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green-striped-gecko / PopGenReport

a simple way to analyse population genetic data using R
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Please remove dependencies on **rgdal**, **rgeos**, and/or **maptools** #8

Open rsbivand opened 1 year 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.

rsbivand commented 1 year ago

This package has strong dependence on at least one of rgdal, rgeos or maptools, but does not seem to use any functionality in code. The usage may have been in raster, which now uses terra instead, or may be in examples or vignettes. Please move all use of rgdal, rgeos or maptools to Suggests: and protect any use against these packages not being present. The packages will be archived in October 2023. See https://r-spatial.org/r/2022/12/14/evolution2.html and https://rsbivand.github.io/csds_jan23/bivand_csds_ssg_230117.pdf and perhaps view https://www.youtube.com/watch?v=TlpjIqTPMCA&list=PLzREt6r1NenmWEidssmLm-VO_YmAh4pq9&index=1.

rsbivand commented 1 year ago

In addition, CMD check failure in a scenario using sp evolution status 2 (substitute use of rgdal with sf for projection/transformation/CRS) and absence of retiring packages from the library path, also causes dartR to fail because it strongly depends on this package. Please also see https://r-spatial.org/r/2023/04/10/evolution3.html.

mijangos81 commented 1 year ago

Hi,

We have removed all dartR’s dependencies on rgdal, rgeos, and/or maptools

Cheers, Luis

rsbivand commented 1 year ago

Only three months remain to save this package. Please act now!

rsbivand commented 1 year ago

@mijangos81 @green-striped-gecko Less than three weeks remain to fix this. As dartR imports this package, it would be collateral damage if this not fixed.

rsbivand commented 1 year ago

@mijangos81 @green-striped-gecko R spatial infrastructure packages maptools, rgdal and rgeos will be archived by CRAN on Monday, October 16, 2023. Your package does not pass CMD check when these packages are not available. Expect your package to be archived by CRAN October 17-18 as CRAN checks feed through and your package fails, if not updated by Monday, October 16, 2023.

No grace period is anticipated, as you have had sufficient time to update your package to remove dependencies on maptools, rgdal and/or rgeos. It remains the case that many packages importing the raster package needlessly depend on retiring packages, as raster stopped using them a year ago.