Why does updating `rgdal` package in R change output of `sp::CRS` (+towgs84=0,0,0)?

I am not a GIS expert, and this change caused quite some errors in our analysis. So my question is, why this was changed: From rgdal 1.4.8 to 1.5.16, the +towgs84=0,0,0 disappeard in the output of sp::CRS.

I hope for an answer, which is comprehensive to a non-GIS-expert.

Reproducible example if you have NO sp and NO rgdal package installed:

packageurl <- "http://cran.r-project.org/src/contrib/Archive/sp/sp_1.4-1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
 
packageurl <- "http://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.4-8.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

packageVersion("sp")
# [1] ‘1.4.1’
packageVersion("rgdal")
# [1] ‘1.4.8’

sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
# CRS arguments:
#   +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0 

So everything works, that is in our case

spdf <- sp::SpatialPointsDataFrame(
  coords = mission_coords[, c(2,1)],
  data = mission_coords,
  proj4string = sp::CRS(
    "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"))
df_in <- sp::over(spdf , departement_boundaries , fn = NULL)

are ok. (I have problem to make a small reproducible example – the departement_boundaries from Zurich are open source, but its a huge string from dput.)

Now, update both packages

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

and in any case +towgs84=0,0,0 is missing now:

sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs",
        doCheckCRSArgs = TRUE)
# CRS arguments: +proj=longlat +datum=WGS84 +no_defs 
sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs",
        doCheckCRSArgs = FALSE) # ... +ellps=WGS84 is added...(?)
# CRS arguments: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs 

Any ideas for an explanation to a GIS-newbie?

---

@EdzerPebesma’s answer helped me find R spatial follows GDAL and PROJ development to get information:

x <- sp::CRS("+init=epsg:4326")
cat(comment(x), "n")

---

One comment from that site is really unclear to me (perhaps how this relates to +towgs84=?):

• rgdal generates many warnings about discarded PROJ string keys,
  -> See e.g. Warnung in showSRID(uprojargs, format = "PROJ", multiline = "NO")
  Discarded datum WGS_1984 in CRS definition, but +towgs84= values preserved
  from here?
• intended to alert package maintainers and script authors to the need to review code.
  -> To me it is not clear, what I have to do, see the link above.
• It is particularly egregious to assign to the CRS object projargs slot directly,
  and this is unfortunately seem in much code in packages.
  -> Again, what should I do instead?