All the warnings

[Maschette]

Soooo I updated all my packages and now get a warning frenzy when I call SOmap()

Is this a reproj thing @mdsumner?

library(SOmap)
#> Loading required package: raster
#> Loading required package: sp

SOmap()
#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved
#> Loading required namespace: rgeos
#> Warning in proj4string(x): CRS object has comment, which is lost in output

#> Warning in proj4string(x): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved

#> Warning in proj4string(x): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved
#> Warning in proj4string(x): CRS object has comment, which is lost in output
#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved

#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved

#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved

#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved
#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on WGS84 ellipsoid in CRS definition,
#>  but +towgs84= values preserved

#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on WGS84 ellipsoid in CRS definition,
#>  but +towgs84= values preserved
#> Warning: st_crs<- : replacing crs does not reproject data; use st_transform for
#> that

#> Warning: st_crs<- : replacing crs does not reproject data; use st_transform for
#> that
#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum WGS_1984 in CRS definition,
#>  but +towgs84= values preserved
#> Warning in proj4string(x): CRS object has comment, which is lost in output
#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on WGS84 ellipsoid in CRS definition,
#>  but +towgs84= values preserved

#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on WGS84 ellipsoid in CRS definition,
#>  but +towgs84= values preserved

#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO"): Discarded datum Unknown based on WGS84 ellipsoid in CRS definition,
#>  but +towgs84= values preserved

sessionInfo()
#> R version 4.0.0 (2020-04-24)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 17134)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
#> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
#> [5] LC_TIME=English_Australia.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] SOmap_0.5.2.9999 raster_3.1-5     sp_1.4-2        
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.4.6       compiler_4.0.0     pillar_1.4.4       highr_0.8         
#>  [5] class_7.3-16       tools_4.0.0        digest_0.6.25      evaluate_0.14     
#>  [9] lifecycle_0.2.0    tibble_3.0.1       gtable_0.3.0       lattice_0.20-41   
#> [13] pkgconfig_2.0.3    rlang_0.4.6        DBI_1.1.0          reproj_0.4.2.9001 
#> [17] rgdal_1.5-10       yaml_2.2.1         xfun_0.14          e1071_1.7-3       
#> [21] stringr_1.4.0      dplyr_1.0.0        knitr_1.28         rgeos_0.5-3       
#> [25] generics_0.0.2     vctrs_0.3.1        classInt_0.4-3     grid_4.0.0        
#> [29] tidyselect_1.1.0   graticule_0.1.2    glue_1.4.1         sf_0.9-4          
#> [33] R6_2.4.1           rmarkdown_2.1      ggplot2_3.3.2      purrr_0.3.4       
#> [37] magrittr_1.5       units_0.6-7        scales_1.1.1       codetools_0.2-16  
#> [41] htmltools_0.4.0    ellipsis_0.3.1     proj4_1.0-10       assertthat_0.2.1  
#> [45] colorspace_1.4-1   KernSmooth_2.23-16 stringi_1.4.6      munsell_0.5.0     
#> [49] crayon_1.3.4

^{Created on 2020-06-25 by the reprex package (v0.3.0)}

[mdsumner]

ignore it, it's meaningless we can't do much about it apart from

options(warn = -1)

and that'll turn off all warnings until they get turned back on.

it's just how things are for now, it's not reproj but rgdal/sf

[mdsumner]

looks like we can do this with the new rgdal (1.5-12, released 2020-06-26)

options("rgdal_show_exportToProj4_warnings"="none")

so this would go into our zzz.R, but the problem with that is it masks it for any use of rgdal if SOmap is loaded, so maybe that's too much

[mdsumner]

also, it only applies if this option is set before rgdal is loaded - on the whole, I think it's worthwhile but perhaps not worth conditioning SOmap on this version of rgdal

[raymondben]

dev version now has quietly(...) wrapped inside top-level functions, which selectively suppresses warnings. Currently only warnings with the string "Discarded datum WGS_1984" are suppressed. @mdsumner SOauto_crop throws "NULL source CRS comment, falling back to PROJ string" warnings - should these be suppressed too? I think they come from spTransform

[mdsumner]

yes I don't see any use for these warnings in this context at all - that particular warning is saying

"this S4-class 'CRS' object has an empty value in the comment attribute"

the comment attribute is a hidden attribute, using the comment() mechanism - and it's been retrofit in sp to store WKT2, so that the back-end can transform using a full CRS, while the front-end presents only a PROJ.4 string. It's a kind of backwards compatibility.

(in sf context, sf only stores $input and $wkt now, and $wkt cannot be NULL, the $proj4string apparent value in sf is a dynamic function call)

[raymondben]

Thanks. https://github.com/AustralianAntarcticDivision/SOmap/commit/abee8fdc1d7dbc0c800020e9d9ce160db4e5e971. I think this is OK as a workaround.