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

[Adam H Sparks]

Thanks, Loïc, I read the NEWS but didn't fully understand/realise that was
what was happening here.

On 17 May 2016 at 18:03, Loïc Dutrieux <loic.dutrieux at wur.nl> wrote:

> 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.
>>
>>
>>
>>
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-- 
Adam Sparks
Associate Professor Field Crops Pathology
Centre for Crop Health
University of Southern Queensland
Toowoomba, QLD, AU

@adamhsparks <https://twitter.com/adamhsparks>

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