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spTransform failing with provided CRS string #48

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everydayduffy opened this issue Feb 26, 2021 · 36 comments
Open

spTransform failing with provided CRS string #48

everydayduffy opened this issue Feb 26, 2021 · 36 comments

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@everydayduffy
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Hello,

I'm afraid this is another issue likely related to the recent large changes to PROJ & GDAL. I get the following error when running:

elevation <- elevatr::get_elev_raster(lake,z = 9)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'CRSobj' in selecting a method for function 'spTransform': NA

I've narrowed it down to this line of code:

elevatr/R/internal.R

Line 196 in 4c45d54

locations <- sp::spTransform(locations, sp::CRS("+init=EPSG:4326"))

...and found that changing it to:

locations <- sp::spTransform(locations, sp::CRS("+proj=longlat +datum=WGS84 +no_defs"))

...resolves the issue.

I think this shouldn't be a breaking change and wondered whether you might consider implementing it?

Here is my sessioninfo / rgdal loading text if useful:

Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

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

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

other attached packages:
[1] rgdal_1.5-23  elevatr_0.3.1 raster_3.4-5  sp_1.4-5      sf_0.9-7     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         magrittr_2.0.1     hms_1.0.0          progress_1.2.2    
 [5] units_0.6-7        tidyselect_1.1.0   lattice_0.20-41    R6_2.5.0          
 [9] rlang_0.4.10       httr_1.4.2         dplyr_1.0.4        tools_4.0.3       
[13] grid_4.0.3         KernSmooth_2.23-18 e1071_1.7-4        DBI_1.1.1         
[17] ellipsis_0.3.1     class_7.3-18       tibble_3.0.6       lifecycle_0.2.0   
[21] crayon_1.4.1       purrr_0.3.4        codetools_0.2-18   vctrs_0.3.6       
[25] curl_4.3           glue_1.4.2         compiler_4.0.3     pillar_1.4.7      
[29] prettyunits_1.1.1  generics_0.1.0     classInt_0.4-3     pkgconfig_2.0.3 ```

# when loading rgdal

Loading required package: sp
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: C:/R/R403/library/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: C:/R/R403/library/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was C:/R/R403/library/rgdal/proj

P.S I think in the much longer term, switching to sf/stars/terra would help solve such issues, but understand that would be a massive undertaking. Oh and thank you for making a very useful package!
@jhollist
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jhollist commented Feb 26, 2021 via email

@everydayduffy
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Thanks for the quick response. I rolled back the version to see if the issue persisted. Have updated and confirm that I get the same error in 0.3.1 & 0.3.4

@jhollist
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I am not able to recreate this on my machine with the same versions as you (only diff is a slightly older OS)

Here's my sessionInfo():
R version 4.0.3 (2020-10-10)
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] sf_0.9-7 raster_3.4-5 elevatr_0.3.4 rgdal_1.5-23 sp_1.4-5

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 magrittr_2.0.1 hms_1.0.0 progress_1.2.2
[5] units_0.6-7 tidyselect_1.1.0 lattice_0.20-41 R6_2.5.0
[9] rlang_0.4.10 httr_1.4.2 dplyr_1.0.2 tools_4.0.3
[13] grid_4.0.3 KernSmooth_2.23-17 e1071_1.7-4 DBI_1.1.1
[17] ellipsis_0.3.1 class_7.3-17 yaml_2.2.1 tibble_3.0.5
[21] lifecycle_0.2.0 crayon_1.4.1 purrr_0.3.4 codetools_0.2-16
[25] vctrs_0.3.6 curl_4.3 glue_1.4.2 compiler_4.0.3
[29] pillar_1.4.7 prettyunits_1.1.1 generics_0.1.0 classInt_0.4-3
[33] pkgconfig_2.0.3

@jhollist
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jhollist commented Feb 26, 2021 •
edited

Oh, and totally agree about the switch to sf. On my list. Need to think on the raster to stars or terra switch.

@everydayduffy
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Out of interest, could you share the output when you load rgdal for the first time please? I think our underlying libraries might be different versions...

