Merge in v3.4.4 to main (#5480)

* Cherry-pick from #5327

* Add a NEWS item

* Hotfix 3.4.4 (#5449)

* is.atomic() --> is.atomic() || is.null()

* Polish news

* Put is.null() first

* Cherrypick rgeos removal from description (#5453)

* Remove rgeos from the dependency (#5242)

---------

Co-authored-by: Hiroaki Yutani <[email protected]>

* run revdepcheck

* Update CRAN comments

* Increment version number to 3.4.4

* Fix Version 3.4.4 NEWS Typo (#5479)

Change "the upcoming retirement of rproj, rgeos, and maptools"
to "the upcoming retirement of rgdal, rgeos, and maptools"

* Increment version number to 3.4.4.9000

---------

Co-authored-by: Hiroaki Yutani <[email protected]>
Co-authored-by: Thomas Lin Pedersen <[email protected]>
Co-authored-by: Matt Nield <[email protected]>

Author: 4 people

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: ggplot2
-Version: 3.4.3.9000
+Version: 3.4.4.9000
 Title: Create Elegant Data Visualisations Using the Grammar of Graphics
 Authors@R: c(
     person("Hadley", "Wickham", , "[email protected]", role = "aut",
@@ -54,7 +54,6 @@ Suggests:
     knitr,
     mapproj,
     maps,
-    maptools,
     multcomp,
     munsell,
     nlme,

NEWS.md

@@ -155,6 +155,17 @@
   duplicated coordinates (@teunbrand, #5215).
 * Improve performance of layers without positional scales (@zeehio, #4990)
 
+# ggplot2 3.4.4
+
+This hotfix release adapts to a change in r-devel's `base::is.atomic()` and 
+the upcoming retirement of maptools.
+
+* `fortify()` for sp objects (e.g., `SpatialPolygonsDataFrame`) is now deprecated
+  and will be removed soon in support of [the upcoming retirement of rgdal, rgeos,
+  and maptools](https://r-spatial.org/r/2023/05/15/evolution4.html). In advance
+  of the whole removal, `fortify(<SpatialPolygonsDataFrame>, region = ...)`
+  no longer works as of this version (@yutannihilation, #5244).
+
 # ggplot2 3.4.3
 This hotfix release addresses a version comparison change in r-devel. There are
 no user-facing or breaking changes.

R/aes-evaluation.R

@@ -226,7 +226,7 @@ is_calculated <- function(x, warn = FALSE) {
     return(TRUE)
   }
   # Support of old recursive behaviour
-  if (is.atomic(x)) {
+  if (is.null(x) || is.atomic(x)) {
     FALSE
   } else if (is.symbol(x)) {
     res <- is_dotted_var(as.character(x))
@@ -266,7 +266,7 @@ is_staged <- function(x) {
 
 # Strip dots from expressions
 strip_dots <- function(expr, env, strip_pronoun = FALSE) {
-  if (is.atomic(expr)) {
+  if (is.null(expr) || is.atomic(expr)) {
     expr
   } else if (is.name(expr)) {
     expr_ch <- as.character(expr)
@@ -324,7 +324,7 @@ strip_stage <- function(expr) {
 make_labels <- function(mapping) {
   default_label <- function(aesthetic, mapping) {
     # e.g., geom_smooth(aes(colour = "loess")) or aes(y = NULL)
-    if (is.atomic(mapping)) {
+    if (is.null(mapping) || is.atomic(mapping)) {
       return(aesthetic)
     }
     mapping <- strip_stage(mapping)

R/aes.R

@@ -285,7 +285,7 @@ aes_ <- function(x, y, ...) {
   as_quosure_aes <- function(x) {
     if (is.formula(x) && length(x) == 2) {
       as_quosure(x)
-    } else if (is.call(x) || is.name(x) || is.atomic(x)) {
+    } else if (is.null(x) || is.call(x) || is.name(x) || is.atomic(x)) {
       new_aesthetic(x, caller_env)
     } else {
       cli::cli_abort("Aesthetic must be a one-sided formula, call, name, or constant.")

R/fortify-spatial.R

@@ -9,32 +9,31 @@
 #' @param ... not used by this method
 #' @keywords internal
 #' @name fortify.sp
-#' @examples
-#' if (require("maptools")) {
-#'  sids <- system.file("shapes/sids.shp", package="maptools")
-#'  nc1 <- readShapePoly(sids,
-#'    proj4string = CRS("+proj=longlat +datum=NAD27"))
-#'  nc1_df <- fortify(nc1)
-#' }
 NULL
 
 #' @rdname fortify.sp
 #' @export
 #' @method fortify SpatialPolygonsDataFrame
 fortify.SpatialPolygonsDataFrame <- function(model, data, region = NULL, ...) {
+  deprecate_warn0("3.4.4",
+    I("`fortify(<SpatialPolygonsDataFrame>)`"),
+    details = "Please migrate to sf."
+  )
+
   attr <- as.data.frame(model)
   # If not specified, split into regions based on polygons
   if (is.null(region)) {
-    coords <- lapply(model@polygons,fortify)
+    # Suppress duplicated warnings
+    withr::with_options(list(lifecycle_verbosity = "quiet"), {
+      coords <- lapply(model@polygons,fortify)
+    })
     coords <- vec_rbind0(!!!coords)
     cli::cli_inform("Regions defined for each Polygons")
   } else {
-    cp <- sp::polygons(model)
-
-    # Union together all polygons that make up a region
-    unioned <- maptools::unionSpatialPolygons(cp, attr[, region])
-    coords <- fortify(unioned)
-    coords$order <- 1:nrow(coords)
+    lifecycle::deprecate_stop("3.4.4",
+      I("`fortify(<SpatialPolygonsDataFrame>, region = ...)` is defunct'"),
+      details = "Please migrate to sf."
+    )
   }
   coords
 }
@@ -43,14 +42,27 @@ fortify.SpatialPolygonsDataFrame <- function(model, data, region = NULL, ...) {
 #' @export
 #' @method fortify SpatialPolygons
 fortify.SpatialPolygons <- function(model, data, ...) {
-  polys <- lapply(model@polygons, fortify)
+  deprecate_warn0("3.4.4",
+    I("`fortify(<SpatialPolygons>)`"),
+    details = "Please migrate to sf."
+  )
+
+  # Suppress duplicated warnings
+  withr::with_options(list(lifecycle_verbosity = "quiet"), {
+    polys <- lapply(model@polygons, fortify)
+  })
   vec_rbind0(!!!polys)
 }
 
