R Under development (unstable) (2023-09-30 r85239 ucrt) -- "Unsuffered Consequences"
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> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
> data(meuse)
> x = meuse
> 
> coordinates(x) <- c("x", "y")
> try(proj4string(x) <- 1.5)
Error : unable to find an inherited method for function 'proj4string<-' for signature 'obj = "SpatialPointsDataFrame", value = "numeric"'
> try(coordinates(a) <- cbind(1:10, 10:1))
Error : object 'a' not found
> # fails because a is not found; passes if a assigned NULL, see pass1.R
> 
> x = meuse
> # invalid coordinate formulae:
> try(coordinates(x) <- ~log(x)+sqrt(y)) # no expressions allowed
Error in `[.data.frame`(object, , -coord.numbers, drop = FALSE) : 
  undefined columns selected
> try(coordinates(x) <- ~x+y+z) # z is not present
Error in eval(predvars, data, env) : object 'z' not found
> x$x2 = x$x^2
> x$y2 = x$y^2
> try(coordinates(x) <- ~x+y+x2+y2) # 4D now passes check...
> x = meuse
> try(coordinates(x) <- ~x) # 1D not allowed
Error in validObject(.Object) : 
  invalid class "SpatialPoints" object: spatial.dimension should be 2 or more
> 
> # is.na.sp.coords
> a = data.frame(cbind(xx=c(1,NA,2,10),yy=c(2,NA,NA,20)))
> try(coordinates(a) <- c("xx", "yy")) # should fail!
Error in `coordinates<-`(`*tmp*`, value = c("xx", "yy")) : 
  coordinates are not allowed to contain missing values
> 
> x = meuse[1:4,]
> coordinates(x) = c(1,2)
> # this should fail -- zinc is not a row:
> #(and will break automatic testing, so outcommented!)
> #try(q <- x["zinc",])
> # this will issue warning under S-Plus, or a silent rename under R
> try(x[c("zinc", "copper", "zinc")])
       coordinates zinc copper zinc.1
1 (181072, 333611) 1022     85   1022
2 (181025, 333558) 1141     81   1141
3 (181165, 333537)  640     68    640
4 (181298, 333484)  257     81    257
> 
> # this will fail, as "x" is not in the data part:
> try(x[c("zinc", "x", "copper", "zinc")])
Error in `[.data.frame`(x@data, i, j, ..., drop = FALSE) : 
  undefined columns selected
> 
> # row index containing missing values will fail:
> try(xx <- x[c(1:3,NA),])
Error in x[c(1:3, NA), ] : NAs not permitted in row index
> 
> xx = data.frame(x=1:10, y=1:10)
> 
> # fails; use SpatialPoints() to create points without attribute 
> try(coordinates(xx) <- c("x", "y")) 
> 
> x = matrix(3, 5, 2)
> dimnames(x) = list(c(1,1:4), NULL)
> y = data.frame(a = 1:5, b = 5:1)
> try(SpatialPointsDataFrame(x, y)) # will complain:
Error in SpatialPointsDataFrame(x, y) : 
  row.names of data and dimnames of coords do not match
In addition: Warning message:
In SpatialPointsDataFrame(x, y) :
  forming a SpatialPointsDataFrame based on maching IDs, not on record order. Use match.ID = FALSE to match on record order
> SpatialPointsDataFrame(x, y, match.ID = FALSE) # won't complain
  coordinates a b
1      (3, 3) 1 5
2      (3, 3) 2 4
3      (3, 3) 3 3
4      (3, 3) 4 2
5      (3, 3) 5 1
Warning messages:
1: In validityMethod(object) :
  duplicate rownames are interpreted by rgeos as MultiPoints; use SpatialMultiPoints to define these; in future sp versions this warning will become an error
2: In validityMethod(as(object, superClass)) :
