ropensci / CoordinateCleaner

Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.
https://docs.ropensci.org/CoordinateCleaner/
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Please remove dependencies on **rgdal**, **rgeos**, and/or **maptools** #78

Closed rsbivand closed 9 months ago

rsbivand commented 1 year ago

This package depends on (depends, imports or suggests) raster and one or more of the retiring packages rgdal, rgeos or maptools (https://r-spatial.org/r/2022/04/12/evolution.html). Since raster 3.6.3, all use of external FOSS library functionality has been transferred to terra, making the retiring packages very likely redundant. It would help greatly if you could remove dependencies on the retiring packages as soon as possible.

Pseudomys commented 1 year ago

Seconded. In the meantime, is it possible to still use this package (I'm wanting to use function cc_outl just now) with rgdal now retired?

azizka commented 1 year ago

working on this, but will take some time.

rsbivand commented 1 year ago

New blog: https://r-spatial.org/r/2023/04/10/evolution3.html. This strong dependence on retiring packages is a problem for a package depending on this package: https://github.com/brunobrr/bdc/issues/253, and will be a problem for any workflows using the package. Best completed in June 2023, last gasp October 2023. In NAMESPACE, you have:

importFrom(rgdal,readOGR) # use st_read() and coerce to sp
importFrom(rgeos,gBuffer) # use st_buffer coercing to sf and back to sp
importFrom(sp,"proj4string<-") # ensure use of WKT-2
importFrom(sp,CRS) # uses st_crs internally in status 2L
importFrom(sp,disaggregate) # probably defunct
importFrom(sp,over) # probably defunct
importFrom(sp,proj4string) # ensure use of WKT-2
importFrom(sp,spTransform) # uses st_transform internally in status 2L

Whether these are actually used or not is unknown, only rgeos::gBuffer was found by pkgapi. I would drop the strong dependencies, comment out the imports, then work around the problems then arising until the output matches the output before changes.

I don't see any relevant updates to the github repo, but maybe you have already made changes on a clone or fork. Since this is an ropensci package, I suggest a review round with them, perhaps also to check workflows not published as packages. @maelle , @Bisaloo suggestions? If you need to raise issues with us, please use https://github.com/r-spatial/evolution/issues.

azizka commented 1 year ago

@BrunoVilela has started working on this issue, this week, will be finished before October. These hint will be very helpful, thanks.

rsbivand commented 1 year ago

Now only three months remain, please submit to CRAN soon @BrunoVilela @kguidonimartins https://github.com/brunobrr/bdc/issues/253

maelle commented 12 months ago

I followed up with the maintainer per email.

rsbivand commented 12 months ago

@maelle Thanks!

rsbivand commented 11 months ago

@azizka @maelle @BrunoVilela The current state of the new_spatial branch passes my CMD check with the forthcoming changes. Please expedite submission to CRAN, as the current release will fail when sp 2.1-0 is submitted (hopefully in early September), freeing sp from the retiring packages. CC @edzer

rsbivand commented 9 months ago

@azizka @maelle @BrunoVilela Action needed immediately; the package will fail CRAN checks as soon as sp 2.1-0 is published, (very soon); rgdal and rgeos have less than three weeks' left.

azizka commented 9 months ago

Thanks, we are working through the issues. Target date was end of this month. @BrunoVilela any news?

rsbivand commented 9 months ago

@azizka Thanks, please try to complete ASAP to avoid a last minute rush. We expect to archive the retiring packages 16 October.

maelle commented 9 months ago

@azizka @BrunoVilela any news? It might be too late to avoid an archival on CRAN now.

rsbivand commented 9 months ago

@maelle 3.0 was published on CRAN 2023-10-03, looks OK, closing here, thanks for your cooperation.

maelle commented 9 months ago

:tada: :relieved: