What do the warnings generated from `raster::crs` in `sp::SpatialPointsDataFrame` mean? [R]

Question

Take the latest versions as described here:

install.packages("rgdal")
# also installing the dependency ‘sp’
packageVersion("sp")
# [1] ‘1.4.2’
packageVersion("rgdal")
# [1] ‘1.5.16’

In this case, the over function returns many warnings which we don't understand:

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

---

Details:

class(spdf)
# [1] "SpatialPointsDataFrame"
# attr(,"package")
# [1] "sp"
class(departement_boundaries)
# [1] "SpatialPolygonsDataFrame"
# attr(,"package")
# [1] "sp"
raster::crs(spdf)
# CRS arguments:
#  +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0 
raster::crs(departement_boundaries)
# CRS arguments:
# +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0 

So everything seems ok to me, but:

df_in <- sp::over(spdf , departement_boundaries , fn = NULL)
# Warnung in showSRID(uprojargs, format = "PROJ", multiline = "NO")
# Discarded datum WGS_1984 in CRS definition,
# but +towgs84= values preserved
# Warnung in showSRID(uprojargs, format = "PROJ", multiline = "NO")
# Discarded datum WGS_1984 in CRS definition,
# but +towgs84= values preserved
# Warnung in showSRID(uprojargs, format = "PROJ", multiline = "NO")
# Discarded datum WGS_1984 in CRS definition,
# but +towgs84= values preserved
# Warnung in showSRID(uprojargs, format = "PROJ", multiline = "NO")
# Discarded datum WGS_1984 in CRS definition,
# but +towgs84= values preserved

Comments:

• I have problems to make a small reproducible example - the departement_boundaries from Zurich are open source, but its a huge string from dput.
• The docs ?sp::over discuss the data.frame cases x = "SpatialPointsDataFrame", y = "SpatialPolygons" and x = "SpatialPoints", y = "SpatialPolygonsDataFrame" but this code ran with previous versions of sp and rgdal (see link above in this question) without errors or warnings.

Answer 1

You don't get errors, you get warnings. When you load rgdal, it prints a message

To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.

when you want to get rid of the warnings, follow that advice, and try setting

options("rgdal_show_exportToProj4_warnings"="none")

(in absence of a reproducible example this is a guess, really - let me know if it worked!)