@jhollist
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They look the same to me:
Loading required package: sp
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: C:/Program Files/R/R-4.0.3/library/rgdal/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: C:/Program Files/R/R-4.0.3/library/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was C:/Program Files/R/R-4.0.3/library/rgdal/proj

@jhollist
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That being said, elevatr wasn't erroring for me, but I can recreate that error on my machine if I run that line on its own.

Could you try: sp::CRS(SRS_string = "EPSG:4326") in that line on your machine to confirm that it fixes the issue?

I am reluctant to roll back to the PROJ4 string since everything is moving in the other direction.

@everydayduffy
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That being said, elevatr wasn't erroring for me, but I can recreate that error on my machine if I run that line on its own.

Could you try: sp::CRS(SRS_string = "EPSG:4326") in that line on your machine to confirm that it fixes the issue?

This is really frustrating, as all I get from running this command on it's own is an NA:

library(sp)
library(rgdal)
sp::CRS(SRS_string = "EPSG:4326")
Error in sp::CRS(SRS_string = "EPSG:4326") : NA

And the same happens when placed within the spTransform:

locations <- sp::spTransform(locations, sp::CRS(SRS_string = "EPSG:4326")) 
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'CRSobj' in selecting a method for function 'spTransform': NA

I'm a bit stumped as to where the differences are in our setups, and why this doesn't work for me.

I am reluctant to roll back to the PROJ4 string since everything is moving in the other direction.

No worries, that's understandable.

For now I've taken a fork and done an alternative install, so I have a working version to use!

@jhollist
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I am totally baffled by this one. I can't seem to recreate the error on my machine now. Happened once, but not now...

Maybe a wholesale upgrade to 4.0.4 with all new packages would fix it? Or, your own version should work for now. Sorry about this. I'll admit to having about a 10% understanding of the PROJ/GDAL changes and what needs to happen on my end. From what I can tell, PROJ4 is what is going away, replaced by WKT or other methods that can more completely/acurately describe the CRS.

Another option is to roll back to elevatr 0.2.0. If the AWS tiles are what you want then I think the results should be the same.

@everydayduffy
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Haha no worries, it is very difficult to pin down... Just for the record, I did a clean install of R4.0.4 and got the following:

library(elevatr)
data(lake)
x <- get_elev_raster(lake, z = 12)
Error in sp::CRS(prj) : 
  PROJ4 argument-value pairs must begin with +: PROJCRS["unknown",
  BASEGEOGCRS["unknown",
 DATUM["North American Datum 1983",
 ELLIPSOID["GRS 1980",6378137,298.257222101,
 LENGTHUNIT["metre",1]],
 ID["EPSG",6269]],
 PRIMEM["Greenwich",0,
 ANGLEUNIT["degree",0.0174532925199433],
 ID["EPSG",8901]]],
 CONVERSION["unknown",
 METHOD["Albers Equal Area",
 ID["EPSG",9822]],
 PARAMETER["Latitude of false origin",40,
 ID["EPSG",8821]],
 PARAMETER["Longitude origin",-96,
 ID["EPSG",8822]],
 1st standard parallel",20,
 ID["EPSG",8823]],
 2nd parallel",60,
 ID["EPSG",8824]],
 PARAMETER["Easting at origin",0,
 LENGTHUNIT["metre",1],
 ID["EPSG",8826]],
 PARAMETER["Northing ID["EPSG",8827]]],
 CS[Cartesian,2],
 AXIS["(E)",east,
 ORDER[1],
 LENGTHUNIT["metre",1,
 ID["EPSG",9001]]],
 AXIS["(N)",north,
 ORDER[2],
 ID["EPSG",9001]]]]

and then when loading rgdal in...

library(rgdal)
library(elevatr)
x <- get_elev_raster(lake, z = 12)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'CRSobj' in selecting a method for function 'spTransform': NA

I think the most solid solution would be switching to sf::st_transform from sp::spTransform. I'd be happy to help you with this for the estimate_raster_size if you'd like? And I agree with your synthesis of the whole situation. It hasn't been that well communicated by those making the sweeping changes IMO.

@jhollist
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jhollist commented Mar 2, 2021

@everydayduffy can you confirm your sp version?

packageVersion("sp")

@everydayduffy
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@jhollist - I've got sp 1.4.5

@everydayduffy
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Hi @jhollist,

Unforutnately, I'm still getting issues with the spTransform line mentioned at the start of this issue thread. It's a bit of a nightmare this rspatial stuff at the moment! Please let me know if I can help with switching at least some parts to an sf framework. Happy to start the ball rolling with a pull request, let me know!

