Remove outdated dependencies; use testthat-3e

See #833

Author: jcheng5

DESCRIPTION

@@ -43,7 +43,7 @@ Imports:
     methods,
     png,
     RColorBrewer,
-    raster,
+    raster (>= 3.6.3),
     scales (>= 1.0.0),
     sp,
     stats,
@@ -54,8 +54,6 @@ Suggests:
     maps,
     sf (>= 0.9-6),
     shiny,
-    rgdal,
-    rgeos,
     R6,
     RJSONIO,
     purrr,
@@ -65,3 +63,4 @@ Suggests:
 RoxygenNote: 7.2.1
 Encoding: UTF-8
 LazyData: true
+Config/testthat/edition: 3

R/layers.R

@@ -232,10 +232,9 @@ epsg3857 <- "+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y
 #' values(r) <- matrix(1:900, nrow(r), ncol(r), byrow = TRUE)
 #' crs(r) <- CRS("+init=epsg:4326")
 #'
-#' if (requireNamespace("rgdal")) {
-#'   leaflet() %>% addTiles() %>%
-#'     addRasterImage(r, colors = "Spectral", opacity = 0.8)
-#' }}
+#' leaflet() %>% addTiles() %>%
+#'   addRasterImage(r, colors = "Spectral", opacity = 0.8)
+#' }
 #' @export
 addRasterImage <- function(
   map,

R/normalize-sp.R

@@ -90,11 +90,24 @@ to_multipolygon_list.SpatialPolygons <- function(pgons) {
 to_multipolygon.Polygons <- function(pgons) {
   if (length(pgons@Polygons) > 1) {
     # If Polygons contains more than one Polygon, then we may be dealing with
-    # a polygon with holes or a multipolygon (potentially with holes). Use
-    # createPolygonsComment to validate and determine what the situation is.
+    # a polygon with holes or a multipolygon (potentially with holes). We used
+    # to use rgeos::createPolygonsComment, but rgeos has been deprecated, so now
+    # we use sf.
     comment <- comment(pgons)
-    if (is.null(comment) || comment == "FALSE")
-      comment <- rgeos::createPolygonsComment(pgons)
+    if (is.null(comment) || comment == "FALSE") {
+      if (any(vapply(pgons@Polygons, methods::slot, logical(1), "hole"))) {
+        if (!require("sf")) {
+          stop("You attempted to use an sp Polygons object that is missing hole ",
+            "information. Leaflet can use the {sf} package to infer hole ",
+            "assignments, but it is not installed. Please install the {sf} ",
+            "package, and try the operation again.")
+        }
+        x <- to_multipolygon_list(sf::st_geometry(sf::st_as_sf(SpatialPolygons(list(pgons)))))
+        return(x[[1]])
+      } else {
+        comment <- paste(collapse = " ", rep_len("0", length(pgons@Polygons)))
+      }
+    }
     pstatus <- as.integer(strsplit(comment, " ")[[1]])
     lapply(which(pstatus == 0L), function(index) {
       # Return a list of rings, exterior first

docs/raster.Rmd

@@ -4,37 +4,31 @@ pagetitle: Leaflet for R - Raster Images
 
 ## Raster Images
 
-Two-dimensional `RasterLayer` objects (from the [`raster` package](http://CRAN.R-project.org/package=raster)) can be turned into images and added to Leaflet maps using the `addRasterImage` function.
+Two-dimensional `SpatRaster` objects (from the [`terra` package](https://CRAN.R-project.org/package=terra)) or `RasterLayer` objects (from the [`raster` package](https://CRAN.R-project.org/package=raster)) can be turned into images and added to Leaflet maps using the `addRasterImage` function.
 
-The `addRasterImage` function works by projecting the `RasterLayer` object to [EPSG:3857](http://spatialreference.org/ref/sr-org/7483/) and encoding each cell to an RGBA color, to produce a PNG image. That image is then embedded in the map widget.
+The `addRasterImage` function works by projecting the `SpatRaster` or `RasterLayer` object to [EPSG:3857](http://spatialreference.org/ref/sr-org/7483/) and encoding each cell to an RGBA color, to produce a PNG image. That image is then embedded in the map widget.
 
