Error: [mask] raster has no values, with certain updatevalue

[mfisher5]

I'd like to set the updatevalue argument of the mask function to "-99" instead of NA. I want to apply a mask of counties (a SpatVector) to rasters of biomass, which may or may not have data for every county in the mask.

I'm able to run one of my rasters (file=SC_s1_2017.tif) through the following code, but the second (file=CC_SC_s1_2017.tif) is returning:

Error: [mask] raster has no values

The second raster is essentially the same as the first, with a slightly larger extent.

I'm running R v4.4.0 (2024-04-24 ucrt) with terra v1.7-82.

I copied some code below that reproduces the error, and attached the three files needed in a zipped folder. Please let me know if there is anything else I should include to help troubleshoot!

library(terra)
# This raster works
x1 <- rast("SC_s1_2017.tif")

# This raster doesn't
x2 <- rast("CC_SC_s1_2017.tif")

x1
#class       : SpatRaster 
#dimensions  : 7814, 10932, 1  (nrow, ncol, nlyr)
#resolution  : 0.000338, 0.00027  (x, y)
#extent      : -120.6634, -116.9684, 32.42012, 34.5299  (xmin, xmax, ymin, ymax)
#coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#source      : SC_Spores_per_cell_s1_2017-2020_30m_SpatRaster.tif 
#name        : Spores_per_cell_2017 
#min value   :          0.00000e+00 
#max value   :          1.50621e+14

x2
#class       : SpatRaster 
#dimensions  : 17268, 16349, 1  (nrow, ncol, nlyr)
#resolution  : 0.000338, 0.00027  (x, y)
#extent      : -122.4944, -116.9684, 32.42012, 37.08248  (xmin, xmax, ymin, ymax)
#coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#source      : CC_SC_Spores_per_cell_s1_2017-2024_30m_SpatRaster.tif 
#name        : Spores_per_cell_2017 
#min value   :         0.000000e+00 
#max value   :         1.725145e+14 

This is the mask, a SpatVector of California counties

county_waters3 <- readRDS("ca_counties_3nm_waters_20241009.RDS")
# project to same CRS as x
waters3_project <- terra::project(county_waters3,  x1)  

Mask a county not in the raster (too far north)

y <- waters3_project[waters3_project$subregion=='del_norte']
# Both of these work
x1_countyNA <- terra::mask(x1, mask=y, touches=TRUE, updatevalue=NA)
x1_county99 <- terra::mask(x1, mask=y, touches=TRUE, updatevalue=-99)

# So does this
x2_countyNA <- terra::mask(x2, mask=y, touches=TRUE, updatevalue=NA)

# But this doesn't
x2_county99 <- terra::mask(x2, mask=y, touches=TRUE, updatevalue=-99)
#Error: [mask] raster has no values**

terra_issue_mf.zip

[rhijmans]

I cannot reproduce this error. I assume you are not using the current version of "terra".

[rhijmans]

The version you mention is behind the current CRAN version. But instead of making a statement, I would need to see what is actually printed when you run library(terra) or what is returned by sessionInfo(). Can you please try with the current CRAN version and let me know if it works with that version?

[mfisher5]

I updated terra and re-started R, and am unfortunately still getting the same error message.
I'm waiting on IT to update R from v4.4.0 to 4.4.1; I can try it again once that is complete!

> library(terra)
terra 1.7.83
Warning message:
package ‘terra’ was built under R version 4.4.1 

> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] tidyterra_0.6.1 raster_3.6-30   sp_2.1-4        tictoc_1.2.1    here_1.0.1      magrittr_2.0.3  lubridate_1.9.3
 [8] forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2     readr_2.1.5     tidyr_1.3.1     tibble_3.2.1   
[15] ggplot2_3.5.1   tidyverse_2.0.0 terra_1.7-83   

loaded via a namespace (and not attached):
 [1] utf8_1.2.4         generics_0.1.3     class_7.3-22       KernSmooth_2.23-22 stringi_1.8.4      lattice_0.22-6    
 [7] hms_1.1.3          digest_0.6.37      evaluate_1.0.1     grid_4.4.0         timechange_0.3.0   fastmap_1.2.0     
[13] rprojroot_2.0.4    e1071_1.7-16       DBI_1.2.3          fansi_1.0.6        scales_1.3.0       codetools_0.2-20  
[19] cli_3.6.2          rlang_1.1.4        units_0.8-5        munsell_0.5.1      withr_3.0.2        yaml_2.3.10       
[25] tools_4.4.0        tzdb_0.4.0         colorspace_2.1-1   vctrs_0.6.5        R6_2.5.1           proxy_0.4-27      
[31] classInt_0.4-10    lifecycle_1.0.4    pkgconfig_2.0.3    pillar_1.9.0       gtable_0.3.6       data.table_1.16.2 
[37] glue_1.8.0         Rcpp_1.0.13-1      sf_1.0-18          xfun_0.49          tidyselect_1.2.1   rstudioapi_0.17.1 
[43] knitr_1.48         farver_2.1.2       htmltools_0.5.8.1  labeling_0.4.3     rmarkdown_2.29     compiler_4.4.0    

[mfisher5]

My R is now updated! And I am still getting the error.

