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Fix/CRAN NOTE #9565

Merged
merged 4 commits into from
Dec 20, 2024
Merged

Fix/CRAN NOTE #9565

merged 4 commits into from
Dec 20, 2024

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dcollins15
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This PR implements two quick fixes to address the following NOTE currently being thrown by R CMD check:

❯ checking CRAN incoming feasibility ... [10s/64s] NOTE
  Maintainer: ‘Rahul Satija <[email protected]>’
  
  Version contains large components (5.1.0.9017)
  
  Suggests or Enhances not in mainstream repositories:
    BPCells, enrichR, presto
  Availability using Additional_repositories specification:
    BPCells   yes   https://bnprks.r-universe.dev/   
    presto    yes   https://satijalab.r-universe.dev/
    enrichR    no   ?                               
  
  Found the following URLs which should use \doi (with the DOI name only):
    File ‘MULTIseqDemux.Rd’:
      https://doi.org/10.1038/s41592-019-0433-8

enrichR was dropped from CRAN on 2024-11-04. Thankfully, it is available from https://cran.r-universe.dev, so we can just add that as an additional repo for now. The only other alternative would be completely deprecating DEenrichRPlot so that we can drop the dependency, but I'd rather not introduce a breaking change during a minor release if we don't have to.

The MULTIseqDemux reference link was recently updated in #8180—I missed the change during my review but it was probably trying to address previous flakiness in CRAN checks caused by the old link. Hopefully, using the DOI name only will cause fewer issues for us in the future.

@dcollins15 dcollins15 marked this pull request as ready for review December 20, 2024 19:09
@dcollins15 dcollins15 requested a review from rsatija December 20, 2024 19:36
@dcollins15 dcollins15 merged commit db8e8f5 into develop Dec 20, 2024
1 of 3 checks passed
@dcollins15 dcollins15 deleted the fix/cran-notes branch December 20, 2024 19:36
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