@arielfuentes
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Hi @jhollist I have the same issue using the example code, this is my session info:

R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

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

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

other attached packages:
[1] sf_0.9-5         ggplot2_3.3.3    reshape2_1.4.4   rayshader_0.19.2 elevatr_0.3.4    raster_3.3-13   
[7] sp_1.4-2        

loaded via a namespace (and not attached):
 [1] progress_1.2.2          tidyselect_1.1.0        xfun_0.17               purrr_0.3.4            
 [5] lattice_0.20-41         colorspace_1.4-1        vctrs_0.3.4             generics_0.1.0         
 [9] miniUI_0.1.1.1          htmltools_0.5.0         rlang_0.4.10            manipulateWidget_0.10.1
[13] e1071_1.7-3             pillar_1.6.0            later_1.1.0.1           withr_2.2.0            
[17] glue_1.4.2              DBI_1.1.1               foreach_1.5.1           lifecycle_1.0.0        
[21] plyr_1.8.6              stringr_1.4.0           munsell_0.5.0           gtable_0.3.0           
[25] htmlwidgets_1.5.3       codetools_0.2-18        knitr_1.33              fastmap_1.0.1          
[29] doParallel_1.0.16       httpuv_1.5.4            crosstalk_1.1.1         parallel_4.0.5         
[33] class_7.3-18            Rcpp_1.0.5              KernSmooth_2.23-18      xtable_1.8-4           
[37] scales_1.1.1            promises_1.1.1          classInt_0.4-3          webshot_0.5.2          
[41] jsonlite_1.7.1          mime_0.9                hms_1.0.0               digest_0.6.25          
[45] stringi_1.5.3           dplyr_1.0.2             shiny_1.5.0             grid_4.0.5             
[49] rgdal_1.5-16            tools_4.0.5             magrittr_2.0.1          rgl_0.100.54           
[53] tibble_3.0.6            crayon_1.4.1            pkgconfig_2.0.3         ellipsis_0.3.1         
[57] prettyunits_1.1.1       rstudioapi_0.13         iterators_1.0.13        R6_2.5.0               
[61] units_0.6-7             compiler_4.0.5

@jhollist
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jhollist commented May 6, 2021

@arielfuentes Which code exactly is throwing the error? I had an issue in the development version that was causing my vignette some problems. I think I have that fixed (not yet pushed), but without know your exact issue hard to say what the problem is. If you can provide a reproducible example, I will take a look.

@arielfuentes
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@jhollist Even though I'm not on my laptop the code was the following:

mt_mans <- data.frame(x = -72.8145, y = 44.5438)
mts <- rbind(mt_wash,mt_mans)
ll_prj <- "EPSG:4326"
mts_sp <- sp::SpatialPoints(sp::coordinates(mts), 
                            proj4string = sp::CRS(ll_prj)) 
get_elev_point(locations = mts_sp)

But in the PC at my office works and I don't know why (it is very good news though), my session info on this machine is:

Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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

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

other attached packages:
[1] elevatr_0.3.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         magrittr_2.0.1     hms_1.0.0          progress_1.2.2    
 [5] units_0.6-7        tidyselect_1.1.0   lattice_0.20-41    R6_2.5.0          
 [9] rlang_0.4.10       fansi_0.4.2        httr_1.4.2         dplyr_1.0.2       
[13] tools_4.0.3        rgdal_1.5-23       grid_4.0.3         xfun_0.18         
[17] tinytex_0.26       KernSmooth_2.23-17 utf8_1.2.1         e1071_1.7-4       
[21] DBI_1.1.0          ellipsis_0.3.1     class_7.3-17       tibble_3.0.4      
[25] lifecycle_1.0.0    sf_0.9-6           crayon_1.4.1       purrr_0.3.4       
[29] vctrs_0.3.4        curl_4.3           glue_1.4.2         sp_1.4-4          
[33] compiler_4.0.3     pillar_1.5.1       prettyunits_1.1.1  generics_0.1.0    
[37] classInt_0.4-3     jsonlite_1.7.1     pkgconfig_2.0.3

What could be the reason that it works on a machine and not on the other?

