Submit 5.3.0 to CRAN (#271)

* Bump version

* Update documentation

* Update changelog

* Update documentation

* Update documentation

* Update cran-comments.md

Author: anashen

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SeuratObject
 Title: Data Structures for Single Cell Data
-Version: 5.2.1.9001
+Version: 5.3.0
 Authors@R: c(
   person(given = 'Paul', family = 'Hoffman', email = 'hoff0792@alumni.umn.edu', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')),
   person(given = 'Rahul', family = 'Satija', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),

NEWS.md

@@ -1,7 +1,15 @@
-# Unreleased
+# SeuratObject 5.3.0
 
-## Changes
+## Changes:
  - Update `subset.Seurat` to no longer call `droplevels` on the input's cell-level `meta.data` slot; update `subset.Assay` to no longer call `droplevels` on the input's feature-level `meta.features` slot; update `subset.StdAssay` to no longer call `droplevels` on the input's feature-level `meta.data` slot (reverting #251, see discussion in #247)
+ - Add `drop = FALSE` when retrieving data in `LayerData.Assay` to preserve dimensions when subsetting to the requested cells (#261)
+ - Update `sf.data` slot in the `Segmentation` class to store a `data.frame` in accordance with changes in loading Visium segmentations (#267)
+ - Add `compact` slot to the `Segmentation` class to denote whether the object only stores segmentation information in the `sf.data` slot, or also the `sp`-inherited slots (#267)
+ - Update `CreateSegmentation`, `CreateSegmentation.data.frame`, `CreateSegmentation.sf`, and methods interacting with `Segmentation` objects (`Cells.Segmentation`, `RenameCells.Segmentation`, `Crop.Segmentation`, `subset.Segmentation`, `[[<-`, `coordinates`, `Overlay`, `show`, `setValidity`) to account for the addition of `compact` and the update to `sf.data`
+   - For a detailed description of changes, see [#267](https://github.com/satijalab/seurat-object/pull/267)
+ - Add `coords_x_orientation` slot to the `FOV` class to hold the orientation of the x-axis for spatial data (to mark whether the coordinate system of a spatial object has been updated)
+ - Update `UpdateSeuratObject` to check whether an object requires an update to the coordinate system based on the existence and value of the `coords_x_orientation` slot (currently only relevant for Visium objects)
+ - Add method `safeValidityCheck` to show an improved error message suggesting to run `UpdateSeuratObject` when a "slots in class definition but not in object" error is thrown by R's internal object validation; use in `FOV`-interacting methods
 
 # SeuratObject 5.2.0
 

R/seurat.R

@@ -628,6 +628,7 @@ RenameAssays <- function(
 #' @order 1
 #'
 #' @examples
+#' \dontrun{
 #' if (requireNamespace("fs", quietly = TRUE)) {
 #'   # Write out with DelayedArray
 #'   if (requireNamespace("HDF5Array", quietly = TRUE)) {
@@ -678,6 +679,7 @@ RenameAssays <- function(
 #'     pbmc2[["disk"]]
 #'   }
 #' }
+#' }
 #'
 SaveSeuratRds <- function(
   object,

R/utils.R

@@ -1338,8 +1338,6 @@ ListToS4 <- function(x) {
 #' \code{PackageCheck} was deprecated in version 5.0.0; please use
 #' \code{\link[rlang:check_installed]{rlang::check_installed}()} instead
 #'
-#' @examples
-#' PackageCheck("SeuratObject", error = FALSE)
 #'
 PackageCheck <- function(..., error = TRUE) {
   .Deprecate(

cran-comments.md

@@ -0,0 +1,44 @@
+# SeuratObject v5.3.0
+
+## Test environments
+* local Ubuntu 20.04.6 install (R 4.3.2)
+* local macOS 15.6 (R 4.5.1)
+* win-builder
+  * R-oldrelease (R 4.4.3)
+  * R-release (R 4.5.2)
+  * R-devel (R 4.6.0)
+
+## R CMD check results
+
+There were no ERRORs or WARNINGs.
+
+There were two NOTEs given by win-builder (oldrel):
+- - -
+```
+* checking CRAN incoming feasibility ... [21s] NOTE
+Maintainer: 'Rahul Satija <seurat@nygenome.org>'
+
+Suggests or Enhances not in mainstream repositories:
+  BPCells
+Availability using Additional_repositories specification:
+  BPCells   yes   https://bnprks.r-universe.dev
+```
+
+Rahul Satija is the maintainer and the email is correct. 
+
+BPCells is hosted on R-universe and used conditionally in SeuratObject.
+
+```
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: 'BPCells'
+```
+
+BPCells is hosted on R-universe and used conditionally in SeuratObject.
+
+## Downstream dependencies
+
+We checked 63 reverse dependencies (25 from CRAN + 38 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+Reverse dependency checks gave ERRORs in 5 packages: Platypus (examples), SCpubr (tests), Seurat (examples, tests), XYomics (vignettes), scpoisson (examples, vignettes). All of these ERRORs are regarding the defunctation of the `slot` argument in `GetAssayData` and `SetAssayData`, which was deprecated in our package three releases ago (v5.0.0, 2023-10-26) and announced then as slated for eventual defunctation.
+
+Besides this point, this update does not affect the functionality of any of the dependencies.