> x2_county99 <- terra::mask(x2, mask=y, touches=TRUE, updatevalue=-99)
Error: [mask] raster has no values
> sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] tidyterra_0.6.1 raster_3.6-30   sp_2.1-4        tictoc_1.2.1    here_1.0.1      magrittr_2.0.3  lubridate_1.9.3
 [8] forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2     readr_2.1.5     tidyr_1.3.1     tibble_3.2.1   
[15] ggplot2_3.5.1   tidyverse_2.0.0 terra_1.7-83   

loaded via a namespace (and not attached):
 [1] utf8_1.2.4         generics_0.1.3     class_7.3-22       KernSmooth_2.23-24 stringi_1.8.4      lattice_0.22-6    
 [7] hms_1.1.3          digest_0.6.37      evaluate_1.0.1     grid_4.4.2         timechange_0.3.0   fastmap_1.2.0     
[13] rprojroot_2.0.4    e1071_1.7-16       DBI_1.2.3          fansi_1.0.6        scales_1.3.0       codetools_0.2-20  
[19] cli_3.6.2          rlang_1.1.4        units_0.8-5        munsell_0.5.1      withr_3.0.2        yaml_2.3.10       
[25] tools_4.4.2        tzdb_0.4.0         colorspace_2.1-1   vctrs_0.6.5        R6_2.5.1           proxy_0.4-27      
[31] classInt_0.4-10    lifecycle_1.0.4    pkgconfig_2.0.3    pillar_1.9.0       gtable_0.3.6       data.table_1.16.2 
[37] glue_1.8.0         Rcpp_1.0.13-1      sf_1.0-18          xfun_0.49          tidyselect_1.2.1   rstudioapi_0.17.1 
[43] knitr_1.48         farver_2.1.2       htmltools_0.5.8.1  labeling_0.4.3     rmarkdown_2.29     compiler_4.4.2    

[rhijmans]

Can you please run the code above (that I simplified) in a clean R session, outside of R Studio? Since this works for me in windows it really ought to work for you too. And if it does not that is most likely because an old session is interfering. R-Studio tends to load those. If an old session is loaded you can remote it with unlink(".RData") and close R and start again.

[mfisher5]

I ran my original code in R, outside of RStudio - I'm still getting the same error. Was there another version of the code that you meant to share with your previous comment?
I re-downloaded the files that I attached to my first comment on this issue, to make sure we're definitely using the same files.
I could try uninstalling and re-installing the base packages in the session, to make sure everything is up to date?

Thanks for taking so much time trying to figure this out!

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> library(here)
here() starts at C:/Users/marfishe/OneDrive - University of California, Davis/Documents
> library(terra)
terra 1.7.83
> x2 <- rast(here("california-kelp-SEN/R/testing/terra_issue/CC_SC_s1_2017.tif"))
> x2
class       : SpatRaster 
dimensions  : 17268, 16349, 1  (nrow, ncol, nlyr)
resolution  : 0.000338, 0.00027  (x, y)
extent      : -122.4944, -116.9684, 32.42012, 37.08248  (xmin, xmax, ymin, ymax)
coord. ref. : lon/lat WGS 84 (EPSG:4326) 
source      : CC_SC_s1_2017.tif 
name        : Spores_per_cell_2017 
min value   :         0.000000e+00 
max value   :         1.725145e+14 
> county_waters3 <- readRDS(here("california-kelp-SEN/R/testing/terra_issue/ca_counties_3nm_waters_20241009.RDS"))
> county_waters3
 class       : SpatVector 
 geometry    : polygons 
 dimensions  : 25, 1  (geometries, attributes)
 extent      : -124.475, -117.097, 32.53501, 41.99988  (xmin, xmax, ymin, ymax)
 coord. ref. : lon/lat WGS 84 (EPSG:4326) 
 names       :   subregion
 type        :       <chr>
 values      :   del_norte
                  humboldt
               los_angeles
> waters3_project <- terra::project(county_waters3,  x2)
> waters3_project
 class       : SpatVector 
 geometry    : polygons 
 dimensions  : 25, 1  (geometries, attributes)
 extent      : -124.475, -117.097, 32.53501, 41.99988  (xmin, xmax, ymin, ymax)
 coord. ref. : lon/lat WGS 84 (EPSG:4326) 
 names       :   subregion
 type        :       <chr>
 values      :   del_norte
                  humboldt
               los_angeles
> y <- waters3_project[waters3_project$subregion=='del_norte']
> plot(y)
> y
 class       : SpatVector 
 geometry    : polygons 
 dimensions  : 1, 1  (geometries, attributes)
 extent      : -124.3227, -124.0652, 41.46474, 41.99988  (xmin, xmax, ymin, ymax)
 coord. ref. : lon/lat WGS 84 (EPSG:4326) 
 names       : subregion
 type        :     <chr>
 values      : del_norte
> x2_county99 <- terra::mask(x2, mask=y, touches=TRUE, updatevalue=-99)
Error: [mask] raster has no values

> sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] terra_1.7-83 here_1.0.1  

loaded via a namespace (and not attached):
[1] compiler_4.4.2   rprojroot_2.0.4  tools_4.4.2      Rcpp_1.0.13-1    codetools_0.2-20

[kadyb]

I could reproduce this issue. Could @rhijmans reproduce if you set the terraOptions(memfrac=0.1) maybe?

[rhijmans]

I think this has now been fixed. I was able to reproduce the problem with terraOptions(todisk=TRUE).

[kadyb]

I tested and after updating to dev version, this example works for me.

[mfisher5]

It's working for me too! thanks so much!