  duplicate rownames are interpreted by rgeos as MultiPoints; use SpatialMultiPoints to define these; in future sp versions this warning will become an error
> 
> Sr1 = Polygon(cbind(c(2,4,4,1,2),c(2,3,5,4,2)))
> Sr2 = Polygon(cbind(c(5,4,2,5),c(2,3,2,2)))
> Sr3 = Polygon(cbind(c(4,4,5,10,4),c(5,3,2,5,5)))
> Sr4 = Polygon(cbind(c(5,6,6,5,5),c(4,4,3,3,4)), hole = TRUE)
> 
> Srs1 = Polygons(list(Sr1), "s1")
> Srs2 = Polygons(list(Sr2), "s2")
> Srs3 = Polygons(list(Sr3, Sr4), "s2")
> try(SR <- SpatialPolygons(list(Srs1,Srs2,Srs3))) # will complain
Error in validObject(res) : 
  invalid class "SpatialPolygons" object: non-unique Polygons ID slot values
> Srs3 = Polygons(list(Sr3, Sr4), "s3/4")
> SR = SpatialPolygons(list(Srs1,Srs2,Srs3)) # won't complain
> try(SRx <- SR[c(1,2,NA),])
Error in SR[c(1, 2, NA), ] : NAs not permitted in row index
> 
> attr = data.frame(a=1:3, b=3:1, row.names=c("s1", "s2", "s3"))
> try(SrDf <- SpatialPolygonsDataFrame(SR, attr)) # will complain
Error in SpatialPolygonsDataFrame(SR, attr) : 
  row.names of data and Polygons IDs do not match
> SrDf = SpatialPolygonsDataFrame(SR, attr, match.ID = FALSE) # won't complain
> attr = data.frame(a=1:3, b=3:1, row.names=c("s1", "s2", "s3/4"))
> SrDf = SpatialPolygonsDataFrame(SR, attr) # won't complain
> 
> l1 = cbind(c(1,2,3),c(3,2,2))
> l1a = cbind(l1[,1]+.05,l1[,2]+.05)
> l2 = cbind(c(1,2,3),c(1,1.5,1))
> Sl1 = Line(l1)
> Sl1a = Line(l1a)
> Sl2 = Line(l2)
> S1 = Lines(list(Sl1, Sl1a), ID="a")
> S2 = Lines(list(Sl2), ID="b")
> S3 = Lines(list(Sl2), ID="a")
> Sl = SpatialLines(list(S1,S2)) # won't complain
> try(Sl1 <- SpatialLines(list(S1,S3))) # will complain
Error in validObject(.Object) : 
  invalid class "SpatialLines" object: non-unique Lines ID slot values
> try(Sl1 <- Sl[c(NA,2),]) # will fail
Error in Sl[c(NA, 2), ] : NAs not permitted in row index
> 
> df = data.frame(z = c(1,2), row.names=sapply(slot(Sl, "lines"), function(x) slot(x, "ID")))
> Sldf = SpatialLinesDataFrame(Sl, data = df) # won't complain
> df1 = data.frame(z = c(1,2))
> try(Sldf1 <- SpatialLinesDataFrame(Sl, data = df1)) # will complain
Error in SpatialLinesDataFrame(Sl, data = df1) : 
  row.names of data and Lines IDs do not match
> Sldf1 = SpatialLinesDataFrame(Sl, data = df1, match.ID = FALSE) # won't complain
> try(Sldf1 <- Sldf1[c(1,NA),])
Error in Sldf1[c(1, NA), ] : NAs not permitted in row index
> 
> data(meuse.grid)
> gridded(meuse.grid) = ~x+y
> try(x <- meuse.grid[c(1:10,NA,12),])
Error in meuse.grid[c(1:10, NA, 12), ] : NAs not permitted in row index
> fullgrid(meuse.grid) = TRUE
> try(x <- meuse.grid[c(1:10,NA,12),])
Error in meuse.grid[c(1:10, NA, 12), ] : NAs not permitted in index
> 
> try(x <- meuse[[c("zinc", "cadmium")]])
Error in .subset2(x, i, exact = exact) : subscript out of bounds
> try(meuse[[c("zn", "cd")]] <- cbind(meuse$zinc, meuse$cadmium))
Error in `[[<-`(`*tmp*`, i, value = value) : no such index at level 1

> 
> data(meuse.grid)
> coordinates(meuse.grid) <- c("x", "y")
> gridded(meuse.grid) <- TRUE
> gridparameters(meuse.grid)
  cellcentre.offset cellsize cells.dim
x            178460       40        78
y            329620       40       104