-It's important that the `RasterLayer` object is tagged with a proper coordinate reference system. Many raster files contain this information, but some do not. Here is how you'd tag a raster layer object "`r`" which contains WGS84 data:
+It's important that the raster object is tagged with a proper coordinate reference system. Many raster files contain this information, but some do not. Here is how you'd tag a raster object "`r`" which contains WGS84 data:
 
 ```r
-crs(r) <- sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
+crs(r) <- "+proj=longlat +datum=WGS84"
 ```
 
 ### Large Raster Warning
 
 Because the `addRasterImage` function embeds the image in the map widget, it will increase the size of the generated HTML proportionally. In order to avoid unacceptable download times and memory usage, `addRasterImage` will error when the PNG is beyond the size indicated by the `maxBytes` argument (defaults to 4 megabytes).
 
-If you have a large raster layer, you can provide a larger number of bytes and see how it goes, or use `raster::resample` or `raster::aggregate` to decrease the number of cells.
+If you have a large raster layer, you can provide a larger number of bytes and see how it goes, or use `terra::resample`, `raster::resample`, or `raster::aggregate` to decrease the number of cells.
 
 ### Projection Performance
 
-The `addRasterImage` function projects using `raster::projectRaster`, which can take a while on all but the smallest rasters. To improve performance, the first thing to do is install a new version of `raster`; version 2.4 includes optimizations that speed up bilinear projection by about 10X. This version has not yet been released to CRAN at the time of this writing (June 17, 2015) but can be installed directly from R-Forge:
-
-```r
-install.packages('raster', repos = 'http://r-forge.r-project.org/', type = 'source')
-```
-
-If you have a large raster layer or expect to call `addRasterImage` on the same raster layer many times, you can perform the [EPSG:3857](http://spatialreference.org/ref/sr-org/7483/) projection yourself (either using `leaflet::projectRasterForLeaflet` or using another GIS library or program) and call `addRasterImage` with `project = FALSE`.
+The `addRasterImage` function projects using `terra::project` or `raster::projectRaster`, which can take a while on all but the smallest rasters. If you have a large raster layer or expect to call `addRasterImage` on the same raster layer many times, you can perform the [EPSG:3857](http://spatialreference.org/ref/sr-org/7483/) projection yourself (either using `leaflet::projectRasterForLeaflet` or using another GIS library or program) and call `addRasterImage` with `project = FALSE`.
 
 Be sure that your pre-projected raster layer is tagged with an accurate extent and CRS, as these values are still needed to place the image in the proper position on the map.
 
 ### Coloring
 
-In order to render the `RasterLayer` as an image, each cell value must be converted to an RGB(A) color. You can specify the color scale using the `colors` argument, which accepts a variety of color specifications:
+In order to render the raster object as an image, each cell value must be converted to an RGB(A) color. You can specify the color scale using the `colors` argument, which accepts a variety of color specifications:
 
 * The name of a [Color Brewer 2](http://colorbrewer2.org/) palette. If no `colors` argument is provided, then `"Spectral"` is the default.
 * A vector that represents the ordered list of colors to map to the data. Any color specification that is accepted by `grDevices::col2rgb` can be used, including `"#RRGGBB"` and `"#RRGGBBAA"` forms. Example: `colors = c("#E0F3DB", "#A8DDB5", "#43A2CA")`.

