Merge pull request #123 from mojaveazure/release/4.1.4

Release 4.1.4

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 4.1.3
-Date: 2022-11-07
+Version: 4.1.4
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
@@ -29,7 +28,7 @@ BugReports:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends:
     R (>= 4.0.0),
     sp (>= 1.5.0)
@@ -38,7 +37,7 @@ Imports:
     future.apply,
     grDevices,
     grid,
-    Matrix (>= 1.5.0),
+    Matrix (>= 1.6.1),
     methods,
     progressr,
     Rcpp (>= 1.0.5),
@@ -48,7 +47,7 @@ Imports:
     utils
 Suggests:
     ggplot2,
-    rgeos,
+    sf,
     testthat
 Collate:
     'RcppExports.R'

NEWS.md

@@ -1,6 +1,12 @@
+# SeuratObject 4.1.4
+## Changes
+- Fixes for `CellsByIdentities` (#80)
+- Remove {rgeos} from Suggests and replace with {sf} due to {rgeos} package retirement
+- New check for potential binary breaks between dependencies and SeuratObject
+
 # SeuratObject 4.1.3
 ## Changes
-- Move {rgeos} to Suggests; segmentation simplification now requires {regos} to be installed manually
+- Move {rgeos} to Suggests; segmentation simplification now requires {rgeos} to be installed manually
 - Move {sp} to Depends
 
 ## Added

R/generics.R

@@ -1064,7 +1064,6 @@ SetIdent <- function(object, ...) {
 
 #' Simplify Geometry
 #'
-#' @inheritParams rgeos::gSimplify
 #' @param coords ...
 #'
 #' @return ...

R/seurat.R

@@ -232,7 +232,7 @@ CellsByIdentities <- function(
     USE.NAMES = TRUE
   )
   if (any(is.na(x = Idents(object = object)[cells]))) {
-    cells.idents["NA"] <- names(x = which(x = is.na(x = Idents(object = object)[cells])))
+    cells.idents[["NA"]] <- names(x = which(x = is.na(x = Idents(object = object)[cells])))
   }
   return(cells.idents)
 }

R/utils.R

@@ -708,35 +708,43 @@ S4ToList.list <- function(object) {
   return(object)
 }
 
+#' Simplify segmentations by reducing the number of vertices
+#'
+#' @param coords A `Segmentation` object
+#' @param tol Numerical tolerance value to be used by the Douglas-Peuker algorithm
+#' @param topologyPreserve Logical determining if the algorithm should attempt to preserve the topology of the original geometry
+#'
+#' @return A `Segmentation` object with simplified segmentation vertices
+#' 
 #' @rdname Simplify
 #' @method Simplify Spatial
 #' @export
 #'
 Simplify.Spatial <- function(coords, tol, topologyPreserve = TRUE) {
-  if (!PackageCheck('rgeos', error = FALSE)) {
-    stop("'Simplify' requires rgeos to be installed", call. = FALSE)
+  if (!PackageCheck("sf", error = FALSE)) {
+    stop("'Simplify' requires sf to be installed", call. = FALSE)
   }
   class.orig <- class(x = coords)
+  coords.orig <- coords
   dest <- ifelse(
-    test = grepl(pattern = '^Spatial', x = class.orig),
+    test = grepl(pattern = "^Spatial", x = class.orig), 
     yes = class.orig,
-    no = grep(
-      pattern = '^Spatial',
-      x = .Contains(object = coords),
-      value = TRUE
-    )[1L]
-  )
-  coords <- rgeos::gSimplify(
-    spgeom = as(object = coords, Class = dest),
-    tol = as.numeric(x = tol),
-    topologyPreserve = isTRUE(x = topologyPreserve)
-  )
-  coords <- tryCatch(
-    expr = as(object = coords, Class = class.orig),
-    error = function(...) {
-      return(coords)
-    }
-  )
+    no = grep(pattern = "^Spatial", x = .Contains(object = coords), value = TRUE)[1L])
+  x <- sf::st_as_sfc(as(object = coords, Class = dest))
+  coords <- sf::st_simplify(
+    x = x,
+    dTolerance = as.numeric(x = tol),
+    preserveTopology = isTRUE(x = topologyPreserve))
+  coords <- sf::st_sf(geometry = coords)
+  coords <- as(coords, Class = "Spatial")
+  coords <- as(coords, Class = "Segmentation")
+  slot(object = coords, name = "polygons") <- mapply(
+    FUN = function(x, y) {
+      slot(object = x, name = "ID") <- y
+      return(x)
+    },
+    slot(object = coords, name = "polygons"),
+    Cells(coords.orig))
   return(coords)
 }
 

R/zzz.R

@@ -1,6 +1,6 @@
 #' @importFrom sp bbox over
 #' @importFrom Rcpp evalCpp
-#' @importFrom utils head tail
+#' @importFrom utils head tail packageVersion
 #' @importFrom methods new setClass setClassUnion setMethod setOldClass
 #' setValidity slot slot<- validObject
 #' @importClassesFrom Matrix dgCMatrix
@@ -24,6 +24,15 @@ Seurat.options <- list(
   progressr.clear = FALSE
 )
 
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+# Built With
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+.BuiltWith <- c(
+  R = format(x = getRversion()),
+  Matrix = format(x = packageVersion(pkg = "Matrix"))
+)
+
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 # Reexports
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -460,6 +469,32 @@ NameIndex <- function(x, names, MARGIN) {
 # Hooks
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+.onAttach <- function(libname, pkgname) {
+  for (i in names(x = .BuiltWith)) {
+    current <- switch(EXPR = i, R = getRversion(), packageVersion(pkg = i))
+    if (current > .BuiltWith[i]) {
+      msg <- paste(
+        sQuote(x = pkgname),
+        "was built",
+        switch(
+          EXPR = i,
+          R = "under R",
+          paste("with package", sQuote(x = i))
+        ),
+        .BuiltWith[i],
+        "but the current version is",
+        paste0(current, ';'),
+        "it is recomended that you reinstall ",
+        sQuote(x = pkgname),
+        " as the ABI for",
+        switch(EXPR = i, R = i, sQuote(x = i)),
+        "may have changed"
+      )
+      packageStartupMessage(paste(strwrap(x = msg), collapse = '\n'))
+    }
+  }
+}
+
 .onLoad <- function(libname, pkgname) {
   toset <- setdiff(x = names(x = Seurat.options), y = names(x = options()))
   if (length(x = toset)) {

cran-comments.md

@@ -1,7 +1,7 @@
-# SeuratObject v4.1.3
+# SeuratObject v4.1.4
 
 ## Test environments
-* local ubuntu 20.04 install, R 4.2.0
+* local ubuntu 22.04 install, R 4.2.3
 * win-builder (oldrelease, release, devel)
 
 ## R CMD check results
@@ -12,6 +12,6 @@ There were no ERRORs, WARNINGs, or NOTEs
 
 There is one package that depends on SeuratObject: tidyseurat; this update does not impact its functionality
 
-There are six packages that import SeuratObject: bbknnR, CAMML, Platypus, scpoisson, Seurat, and Signac; this update does not impact their functionality
+There are six packages that import SeuratObject: bbknnR, CAMML, scCustomize, scpoisson, Seurat, and Signac; this update does not impact their functionality
 
-There are five packages that suggest SeuratObject: cellpypes, scOntoMatch, singleCellHaystack, SPECK, and VAM; this update does not impact their functionality
+There are seven packages that suggest SeuratObject: cellpypes, RESET, scOntoMatch, SCpubr, singleCellHaystack, SPECK, and VAM; this update does not impact their functionality