Vulnerability to absence of retiring r-spatial packages

[rsbivand]

00check.log
is a recent check log from running under _SP_EVOLUTION_STATUS_=2 without retiring r-spatial packages (suggested in this package) on the library path. The minimal correction is to check that the package namespaces can be loaded, and if not, do not run those parts of the examples or vignettes. It would be safer in the longer term to replace retiring r-spatial packages with active r-spatial/rspatial packages (see https://r-spatial.org/r/2022/04/12/evolution.html, https://r-spatial.org/r/2022/12/14/evolution2.html).

[clnsmth]

Thanks for reaching out @rsbivand. I agree, the preferred approach is to replace the retiring R spatial packages with active ones.

@sokole, do you have any cycles to put into this? I think you are most familiar with this part of the code base.

[sokole]

@clnsmth I'll try to address this in my next pull request to dev.

[rsbivand]

Please also see https://r-spatial.org/r/2023/04/10/evolution3.html, fix best by June, latest October 2023.

[sokole]

thanks for the link @rsbivand

[pdil]

@sokole Because of this change, usmap_transform from the usmap package now requires the sf package. ecocomDP will result in the following error once usmap is updated soon:

Package: ecocomDP
Check: examples
New result: ERROR
  Running examples in ‘ecocomDP-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_sites
  > ### Title: Plot sites on US map
  > ### Aliases: plot_sites
  > 
  > ### ** Examples
  > 
  > ## Not run: 
  > ##D # Read a dataset of interest
  > ##D dataset <- read_data("edi.193.5")
  > ##D 
  > ##D # Plot the dataset
  > ##D plot_sites(dataset)
  > ##D 
  > ##D # Flatten dataset then plot
  > ##D dataset %>% 
  > ##D   flatten_data() %>% 
  > ##D   plot_sites()
  > ## End(Not run)
  > 
  > # Plot the example dataset
  > plot_sites(ants_L1)
  The legacy packages maptools, rgdal, and rgeos, underpinning this package
  will retire shortly. Please refer to R-spatial evolution reports on
  https://r-spatial.org/r/2023/05/15/evolution4.html for details.
  This package is now running under evolution status 0 
  Please note that 'maptools' will be retired during October 2023,
  plan transition at your earliest convenience (see
  https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
  for guidance);some functionality will be moved to 'sp'.
   Checking rgeos availability: FALSE
  Please note that rgdal will be retired during October 2023,
  plan transition to sf/stars/terra functions using GDAL and PROJ
  at your earliest convenience.
  See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution
  rgdal: version: 1.6-7, (SVN revision 1203)
  Geospatial Data Abstraction Library extensions to R successfully loaded
  Loaded GDAL runtime: GDAL 3.6.2, released 2023/01/02
  Path to GDAL shared files: /usr/share/gdal
   GDAL does not use iconv for recoding strings.
  GDAL binary built with GEOS: TRUE 
  Loaded PROJ runtime: Rel. 9.1.1, December 1st, 2022, [PJ_VERSION: 911]
  Path to PROJ shared files: /home/hornik/.local/share/proj:/usr/share/proj
  PROJ CDN enabled: FALSE
  Linking to sp version:1.6-1
  To mute warnings of possible GDAL/OSR exportToProj4() degradation,
  use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.
  Error in usmap::usmap_transform(cleaned, input_names = c("longitude",  : 
    `sf` must be installed to use `usmap_transform`.
           Use: install.packages("sf") and try again.
  Calls: plot_sites
  Execution halted

The simplest fix would be to add sf to your DESCRIPTION/Suggests and/or importing it whenever usmap_transform() or usmap_crs() is used.

[rsbivand]

And https://r-spatial.org/r/2023/05/15/evolution4.html. Expect package to fail CRAN CMD check with _R_CHECK_SUGGESTS_ONLY_=true when sp 2.0-0 is published very soon, if sf is not added to Suggests:

[rsbivand]

See pdil/usmap#70; new usmap release forthcoming. You need to add sf to Suggests: in DESCRIPTION, if you do so, ecocomDP passes CMD check also with _R_CHECK_SUGGESTS_ONLY_=true.

[sokole]

@clnsmth we have a fix for this, will submit PR this week.

[rsbivand]

Thanks!