man/addRasterImage.Rd

@@ -0,0 +1,53 @@
+# normalize
+
+    [[1]]
+    [[1]][[1]]
+    [[1]][[1]][[1]]
+      lng lat
+    1  -1   1
+    2   1   1
+    3   1  -1
+    4  -1  -1
+    5  -1   1
+    
+    [[1]][[1]][[2]]
+       lng  lat
+    1 -0.5 -0.5
+    2  0.5 -0.5
+    3  0.5  0.5
+    4 -0.5  0.5
+    5 -0.5 -0.5
+    
+    
+    [[1]][[2]]
+    [[1]][[2]][[1]]
+      lng lat
+    1   4   6
+    2   6   6
+    3   6   4
+    4   4   4
+    5   4   6
+    
+    [[1]][[2]][[2]]
+      lng lat
+    1 4.5 4.5
+    2 5.5 4.5
+    3 5.5 5.5
+    4 4.5 5.5
+    5 4.5 4.5
+    
+    [[1]][[2]][[3]]
+       lng  lat
+    1 4.05 4.05
+    2 4.45 4.05
+    3 4.45 4.45
+    4 4.05 4.45
+    5 4.05 4.05
+    
+    
+    
+    attr(,"bbox")
+        [,1] [,2]
+    lng   -1    6
+    lat   -1    6
+

tests/testthat/_snaps/normalize-2.md

@@ -1,5 +1,3 @@
-context("colors")
-
 # Like expect_warning, but returns the result of the expr
 with_warning <- function(expr) {
   expect_warning(result <- force(expr))

tests/testthat/test-colors.R

@@ -1,9 +1,3 @@
-
-
-context("evalFormula")
-
-
-
 test_that("evalFormula() does not discard the class of a list", {
   res <- evalFormula(structure(list(1, ~x, ~x + 1), class = "FOO"), data.frame(x = 2))
 

tests/testthat/test-evalFormula.R

@@ -1,6 +1,3 @@
-
-context("icon")
-
 test_that("icon deduping works", {
   icons <- c("leaf-green.png", "leaf-red.png")
   m <-

tests/testthat/test-icon.R

@@ -1,6 +1,3 @@
-
-context("measure")
-
 test_that("dependency got added", {
   expect_true(
     !is.na(Position(

tests/testthat/test-measure.R

@@ -2,12 +2,11 @@
 expect_maps_equal <- function(m1, m2) {
   attr(m1$x, "leafletData") <- NULL
   attr(m2$x, "leafletData") <- NULL
-  expect_equal(m1, m2, check.environment = FALSE)
+  expect_equal(m1, m2, ignore_function_env = TRUE, ignore_formula_env = TRUE)
 }
 
 test_that("normalize", {
   skip_if_not_installed("sf")
-  skip_if_not_installed("rgeos")
 
   library(sf)
   library(sp)
@@ -101,12 +100,15 @@ test_that("normalize", {
       create_square(1, 5, 5, hole = TRUE),
       create_square(0.4, 4.25, 4.25, hole = TRUE)
     ), "A")
-  comment(polys) <- rgeos::createPolygonsComment(polys)
+  comment(polys) <- "0 0 1 2 2"
 
   spolys <- SpatialPolygons(list(
     polys
   ))
   stspolys <- st_as_sf(spolys)
+
+  testthat::expect_snapshot_output(derivePolygons(spolys))
+
   (l101 <- leaflet(spolys) %>% addPolygons())
   (l102 <- leaflet(stspolys) %>% addPolygons())
   expect_maps_equal(l101, l102)

tests/testthat/test-normalize-2.R

@@ -2,7 +2,7 @@
 expect_maps_equal <- function(m1, m2) {
   attr(m1$x, "leafletData") <- NULL
   attr(m2$x, "leafletData") <- NULL
-  expect_equal(m1, m2, check.environment = FALSE)
+  expect_equal(m1, m2, ignore_function_env = TRUE, ignore_formula_env = TRUE)
 }
 
 
@@ -75,12 +75,12 @@ test_that("normalize terra", {
       create_square(1, 5, 5, hole = TRUE),
       create_square(0.4, 4.25, 4.25, hole = TRUE)
     ), "A")
-  comment(polys) <- rgeos::createPolygonsComment(polys)
+  comment(polys) <- "0 0 1 2 2"
 
   spolys <- SpatialPolygons(list(
     polys
   ))
-  # these "commented" Spatial objects need to go through 
+  # these "commented" Spatial objects need to go through
   # sf for terra to understand them properly
   vpolys = vect(sf::st_as_sf(spolys ))
   (l101 <- leaflet(spolys) %>% addPolygons())

