[R-sig-Geo] Warning when stacking, masking or cropping raster objects

[Loïc Dutrieux]

It's related to a change in R, not in raster. See "DEPRECATED AND 
DEFUNCT" related to R 3.3.0 in https://cran.r-project.org/src/base/NEWS

Cheers,
Loïc

On 05/17/2016 06:20 AM, Thiago V. dos Santos via R-sig-Geo wrote:
> I also noticed those warnings after the last raster update. Here is one simple way to reproduce them:
>
>
> library(raster)
> r <- raster(nrows=100, ncols=100, xmn=5, xmx=10, ymn=46, ymx=51)
> r[] <- 1:ncell(r)
>
> # crop raster with a SpatialPolygon* object
> if (require(rgdal) & require(rgeos)) {
> p <- shapefile(system.file("external/lux.shp", package="raster"))
> }
>
> # Crop and mask
> rc <- crop(r, extent(p))
> rc <- mask(rc, p)
>
>
> I wonder if there are new instructions to crop/mask rasters that are not yet documented...
> Greetings,
>   -- Thiago V. dos Santos
>
> PhD student
> Land and Atmospheric Science
> University of Minnesota
>
>
>
> On Tuesday, May 10, 2016 1:45 AM, Adam H Sparks <adamhsparks at gmail.com> wrote:
> Hi all,
> I'm working on a vignette from the R-OpenSci auunconf,
> https://github.com/saundersk1/auunconf16/blob/master/Vignette%20BoM.Rmd,
> and am suddenly getting warning messages where I've never had any before
> with this process.
>
> In the "Australian Water Availability Project (AWAP)" section, at the very
> end of the file, some grid files are downloaded and saved and GADM level 2
> data are fetched to do cropping and masking.
>
> Two weeks ago when we put this together it all worked with no error
> messages. Today as I'm working on cleaning up the vignette I'm getting
> error messages I've never seen before when doing these things.
>
> For example, the line:
> cfiles <- stack(dir(pattern = "grid$"))
>
> Now returns these warning messages:
> Warning messages:
> 1: In `[<-`(`*tmp*`, j, value = <S4 object of class "RasterLayer">) :
>    implicit list embedding of S4 objects is deprecated
> 2: In `[<-`(`*tmp*`, j, value = <S4 object of class "RasterLayer">) :
>    implicit list embedding of S4 objects is deprecated
> 3: In `[<-`(`*tmp*`, j, value = <S4 object of class "RasterLayer">) :
>    implicit list embedding of S4 objects is deprecated
> 4: In `[<-`(`*tmp*`, j, value = <S4 object of class "RasterLayer">) :
>    implicit list embedding of S4 objects is deprecated
> 5: In `[<-`(`*tmp*`, j, value = <S4 object of class "RasterLayer">) :
>    implicit list embedding of S4 objects is deprecated
> 6: In `[<-`(`*tmp*`, j, value = <S4 object of class "RasterLayer">) :
>    implicit list embedding of S4 objects is deprecated
> 7: In `[<-`(`*tmp*`, nl, value = r) :
>    implicit list embedding of S4 objects is deprecated
>
> When I try to mask I get similar messages about the implicit list embedding
> of S4 objects being deprecated.
>
> For now in the vignette I've suppressed the warning messages as the code
> appears to work, it just gives these warnings, but I'd like to understand
> why I'm getting them.
>
>
>