating diverse spatial datasets—including imaging, spatial 
-transcriptomics, and proteomics—by employing the 
+The `r BiocStyle::Biocpkg("spatialdataR")` package provides an R interface to 
+Python's [spatialdata](https://spatialdata.scverse.org) framework for unified 
+handling of spatial omics data, including tabular annotations, vector- and 
+raster-based components. Developed as part of the [scverse](https://scverse.org) 
+project [@Virshup2023-scverse], `spatialdata` aims to solve the challenges of 
+integrating diverse spatial datasets -- including  -- by employing the 
 [OME-NGFF (Next Generation File Format)](https://ngff.openmicroscopy.org) 
 standard [@Marconato2025-SpatialData].
 
-The Python implementation and core specifications can be found at the 
-[official SpatialData website](https://spatialdata.scverse.org).
+The Python implementation and core specifications are found at the
+[official `spatialdata` website](https://spatialdata.scverse.org).
 
 ## Representation
 
 The core data structure is the `SpatialData` class, which organizes data 
 into 5 coordinated **layers: images, labels, points, shapes, and tables**. 
-Each layer is stored as a list of layer-specific objects that carry associated `SpatialDataAttr` (`@meta` slot), which encode `spatialdata`-specific zarr attributes (*.zattr* for Zarr v2, and *zarr.json* for Zarr v3)
+Each layer is stored as a list of layer-specific objects that carry associated 
+`SpatialDataAttr` (`@meta` slot), which encode `spatialdata`-specific 
+Zarr attributes (*.zattr* for Zarr v2, and *zarr.json* for Zarr v3).
 Together, these layers provide a unified representation of spatial omics data, 
 combining raster, vector, and tabular data within a single coherent framework.
 
@@ -240,7 +242,7 @@ in the correct order (e.g., `scale()` then `translation()`).
 a <- label(sd)
 
 # project into 'global'
-b <- transform(a, "scale")
+b <- spatialdataR::transform(a, "scale")
 
 # compare XY extents
 do.call(rbind, c(a=extent(a), b=extent(b)))
@@ -338,7 +340,7 @@ across objects via `make.names()`, appending a suffix to the element names of
 subsequent objects. Alternatively, names could be customize before combining.
 
 ```{r combine}
-sp <- combine(sd, sd)
+sp <- combine(list(foo=sd, bar=sd))
 cbind(
     original=lengths(colnames(sd)),
     combined=lengths(colnames(sp)))