tests/testthat/test-normalize-3.R

@@ -1,5 +1,3 @@
-context("normalize")
-
 # derivePoints -------------------------------------------------------------
 
 test_that("can get point data from SpatialPointsDataFrame", {
@@ -27,13 +25,13 @@ test_that("derivePolygons works with sf classes", {
 
 verifyPolygonData <- function(x) {
   expect_true(!is.null(attr(x, "bbox", exact = TRUE)))
-  expect_is(x, "list")
+  expect_type(x, "list")
   lapply(x, function(multipolygon) {
-    expect_is(multipolygon, "list")
+    expect_type(multipolygon, "list")
     lapply(multipolygon, function(polygon) {
-      expect_is(polygon, "list")
+      expect_type(polygon, "list")
       lapply(polygon, function(ring) {
-        expect_is(ring, "data.frame")
+        expect_s3_class(ring, "data.frame")
       })
     })
   })
@@ -50,7 +48,7 @@ test_that("derivePolygons normalizes polygon data across sp polygon classes", {
   expect_equal(out[[1]][[1]][[1]]$lng, meuse.riv[, 1])
   expect_equal(out[[1]][[1]][[1]]$lat, meuse.riv[, 2])
   # row/col names are different but values are the same
-  expect_equivalent(attr(out, "bbox"), sp::bbox(meuse.riv))
+  expect_equal(attr(out, "bbox"), sp::bbox(meuse.riv), ignore_attr = TRUE)
 
   polys <- sp::Polygons(list(poly), "river")
   expect_equal(derivePolygons(polys), out)
@@ -72,7 +70,7 @@ test_that("derivePolygons normalizes polygon data across sp line classes", {
   expect_equal(out[[1]][[1]][[1]]$lng, meuse.riv[, 1])
   expect_equal(out[[1]][[1]][[1]]$lat, meuse.riv[, 2])
   # row/col names are different but values are the same
-  expect_equivalent(attr(out, "bbox"), sp::bbox(meuse.riv))
+  expect_equal(attr(out, "bbox"), sp::bbox(meuse.riv), ignore_attr = TRUE)
 
   lines <- sp::Lines(list(line), "river")
   expect_equal(derivePolygons(lines), out)

tests/testthat/test-normalize.R

@@ -2,27 +2,32 @@
 expect_maps_equal <- function(m1, m2) {
   attr(m1$x, "leafletData") <- NULL
   attr(m2$x, "leafletData") <- NULL
-  expect_equal(m1, m2, check.environment = FALSE)
+  expect_equal(m1, m2, ignore_function_env = TRUE, ignore_formula_env = TRUE)
 }
 
+# Some proj4string values differ only by one having whole numbers represented as
+# x while others have x.0. So, strip each trailing .0 value.
+normalize_zero_values <- function(str) {
+  gsub("=(\\d+).0( |$)", "=\\1\\2", str)
+}
 
 test_that("rasters", {
   skip_if_not_installed("terra")
 
   library(terra)
-  library(raster) 
+  library(raster)
 
   lux <- rast(system.file("ex/elev.tif", package="terra"))
   pmerc <- "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs"
 
   plux <- projectRasterForLeaflet(lux, "bilinear")
-  expect_equal(crs(plux, proj=TRUE), pmerc)
+  expect_equal(normalize_zero_values(crs(plux, proj=TRUE)), pmerc)
   test <- projectRasterForLeaflet(raster(lux), "bilinear")
-  expect_equal(proj4string(test), pmerc)
+  expect_equal(normalize_zero_values(proj4string(test)), pmerc)
 
   # terra and raster have different projection algorithms, and while
-  # their outputs are very similar, they are not identical. Hence we need 
-  # to use pre-projected rasters and project=FALSE  
+  # their outputs are very similar, they are not identical. Hence we need
+  # to use pre-projected rasters and project=FALSE
   rtest <- function(x) {
     leaflet() %>% addTiles() %>% addRasterImage(x, project=FALSE)
   }