 #' @rdname fortify.sp
 #' @export
 #' @method fortify Polygons
 fortify.Polygons <- function(model, data, ...) {
+  deprecate_warn0("3.4.4",
+    I("`fortify(<Polygons>)`"),
+    details = "Please migrate to sf."
+  )
+
   subpolys <- model@Polygons
   pieces <- lapply(seq_along(subpolys), function(i) {
     df <- fortify(subpolys[[model@plotOrder[i]]])
@@ -70,6 +82,11 @@ fortify.Polygons <- function(model, data, ...) {
 #' @export
 #' @method fortify Polygon
 fortify.Polygon <- function(model, data, ...) {
+  deprecate_warn0("3.4.4",
+    I("`fortify(<Polygon>)`"),
+    details = "Please migrate to sf."
+  )
+
   df <- as.data.frame(model@coords)
   names(df) <- c("long", "lat")
   df$order <- 1:nrow(df)
@@ -81,6 +98,11 @@ fortify.Polygon <- function(model, data, ...) {
 #' @export
 #' @method fortify SpatialLinesDataFrame
 fortify.SpatialLinesDataFrame <- function(model, data, ...) {
+  deprecate_warn0("3.4.4",
+    I("`fortify(<SpatialLinesDataFrame>)`"),
+    details = "Please migrate to sf."
+  )
+
   lines <- lapply(model@lines, fortify)
   vec_rbind0(!!!lines)
 }
@@ -89,6 +111,11 @@ fortify.SpatialLinesDataFrame <- function(model, data, ...) {
 #' @export
 #' @method fortify Lines
 fortify.Lines <- function(model, data, ...) {
+  deprecate_warn0("3.4.4",
+    I("`fortify(<Lines>)`"),
+    details = "Please migrate to sf."
+  )
+
   lines <- model@Lines
   pieces <- lapply(seq_along(lines), function(i) {
     df <- fortify(lines[[i]])
@@ -108,6 +135,11 @@ fortify.Lines <- function(model, data, ...) {
 #' @export
 #' @method fortify Line
 fortify.Line <- function(model, data, ...) {
+  deprecate_warn0("3.4.4",
+    I("`fortify(<Line>)`"),
+    details = "Please migrate to sf."
+  )
+
   df <- as.data.frame(model@coords)
   names(df) <- c("long", "lat")
   df$order <- 1:nrow(df)

cran-comments.md

@@ -1,5 +1,66 @@
-This is a patch release responding to a request from CRAN about numeric
-version comparisons in R-devel. It also includes a workaround for changes
-in the `stats::density()` function in R-devel that affected visual tests.
-There are no user facing changes, so no reverse dependencies are expected to
-be affected.
+This is a patch release responding to changes in R-devel concerning the behavior
+of `is.atomic()`. Further, it contains the removal of maptools and rgeos which 
+is set for archival soon
+
+## revdepcheck results
+
+We checked 4771 reverse dependencies (4716 from CRAN + 55 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 2 new problems
+ * We failed to check 42 packages
+
+Issues with CRAN packages are summarised below.
+
+### New problems
+(This reports the first line of each new failure)
+
+* jfa
+  checking re-building of vignette outputs ... WARNING
+
+* SCORPIUS
+  checking tests ... ERROR
+
+### Failed to check
+
+* ale             (NA)
+* aPEAR           (NA)
+* bayesdfa        (NA)
+* BrailleR        (NA)
+* CausalImpact    (NA)
+* CensMFM         (NA)
+* cinaR           (NA)
+* fdacluster      (NA)
+* genekitr        (NA)
+* ggPMX           (NA)
+* grandR          (NA)
+* HeckmanEM       (NA)
+* immcp           (NA)
+* loon.ggplot     (NA)
+* MACP            (NA)
+* MarketMatching  (NA)
+* MARVEL          (NA)
+* MSclassifR      (NA)
+* nlmixr2         (NA)
+* nlmixr2extra    (NA)
+* nlmixr2plot     (NA)
+* nlmixr2rpt      (NA)
+* numbat          (NA)
+* oHMMed          (NA)
+* OlinkAnalyze    (NA)
+* OpenMx          (NA)
+* phylosem        (NA)
+* PsychWordVec    (NA)
+* RcppCensSpatial (NA)
+* rmsb            (NA)
+* rstanarm        (NA)
+* RVA             (NA)
+* SCpubr          (NA)
+* SSVS            (NA)
+* streamDAG       (NA)
+* TestAnaAPP      (NA)
+* tidySEM         (NA)
+* tinyarray       (NA)
+* TOmicsVis       (NA)
+* valse           (NA)
+* vivid           (NA)
+* xpose.nlmixr2   (NA)