Release/5.2.0

[dcollins15]

Release Seurat v5.2.0 🚀

• Bump version
• Update changelog
• win-builder
• mac-builder
• Update CRAN comments
• Submit to CRAN
• Resolve issues with submission
• Re-submit to CRAN
• Resolve issues with submission
• Re-submit to CRAN

---

Historically, we have made major/minor version bumps in release/major.minor.patch branches that are merged to develop, which is subsequently merged into master which is then fast-forwarded back into develop. This time though, we'll take a page out of the seurat-object playbook and merge release/5.2.0 directly to master and then fast-forward master back to develop. The results are similar, but this way requires a one-fewer PR.

(In the future, we will likely refine this workflow further)

[dcollins15]

CRAN rejected our submission with the following NOTEs:

The main problem seems to be a bunch of roxygen2 \link{} statements pointing to targets exported by SeuratObject without properly referencing the package:

Check: Rd cross-references, Result: NOTE
  Found the following Rd file(s) with Rd \link{} targets missing package
  anchors:
    CCAIntegration.Rd: DimReduc
    FindNeighbors.Rd: Neighbor, Graph, Graphs
    FindTransferAnchors.Rd: RANN, RcppAnnoy
    IntegrateData.Rd: DimReduc, RANN, Assay
    IntegrateEmbeddings.Rd: DimReduc
    JointPCAIntegration.Rd: DimReduc
    PrepSCTIntegration.Rd: Assay
    RPCAIntegration.Rd: DimReduc
    RunCCA.Rd: merge.Seurat
    SCTAssay-class.Rd: Assay
    TopNeighbors.Rd: Neighbor
    TransferData.Rd: DimReduc, RANN
    fortify-Spatial.Rd: Segmentation-class, Centroids-class,
      Molecules-class
  Please provide package anchors for all Rd \link{} targets not in the
  package itself and the base packages.

It seems like external package links don't point anywhere in either the reference manual or the website's reference pages, even if they're properly formatted—it's unclear what the upside of including them is... For now, I'll address the problematic blocks but it'd probably be worthwhile to do a more comprehensive cleanup of our roxygen2 documentation in the near term.

There is also a bad @reference tag link (I'm pretty sure this is a false positive, but I still think it's worth switching over to just the DOI, at the very least that seems to be less flaky):

Found the following (possibly) invalid URLs:
    URL: https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui
      From: man/RunSPCA.Rd
      Status: 403
      Message: Forbidden
  Please use DOIs for the following publisher URLs:
    https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui

These NOTEs were present in the win-builder output for R-devel but I assumed it was a false positive. Once things are passing with my local version I'll push the changes and then resubmit to CRAN 👍

[dcollins15]

CRAN rejected our submission with the following NOTE:

Check: compilation flags used, Result: WARNING
  Compilation used the following non-portable flag(s):
    '-Wno-missing-template-arg-list-after-template-kw'
  including flag(s) suppressing warnings

[rharao]

@dcollins15 I'm curious about from where the offending compilation flag was picked up. It would have to be a non-CRAN package, right?