Crytpic error in as_Spatial() - "no arguments in initialization list"

[lucas-johnson]

Current Behavior

When converting an sf object to a Spatial object I'm getting a strange error that I don't know how to deal with (see below).

nys <- st_read("~/Documents/CAFRI/data/maps/nys/NYS_Civil_Boundaries_SHP/State_Shoreline.shp")
#>  Reading layer `State_Shoreline' from data source `/Users/lucasj/Documents/CAFRI/data/maps/nys/NYS_Civil_Boundaries_SHP/State_Shoreline.shp' using driver `ESRI Shapefile'
#>  Simple feature collection with 1 feature and 6 fields
#>  geometry type:  MULTIPOLYGON
#>  dimension:      XY
#>  bbox:           xmin: 105571.4 ymin: 4483090 xmax: 764142.8 ymax: 4985444
#>  projected CRS:  NAD83 / UTM zone 18N
sf::as_Spatial(nys)
#>  Error in h(simpleError(msg, call)) : 
#>   error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': no arguments in initialization list
packageVersion("sf")
#> [1] ‘0.9.6’
packageVersion("sp")
#> [1] ‘1.4.4’

sessionInfo()
#>  R version 4.0.1 (2020-06-06)
#>  Platform: x86_64-apple-darwin17.0 (64-bit)
#>  Running under: macOS Catalina 10.15.6

#>  Matrix products: default
#>  BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#>  LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

#>  locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

#>  other attached packages:
#> [1] sf_0.9-6

#>  loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.5.2       rstudioapi_0.11    magrittr_1.5       units_0.6-7        tidyselect_1.1.0   lattice_0.20-41    R6_2.4.1           rlang_0.4.6        dplyr_1.0.0        tools_4.0.1       
#>[11] rgdal_1.5-10       grid_4.0.1         packrat_0.5.0      KernSmooth_2.23-17 e1071_1.7-3        DBI_1.1.0          ellipsis_0.3.1     class_7.3-17       tibble_3.0.1       lifecycle_0.2.0   
#>[21] crayon_1.3.4       purrr_0.3.4        vctrs_0.3.1        glue_1.4.1         sp_1.4-4           compiler_4.0.1     pillar_1.4.4       generics_0.0.2     classInt_0.4-3     pkgconfig_2.0.3  

sf::sf_extSoftVersion()
#>           GEOS           GDAL         proj.4 GDAL_with_GEOS     USE_PROJ_H 
#>        "3.8.1"        "3.1.1"        "6.3.1"         "true"         "true" 
rgdal::rgdal_extSoftVersion()
#>           GDAL GDAL_with_GEOS           PROJ             sp 
#>        "2.4.2"        "FALSE"        "5.2.0"        "1.4-2" 

Desired Behavior

It would be nice to have a more informative error message so I can diagnose the issue. Or perhaps this is a bug and it should be fixed.

[Nowosad]

@lucas-johnson have you tried:

nys_sp = as(nys, "Spatial")

?

[lucas-johnson]

@Nowosad Same result:

nys_sp = as(nys, "Spatial")
#> Error in h(simpleError(msg, call)) : 
#>  error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': no arguments in initialization list

[edzer]

I can't reproduce this, and would need a full reprex.

[lucas-johnson]

@edzer do you need me to share the shapefile? How can I help you get a full reprex?

[edzer]

Yes, or alternatively you try this:

library(sf)
nc = st_read(system.file("gpkg/nc.gpkg", package="sf"))
as_Spatial(nc)

which should work.

[lucas-johnson]

No luck.

library(sf)
nc = st_read(system.file("gpkg/nc.gpkg", package="sf"))
#> Reading layer `nc.gpkg' from data source `/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sf/gpkg/nc.gpkg' using driver `GPKG'
#> Simple feature collection with 100 features and 14 fields
#> geometry type:  MULTIPOLYGON
#> dimension:      XY
#> bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
#> geographic CRS: NAD27
as_Spatial(nc)
#> Error in h(simpleError(msg, call)) : 
#>   error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': no arguments in initialization list

[edzer]

Does it help if you load sp after loading sf?

