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:.
> xy = expand.grid(x = 1:4, y = 1:4)
> xy.sp = SpatialPoints(xy)
> gridded(xy.sp) = T
> # deselect 1 row and 2 col:
> tst = xy.sp[-c(2,6,10,14,9,11,12)]
> tst
Object of class SpatialPixels
Grid topology:
  cellcentre.offset cellsize cells.dim
x                 1        1         4
y                 1        1         4
SpatialPoints:
      x y
 [1,] 1 1
 [2,] 3 1
 [3,] 4 1
 [4,] 1 2
 [5,] 3 2
 [6,] 4 2
 [7,] 1 4
 [8,] 3 4
 [9,] 4 4
Coordinate Reference System (CRS) arguments: NA 
> # convert to SpatialPixelsDataFrame:
> tst = SpatialPixelsDataFrame(tst, data.frame(xx = rnorm(9)))
> spplot(tst["xx"], main = "empty row + col")
> 
> proc.time()
   user  system elapsed 
   0.73    0.12    0.84