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Separate failure policies for R CMD check and BiocCheck - #38
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Rename error_on to rcmdcheck_error_on and add bioccheck_error_on (error or never) so a known, unavoidable BiocCheck ERROR such as a Remotes: dependency not yet in Bioconductor no longer hides R CMD check results. No compatibility alias: the workflow is pre-release with seven known callers, and rename PRs follow on merge. Template, generator, usage docs and canary updated; ADR added as Accepted. Co-authored-by: Claude Code <noreply@anthropic.com>
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BiocCheck raises an ERROR for any
Remotes:orAdditional_repositories:field in DESCRIPTION, and that check cannot be silenced on its own. A package under development that depends on something not yet in Bioconductor is therefore permanently red, which hides the R CMD check results the maintainer does care about (curatedMetagenomicData is the motivating case).This PR gives the two tools separate failure policies:
rcmdcheck_error_on(defaultwarning): the input formerly namederror_on, same four values.bioccheck_error_on(defaulterror):errorkeeps the current behaviour (quit-with-status);neverprints the BiocCheck report without failing the job. BiocCheck warnings and notes never fail the job either way, since BiocCheck only exits non-zero on ERRORs.error_onis removed with no alias. The workflow is pre-release with seven known public callers, all on@main; one-line rename PRs go to each of them as soon as this merges, so the window where they are red is short.Defaults preserve current behaviour for every caller once renamed. The template
ci.yml, the Workflow Generator, the usage guide, technical notes and the canary are updated. ADR 0013 (Accepted) amends ADR 0003; the ADR index also drops the stale "(Proposed)" tag on ADR 0010, which was accepted in #35.Linted with yamllint and actionlint; reviewed by Gemini before opening; canary run on the branch passed.
Drafted with Claude Code.