@jhollist
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jhollist commented May 6, 2021 •
edited

This problem is linked back to how sp, raster, sf, etc. are dealing with coordinate reference systems. There have been a number of changes in the last year or so because the underlying libraries (e.g. GDAL, PROJ, etc.) have been updated. Given all that, the two machines can have different package versions and/or different versions of the underlying libraries. That could easily be the cause of the different behavior on different machines.

I did see different version of rgdal which could be the problem. First thing to try is to make sure all your packages are up to date. At a minimum do fresh installs of rgdal, sp, sf, and raster. After that try again with the examples.

@arielfuentes
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Thank you @jhollist, the lack of update for the sp library was causing the issue.

@jhollist
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@arielfuentes and @everydayduffy I pushed an update to CRAN yesterday that I hope fixes this problem. I am pretty sure it is linked to an older version of PROJ which doesn't like WKT. It might still fail and if so, there is a change for sp that once incorporated will fix it.

@h-a-graham h-a-graham mentioned this issue Nov 22, 2021
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@jhollist
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All, I am going to leave this open as I think I have it solved as well as I can with sp still involved. I have one more release of elevatr slated with sp. I am about 90% of the way done with transitioning solely to sf. Once that is done, this issue will mostly be moot. Will close it when I get the sf changes completed. Thanks for bearing with me on this!

@everydayduffy
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All, I am going to leave this open as I think I have it solved as well as I can with sp still involved. I have one more release of elevatr slated with sp. I am about 90% of the way done with transitioning solely to sf. Once that is done, this issue will mostly be moot. Will close it when I get the sf changes completed. Thanks for bearing with me on this!

Keep up the good work!

@xtimbeau
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xtimbeau commented Feb 3, 2022

Hi to all,
It looks like the issue is back. When using elevatr with updated packages for sp, sf, raster and using GDAL 3.2.1,

> rgdal::getGDALVersionInfo()
[1] "GDAL 3.2.1, released 2020/12/29"

I get the error 'spTransform' : NA in get_elev_raster related to

> sp::CRS(SRS_string = "EPSG:4326")
Error in sp::CRS(SRS_string = "EPSG:4326") : NA

I tried the github version of elevatr, with no changes.
On an other setup linked to GDAL 3.0.2, everything is fine. However, I can't find a way to roll back from 3.2 to 3.0.

Any hints on how to solve this ?

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    
system code page: 65001

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

other attached packages:
 [1] stars_0.5-5       abind_1.4-5       glue_1.6.1        accessibility_0.2 rJava_1.0-6       sf_1.0-5          data.table_1.14.2
 [8] tmap_3.3-2        tictoc_1.0.1      forcats_0.5.1     stringr_1.4.0     dplyr_1.0.7       purrr_0.3.4       readr_2.1.2      
[15] tidyr_1.2.0       tibble_3.1.6      ggplot2_3.3.5     tidyverse_1.3.1  

