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Drop --as-cran from R CMD check - #32
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Bioconductor packages are checked against Bioconductor policy, not CRAN policy, so --as-cran produces NOTEs that are irrelevant here (and can fail the job under error_on: warning). BiocCheck already covers the Bioconductor-specific requirements. Also removes _R_CHECK_CRAN_INCOMING_REMOTE_, which only existed to suppress the remote incoming checks that --as-cran turns on. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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🟢 Approval recommended
The focused changes correctly remove the CRAN-only behavior and its associated configuration.
Review effort: Balanced
Findings: None
What changed in this PR
Removes CRAN-specific checks from the reusable Bioconductor validation workflow.
Changes:
- Drops
--as-cranfromrcmdcheck. - Removes the now-unnecessary CRAN incoming-check environment override.
| File | Description |
|---|---|
.github/workflows/bioccheck.yml |
Aligns package checks with Bioconductor policy. |
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rcmdcheckin the reusablebioccheck.ymlworkflow was running with--as-cran. Bioconductor packages are checked against Bioconductor policy, not CRAN policy, so the CRAN-only checks produce NOTEs that are irrelevant here, and witherror_on: 'warning'they can fail the job for things Bioconductor doesn't care about. Example: https://github.com/waldronlab/curatedMetagenomicData/actions/runs/37500050547/job/112394531507#step:7:79Changes:
args = c("--no-manual", "--as-cran")becomesargs = "--no-manual"_R_CHECK_CRAN_INCOMING_REMOTE_: 'false', which only existed to suppress the remote incoming checks that--as-cranturns onBiocCheck still runs on the tarball and covers the Bioconductor-specific requirements.
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