> 
> image(meuse.grid)
> image(meuse.grid[2])
> image(meuse.grid, 2)
> try(image(meuse.grid, 0))
Error in .subset2(x, i, exact = exact) : subscript out of bounds
> image(meuse.grid[3], breaks=c(0,.2,.5,.8,1), col = bpy.colors(4))
> image(meuse.grid, 3, zlim = c(0,.3))
> image(meuse.grid, 3, zlim = c(.3,.1))
> image(meuse.grid, 3, zlim = c(.2,.8))
> image(meuse.grid, 3, zlim = c(.2,.8), breaks = c(.2,.4,.6,.8), 
+ 	col = bpy.colors(3))
> 
> data(meuse.grid)
> set.seed(1)
> meuse.grid$x <- meuse.grid$x + rnorm(length(meuse.grid$x), 0, 0.0002)
> meuse.grid$y <- meuse.grid$y + rnorm(length(meuse.grid$y), 0, 0.0002)
> coordinates(meuse.grid) <- c("x", "y")
> try(gridded(meuse.grid) <- TRUE)
suggested tolerance minimum: 0.964318 
Error in points2grid(points, tolerance, round) : 
  dimension 1 : coordinate intervals are not constant
> try(meuse.grid <- SpatialPixelsDataFrame(as(meuse.grid, "SpatialPoints"),
+   data=as(meuse.grid, "data.frame"), tolerance=0.077))
> gridparameters(meuse.grid)
  cellcentre.offset cellsize cells.dim
x            178460 39.99912        78
y            329620 39.99920       104
> 
> data(meuse.grid_ll)
> try(gridded(meuse.grid_ll) <- TRUE)
suggested tolerance minimum: 0.818323 
Error in points2grid(points, tolerance, round) : 
  dimension 1 : coordinate intervals are not constant
> try(meuse.grid_ll <- SpatialPixelsDataFrame(as(meuse.grid_ll, "SpatialPoints"), data=as(meuse.grid_ll, "data.frame"), tolerance=0.9))
> gridparameters(meuse.grid_ll)
  cellcentre.offset     cellsize cells.dim
x          5.721109 0.0005312853        84
y         50.955770 0.0003318105       112
> 
> try(CRS("+proj=latlon +ellps=WGS84"))
Coordinate Reference System:
Deprecated Proj.4 representation: +proj=longlat +ellps=WGS84 +no_defs 
WKT2 2019 representation:
GEOGCRS["unknown",
    DATUM["Unknown based on WGS84 ellipsoid",
        ELLIPSOID["WGS 84",6378137,298.257223563,
            LENGTHUNIT["metre",1],
            ID["EPSG",7030]]],
    PRIMEM["Greenwich",0,
        ANGLEUNIT["degree",0.0174532925199433],
        ID["EPSG",8901]],
    CS[ellipsoidal,2],
        AXIS["longitude",east,
            ORDER[1],
            ANGLEUNIT["degree",0.0174532925199433,
                ID["EPSG",9122]]],
        AXIS["latitude",north,
            ORDER[2],
            ANGLEUNIT["degree",0.0174532925199433,
                ID["EPSG",9122]]]] 
> try(CRS("+proj=lonlat +ellps=WGS84"))
Coordinate Reference System:
Deprecated Proj.4 representation: +proj=longlat +ellps=WGS84 +no_defs 
WKT2 2019 representation:
GEOGCRS["unknown",
    DATUM["Unknown based on WGS84 ellipsoid",
        ELLIPSOID["WGS 84",6378137,298.257223563,
            LENGTHUNIT["metre",1],
            ID["EPSG",7030]]],
    PRIMEM["Greenwich",0,
        ANGLEUNIT["degree",0.0174532925199433],
        ID["EPSG",8901]],
    CS[ellipsoidal,2],
        AXIS["longitude",east,
            ORDER[1],
            ANGLEUNIT["degree",0.0174532925199433,
                ID["EPSG",9122]]],
        AXIS["latitude",north,
            ORDER[2],
            ANGLEUNIT["degree",0.0174532925199433,
                ID["EPSG",9122]]]] 
> 
> proc.time()
   user  system elapsed 
   0.82    0.18    0.96