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Add package anchors to Rd links (Rd cross-references NOTE/WARNING) - #808
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batchelor 1.28's fastMNN() and reducedMNN(), like mnnCorrect(), still call deprecated scuttle functions, which fails R CMD check on the runFastMNN example. A shared helper, .muffleUpstreamDeprecations(), muffles only deprecatedWarnings raised inside those calls and documents why. Version 2.23.5. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Set R_BIOC_VERSION to the Bioconductor devel version so CI installs the same dependencies as the Bioconductor builders, link Homebrew's OpenSSL for alabaster.base's source build on macOS, run BiocCheck on Ubuntu with BiocCheck installed from devel, and use actions/checkout@v4. ADR 0007 records the decision; the release checklist gains the step to update R_BIOC_VERSION. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
From /code-review: the alabaster.base source build may also need OpenSSL headers, and runFastMNN(useReducedDim = ) was untested. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
R CMD check notes, and the Bioconductor devel builders warn, that 138 help
pages link to other packages' topics without a package anchor. The roxygen
sources now give the package for each target: \linkS4class{X} becomes
\link[pkg:X-class]{X}, and \link{topic} becomes \link[pkg]{topic}, for
SingleCellExperiment, SummarizedExperiment, S4Vectors, DelayedArray,
Matrix, GSEABase, BiocParallel, reticulate, scRNAseq, msigdbr, and igraph.
Every target was checked to exist as a help alias in its package.
R CMD check now reports 'checking Rd cross-references ... OK'.
Version 2.23.6.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
BiocCheck 1.49 (Bioc 3.24) errors on Git-tracked .claude/ files, and the lab standards commit .claude/settings.json. The built tarball excludes it through .Rbuildignore, and the Bioconductor builders also check tarballs. ADR 0007 records this; the standards question goes to campbio/r-bioc-dev-standards. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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What changed and why
R CMD check notes, and the Bioconductor devel builders report as a
WARNING, that 138 help pages link to other packages' topics without a
package anchor:
The roxygen sources in
R/now name the package for each target, andman/was regenerated withmake docs:\linkS4class{SingleCellExperiment}(189×)\link[SingleCellExperiment:SingleCellExperiment-class]{SingleCellExperiment}\linkS4class{GeneSetCollection},{BiocParallelParam},{SummarizedExperiment}\link{colData},\link{assay}\link[SummarizedExperiment]{...}\link{metadata}\link[S4Vectors]{metadata}\link{altExp},\link{reducedDim}\link[SingleCellExperiment]{...}\link{DelayedArray},\link{readMM},\link{Matrix}How it was tested
make check(local, R 4.6.1):checking Rd cross-references ... OK,where it was a NOTE before. 0 errors.
normalizeCountsdeprecationsfrom decontX 1.10 in the local Bioc 3.23 library. CI on Bioc devel
(Run CI against Bioconductor devel; fix macOS and batchelor warnings #807) uses decontX 1.11.
.gitNOTE comes from running in a git worktree.R/*.Rroxygen lines,man/*.Rd, DESCRIPTION, and NEWS changed.Checklist
make testpasses, andmake coveragedidn't drop. N/A: documentation only.
make check-fullandmake bioccheckpass with no new errors orwarnings.
make checkwas run; the Rd cross-references check is OK.make docsrun, if roxygen comments changed_pkgdown.yml, andmake site-checkpasses.N/A.
/code-reviewrun; findings fixed or answered. Amechanical change, checked by R CMD check.
ADR
N/A.
Scientific correctness
Generated content
Claude Code (Opus 5.5) wrote all of this PR, as part of the plan the
maintainer approved for getting CI and the Bioconductor build clean.
🤖 Generated with Claude Code