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Run CI against Bioconductor devel; fix macOS and batchelor warnings - #807
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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>
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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>
This was referenced Oct 9, 2026
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Reverts the BiocCheck part of 14fc41e (compbiomed#807). That stopgap ran BiocCheck on the built tarball only because the repo tracked .claude/settings.json; now that it doesn't, BiocCheck(".") runs BiocCheckGitClone on the repo again. ADR 0007 (still Proposed) drops the matching bullet and keeps the OpenSSL include-path change from the same commit. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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What changed and why
GitHub CI on
develhas failed for weeks for reasons unrelated to the codeunder test. This PR makes it test what the Bioconductor builders test
(ADR 0007).
checking examples ... WARNINGR_BIOC_VERSION: "3.24"in both workflows, so pak installs Bioc devel packagesfastMNN()/reducedMNN()call deprecated scuttle functionsrunFastMNN()uses.muffleUpstreamDeprecations(), now shared withrunMNNCorrect(), which muffles onlydeprecatedWarnings raised inside batcheloralabaster.basehas no macOS binary and its source build can't link OpenSSLopenssl@3and add its paths toLDFLAGS/CPPFLAGSin~/.R/Makevarsbefore installing dependenciesubuntu-latest, with BiocCheck installed from devel throughextra-packagesAlso:
actions/checkout@v4.R_BIOC_VERSIONat eachBioconductor release.
How it was tested
Locally (R 4.6.1, Bioc 3.23 packages):
runFastMNN()raises nodeprecatedWarning, with or withoutuseReducedDim. The assay case failed first (normalizeCountsfrombatchelor) and passes now. The batch-correction tests pass: 11 tests,
0 failures.
raised. Only the three decontX examples still warn locally, from decontX
1.10; CI on Bioc devel uses decontX 1.11. Before this PR,
runFastMNNalso warned.
one inherited variable name.
The workflow changes can only be confirmed by this PR's own CI run.
The first run builds many Bioconductor devel packages from source and may
take 30–60 minutes.
Checklist
make testpasses, andmake coveragedidn't drop. Only
test-batchCorrectionwas run locally.make check-fullandmake bioccheckpass with no new errors orwarnings. This PR's CI on Bioc devel is the real check.
make docsrun, if roxygen comments changed. N/A._pkgdown.yml, andmake site-checkpasses.N/A.
/code-reviewrun; findings fixed or answered. Nobugs; added the OpenSSL include path and a reducedMNN-path test, as
it suggested.
ADR
dev/adr/0007-ci-against-bioc-devel.md
Scientific correctness
Generated content
Claude Code (Opus 5.5) wrote all of this PR. The maintainer approved the
plan: run CI on Bioc devel, fix macOS, and handle the Rd anchors in a
separate PR.
🤖 Generated with Claude Code