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I'm trying to replicate the following example from package getCRUCLdata:

# Create a raster stack of temperature from tmp
# files in the tempdir() directory.
download.file(
   url = "https://crudata.uea.ac.uk/cru/data/hrg/tmc/grid_10min_tmp.dat.gz",
   destfile = file.path(tempdir(), "grid_10min_tmp.dat.gz")
)
CRU_tmp <- create_CRU_stack(tmp = TRUE, dsn = tempdir())
CRU_tmpcode here

However, all that I get is an error message: 'gzip' not recognized as an internal or external command, operable program or batch file. Can anybody tell me how to fix this?

I'm running on:

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252    
LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                       
LC_TIME=Portuguese_Brazil.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] R.utils_2.9.0      R.oo_1.22.0        R.methodsS3_1.7.1  getCRUCLdata_0.3.0 
raster_2.9-5       sp_1.3-1          

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1        lattice_0.20-38   codetools_0.2-16  digest_0.6.19     
hoardr_0.5.2      rappdirs_0.3.1    grid_3.6.0        R6_2.4.0          
data.table_1.12.2 rgdal_1.4-3       tools_3.6.0      
[12] compiler_3.6.0   

Alternatively, I would like to know how to convert the .dat file, obtained by decompressing the file downloadable from the link in the example, to a raster stack.

3

Code in that package uses gzip to decompress the .gz file:

   wvar <- data.frame(data.table::fread(cmd = paste0("gzip -dc ", 
        files[[1]]), header = FALSE))

gzip is a standard utility with Linux but must be an optional extra for Windows that you don't have, or R isn't finding the gzip binary executable.

Its possible that R code should use the value of the R_GZIPCMD environment variable instead of expecting it in the search path. Perhaps you should file an issue on the package to replace their explicit fread(cmd="gzip....") with something that gets the gzip command from this variable:

> message(Sys.getenv("R_GZIPCMD"))
/bin/gzip -n
  • Thanks, @Spacedman. The interesting situation is that I, indeed, can use gzip out from create_CRU_stack... too strange – perep1972 Jul 27 at 14:39

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