loaded via a namespace (and not attached):
  [1] leafem_0.1.6        colorspace_2.0-2    ellipsis_0.3.2      class_7.3-19        leaflet_2.0.4.1     rgdal_1.5-28       
  [7] rprojroot_2.0.2     gtfsio_1.0.0        base64enc_0.1-3     fs_1.5.2            dichromat_2.0-0     rstudioapi_0.13    
 [13] proxy_0.4-26        listenv_0.8.0       remotes_2.4.2       fansi_1.0.2         lubridate_1.8.0     xml2_1.3.3         
 [19] codetools_0.2-18    cachem_1.0.6        pkgload_1.2.4       jsonlite_1.7.3      tmaptools_3.1-1     broom_0.7.12       
 [25] dbplyr_2.1.1        png_0.1-7           compiler_4.1.2      httr_1.4.2          backports_1.4.1     assertthat_0.2.1   
 [31] fastmap_1.1.0       cli_3.1.1           htmltools_0.5.2     prettyunits_1.1.1   tools_4.1.2         gtable_0.3.0       
 [37] Rcpp_1.0.8          cellranger_1.1.0    raster_3.5-15       vctrs_0.3.8         progressr_0.10.0    leafsync_0.1.0     
 [43] crosstalk_1.2.0     lwgeom_0.2-8        globals_0.14.0      ps_1.6.0            brio_1.1.3          testthat_3.1.2     
 [49] rvest_1.0.2         lifecycle_1.0.1     devtools_2.4.3      XML_3.99-0.8        future_1.23.0       terra_1.5-17       
 [55] scales_1.1.1        tidytransit_1.3.0   hms_1.1.1           geodist_0.0.7       parallel_4.1.2      RColorBrewer_1.1-2 
 [61] qs_0.25.2           curl_4.3.2          memoise_2.0.1       stringi_1.7.6       desc_1.4.0          checkmate_2.0.0    
 [67] e1071_1.7-9         zip_2.2.0           pkgbuild_1.3.1      rlang_1.0.1         pkgconfig_2.0.3     lattice_0.20-45    
 [73] elevatr_0.4.2       htmlwidgets_1.5.4   processx_3.5.2      tidyselect_1.1.1    parallelly_1.30.0   magrittr_2.0.2     
 [79] R6_2.5.1            generics_0.1.2      DBI_1.1.2           pillar_1.7.0        haven_2.4.3         withr_2.4.3        
 [85] units_0.7-2         sp_1.4-7            modelr_0.1.8        crayon_1.4.2        KernSmooth_2.23-20  utf8_1.2.2         
 [91] RApiSerialize_0.1.0 tzdb_0.2.0          progress_1.2.2      usethis_2.1.5       grid_4.1.2          readxl_1.3.1       
 [97] callr_3.7.0         reprex_2.0.1        digest_0.6.29       classInt_0.4-3      RcppParallel_5.1.5  munsell_0.5.0      
[103] stringfish_0.15.5   viridisLite_0.4.0   sessioninfo_1.2.2

@jhollist
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jhollist commented Feb 3, 2022

I am not able to recreate your issue with sp::CRS(SRS_string = "EPSG:4326"). I get a valid WKT and all our versions appear to match with one exception. I noticed that you are on the dev version of sp. Current CRAN version is 1.4-6. Maybe try a reinstall of sp from CRAN?

That being said, current dev version and CRAN versions both worked fine for me.

@xtimbeau
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xtimbeau commented Feb 3, 2022

sp dev or CRAN give the same result on my system. I think it is related to GDAL version ?

@jhollist
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jhollist commented Feb 3, 2022

I am on the same GDAL version. Tracking down these small differences can be a challenge!

@xtimbeau
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xtimbeau commented Feb 3, 2022 via email

@jhollist
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jhollist commented Feb 3, 2022

7.2.1

@xtimbeau
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xtimbeau commented Feb 3, 2022 via email

@jhollist
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jhollist commented Feb 3, 2022

That sounds promising! Let me know if that was the issue. I wouldn't be surprised if some of the issues others reported that we couldn't track down were caused by similar things.

@xtimbeau
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xtimbeau commented Feb 4, 2022 via email

@fipoucat
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fipoucat commented Mar 5, 2022

I am having the same issue: on window 11

downloading DEM via package elevatr
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'CRSobj' in selecting a method for function 'spTransform': NA

In case you sokved the problem?, what can you suggest?

Thanks

@xtimbeau
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xtimbeau commented Mar 5, 2022

check that rgdal::get_proj_search_paths() points to the proj folder inside rgdal (it should be something like "....../rlibs/4.1.2/rgdal/proj".
If not, change it using rgdal::set_proj_search_paths() or by setting an environ variable PROJ_USER_WRITABLE_DIRECTORY to the correct path (in .Renviron for instance). That should help.

@fipoucat
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fipoucat commented Mar 6, 2022 via email

@jhollist
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jhollist commented Mar 6, 2022 via email

@fipoucat
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fipoucat commented Mar 6, 2022 via email

@jhollist jhollist mentioned this issue Mar 7, 2022
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@jhollist
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jhollist commented Mar 9, 2022

@fipoucat Go ahead an update raster, sf, rgdal, and sp and try to run again. That might fix the issue.

@ckluss ckluss mentioned this issue Mar 18, 2022
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@fipoucat @jhollist @arielfuentes @everydayduffy @xtimbeau