Sources and refresh baseline
This file records where each summary came from and the exact upstream state it was generated against. Use it to detect drift and to refresh only what changed: compare the live upstream against the pins below, and re-derive only the knowledge files the changed chapters map to.
Tracked upstreams (update every pin on every refresh)
Four upstreams, not one. A change to any of them can silently invalidate the guidance here.
| Upstream | Pin | Verified | Invalidates |
|---|---|---|---|
Bioconductor/pkgrevdocs (devel) | 9b078ea2a0ec05274be83cb12ea75473c6d0c808 (committed 2026-07-20) | 2026-08-14 | all of knowledge/ |
Bioconductor/BiocContributions .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE.md | blob a9e7b0e39fbf (repo devel at 2e040ee3, 2026-07-22) | 2026-08-18 | the pre-submission gate wording in ../SKILL.md |
| Bioconductor/BiocCheck | release 1.48.1, devel 1.49.30 | 2026-08-14 | what “BiocCheck clean” means |
| lcolladotor/biocthis | release 1.22.0, devel 1.23.0 | 2026-08-14 | the scaffolding guidance in ../SKILL.md |
Bioconductor cycle at the last refresh: Bioconductor release 3.23, devel 3.24, both on R 4.6.0 (source: https://bioconductor.org/config.yaml). Check that triple against config.yaml before relying on it - it changes twice a year, and an agent that is not given it will invent one.
Other baseline facts:
- Rendered guide: https://contributions.bioconductor.org
- Summaries fetched: 2026-08-14. Every summary now carries that stamp. The earlier 2026-07-23 pass is still the origin of most of the prose, but the pkgrevdocs pin was re-verified on 2026-08-14 and no mapped chapter had changed between the two dates, so the later date is the one each file can actually back.
Machine-readable endpoints used for drift detection:
- pkgrevdocs commit:
https://api.github.com/repos/Bioconductor/pkgrevdocs/commits/devel, fieldsha - changed files since the pin:
https://github.com/Bioconductor/pkgrevdocs/compare/<pinned>...devel - chapter order:
https://raw.githubusercontent.com/Bioconductor/pkgrevdocs/devel/_bookdown.yml - BiocCheck / biocthis versions:
https://bioconductor.org/packages/release/bioc/VIEWSand.../devel/bioc/VIEWS(parsePackage:/Version:pairs - the HTML landing pages are not reliably parseable) - Bioconductor release/devel pair and their R version:
https://bioconductor.org/config.yaml
Chapter map: .Rmd source -> rendered slug -> knowledge file
Two columns are needed, not one. The GitHub compare API reports changed .Rmd filenames, while every Source: footer in knowledge/ cites a rendered slug - and they routinely differ (package-maintainence.Rmd renders to package-maintenance.html, note the upstream misspelling; bioc-classes-methods.Rmd renders to reusebioc.html). A drift report can only be scoped to the right files by joining through this table.
Rendered pages live at https://contributions.bioconductor.org/<slug>.html. Chapter order and .Rmd names come from _bookdown.yml; slugs come from each chapter’s {#id} anchor.
| .Rmd | Slug | Ch | Knowledge file |
|---|---|---|---|
index.Rmd | index | - | not summarized (welcome page, no rules) |
package-submission.Rmd | submission-overview | - | 01-submissions.md |
package-submission.Rmd | bioconductor-package-submissions | 1 | 01-submissions.md |
devguide-introduction.Rmd | develop-overview | - | not summarized (part overview, no rules) |
package-name.Rmd | package-name | 2 | development/package-name.md |
general-package-development.Rmd | general | 3 | development/general-dev.md |
important-bioc-features.Rmd | important-bioconductor-package-development-features | 4 | development/general-dev.md |
bioc-classes-methods.Rmd | reusebioc | 5 | development/methods-classes.md |
readme-file.Rmd | readme | 6 | development/metadata-files.md |
description-file.Rmd | description | 7 | development/metadata-files.md |
namespace-file.Rmd | namespace | 8 | development/metadata-files.md |
news-file.Rmd | news | 9 | development/metadata-files.md |
license-file.Rmd | license | 10 | development/metadata-files.md |
citation-file.Rmd | citation | 11 | development/metadata-files.md |
install-file.Rmd | sysdep | 12 | development/metadata-files.md |
documentation.Rmd | docs | 13 | development/documentation.md |
package-data.Rmd | data | 14 | development/data.md |
unit-tests.Rmd | tests | 15 | development/tests.md |
r-code.Rmd | r-code | 16 | development/r-code.md |
fortran-C-python.Rmd | other-than-Rcode | 17 | development/compiled-thirdparty.md |
shiny-apps.Rmd | shiny | 18 | development/shiny.md |
ai-policy-third-party.Rmd | ai-policy-third-party | 19 | development/ai-policy.md |
non-software-packages.Rmd | non-software | 20 | development/non-software-pkgs.md |
gitignore-file.Rmd | gitignore | 21 | development/gitignore.md |
build-check-bioccheck.Rmd | build-check-bioccheck | 22 | development/build-check-bioccheck.md |
devguide-conclusion.Rmd | conclusion | 23 | development/build-check-bioccheck.md |
package-maintainence.Rmd | package-maintenance | - | not summarized (part overview, no rules) |
git-version-control.Rmd | git-version-control | 24 | maintenance.md |
version-numbering.Rmd | versionnum | 25 | maintenance.md |
troubleshoot-build-report.Rmd | troubleshooting-build-report | 26 | maintenance.md |
debugging-c-code.Rmd | debugging-cc-code | 27 | maintenance.md |
deprecation.Rmd | deprecation | 28 | maintenance.md |
package-end-of-life.Rmd | package-end-of-life-policy | 29 | maintenance.md |
branch-rename-faq.Rmd | branch-rename-faqs | 30 | maintenance.md |
review-overview.Rmd | reviewer-resources-overview | - | reviewer.md |
review-expectations.Rmd | review-expectation | 31 | reviewer.md |
review-resources-and-tools.Rmd | reviewtools | 32 | reviewer.md |
volunteer-to-review.Rmd | review-volunteer-chapter | 33 | reviewer.md |
appendix.Rmd | - | - | no page (part marker only) |
devel-branch.Rmd | use-devel | A | appendices.md |
advanced-build-options.Rmd | advanced-build-options | B | appendices.md |
web-query.Rmd | querying-web-resources | C | appendices.md |
c-and-fortran.Rmd | c-fortran | D | appendices.md |
mavericks.Rmd | cmavericks-best-practices | E | appendices.md |
debug-rd-links.Rmd | man-links | F | appendices.md |
news-for-bookdown.Rmd | booknews | G | appendices.md |
references.Rmd | references-1 | H | appendices.md |
Three slugs are deliberately marked “not summarized”: index, develop-overview and package-maintenance are welcome or part-overview pages whose entire body is a sentence or two of orientation. They carry no rules to summarize. They are listed anyway so that a chapter-coverage check can tell “we decided not to summarize this” apart from “we missed a chapter”.
Not chapter-derived (maintain by hand)
index.md (router), workflow.md (runbook), and this file.