[lucas-johnson]

No, unfortunately it does not:

library(sf)
#> Linking to GEOS 3.8.1, GDAL 3.1.1, PROJ 6.3.1
#> Warning message:
#> package ‘sf’ was built under R version 4.0.2 
library(sp)
#> Warning message:
#> package ‘sp’ was built under R version 4.0.2 
nc = st_read(system.file("gpkg/nc.gpkg", package="sf"))
#> Reading layer `nc.gpkg' from data source `/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sf/gpkg/nc.gpkg' using driver `GPKG'
#> Simple feature collection with 100 features and 14 fields
#> geometry type:  MULTIPOLYGON
#> dimension:      XY
#> bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
#> geographic CRS: NAD27
as_Spatial(nc)
#> Error in h(simpleError(msg, call)) : 
#>   error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': no arguments in initialization list

[edzer]

update rgdal?

[jmhatch]

I'm also having an issue with as_Spatial(). reprex below.

library(sf)
library(sp)
library(dplyr)

ex_poly = data.frame(x = c(-75.927511,-75.523696,-75.449457,-75.797533,-75.927511), y = c(35.128219,35.274408,35.100152,34.998016,35.128219)) %>% st_as_sf(coords = c('x', 'y'), crs = 4326) %>% st_combine() %>% st_cast('POLYGON')

## convert to sp object
ex_poly %>% as_Spatial()

#> Error in (function (classes, fdef, mtable)  : 
#>   unable to find an inherited method for function ‘coordinates’ for signature ‘"XY"’`

Also tried this:

## convert to sp object
ex_poly %>% st_sf() %>% as_Spatial()

#Error in (function (classes, fdef, mtable)  : 
#>   unable to find an inherited method for function ‘coordinates’ for signature ‘"XY"’`

Not sure if I'm doing something incorrectly.

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] dplyr_0.8.5 sp_1.4-1    sf_0.9-4   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         rstudioapi_0.11    magrittr_1.5       units_0.6-5        tidyselect_1.1.0  
 [6] here_0.1           lattice_0.20-38    R6_2.4.1           rlang_0.4.7        tools_3.6.1       
[11] grid_3.6.1         packrat_0.5.0      KernSmooth_2.23-15 e1071_1.7-3        DBI_1.1.0         
[16] ellipsis_0.3.1     class_7.3-15       rprojroot_1.3-2    assertthat_0.2.1   tibble_3.0.3      
[21] lifecycle_0.2.0    crayon_1.3.4       purrr_0.3.3        vctrs_0.3.2        glue_1.4.2        
[26] compiler_3.6.1     pillar_1.4.6       backports_1.1.5    classInt_0.4-2     pkgconfig_2.0.3   
  

[lucas-johnson]

Updating rgdal worked.

Old rgdal version: 1.5.10
New rgdal version: 1.5.18

remove.packages("rgdal")
#>Removing package from ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
#>(as ‘lib’ is unspecified)
install.packages("rgdal")
#>trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgdal_1.5-18.tgz'
#>Content type 'application/x-gzip' length 83963272 bytes (80.1 MB)
#>==================================================
#>downloaded 80.1 MB


#>The downloaded binary packages are in
#>	/var/folders/_c/bcw1j0251k12c8hqxpqpb7nr0000gn/T//RtmpS9Wnpi/downloaded_packages
library(sf)
#>Linking to GEOS 3.8.1, GDAL 3.1.1, PROJ 6.3.1
#>Warning message:
#>package ‘sf’ was built under R version 4.0.2 
nc = st_read(system.file("gpkg/nc.gpkg", package="sf"))
#>Reading layer `nc.gpkg' from data source `/Library/Frameworks/R.framework/Versions/4.0/Resources/library/sf/gpkg/nc.gpkg' using driver `GPKG'
#>Simple feature collection with 100 features and 14 fields
#>geometry type:  MULTIPOLYGON
#>dimension:      XY
#>bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
#>geographic CRS: NAD27
sp_nc <- as_Spatial(nc)

Thanks for the help!

[edzer]

Good to hear that. @jmhatch your problem is another one, I'm close to fixing it.