[Bioc-devel] BioConductor package vulnerabilities to R-spatial evolution process

Roger Bivand Roger@B|v@nd @end|ng |rom nhh@no
Sat Jun 3 15:09:43 CEST 2023

Packages: GSCA, Cardinal, cellmigRation, flowDensity, MoleculeExperiment, SPIAT, stJoincount, structToolbox, synergyfinder have strong dependencies on CRAN package sp; mtbls2 has a weak dependency. 

The evolution project https://github.com/r-spatial/evolution, https://www.r-consortium.org/all-projects/awarded-projects/2021-group-2#Preparing%20CRAN%20for%20the%20Retirement%20of%20rgdal,%20rgeos%20and%20maptools, has now published four reports, most recently https://r-spatial.org/r/2023/05/15/evolution4.html with links to the three previous ones. 

The sp package was written before the rgdal and rgeos packages, but rgdal, rgeos and maptools are being retired/archived in October 2023 because better alternatives exist, through the CRAN sf and terra packages. The continued use of sp is possible, rather for older existing packages, by coercion to and from classes used in sf and terra.

The new BioConductor package MoleculeExperiment has a new strong dependency on sp; I have raised an issue there: https://github.com/SydneyBioX/MoleculeExperiment/issues/1, but feel that BioConductor developers generally need to be warned off unconsidered new use of sp in ignorance of impending changes. sp 1.6-1 now on load issues a message informing of the need for care, so one can hope that maintainers will be attentive. Please alert any potentially affected as soon as possible, and post issues on https://github.com/r-spatial/evolution/issues - I do not follow this list carefully.

Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
Roger.Bivand using nhh.no

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