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ci: Check Bioconductor reverse dependencies in revdep4 #2994

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d0cd59f
ci: Check Bioconductor reverse dependencies in revdep4
claude Oct 18, 2026
65912b4
docs: Say what a reverse-dependency run covers
claude Oct 18, 2026
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167 changes: 167 additions & 0 deletions .github/revdepx/bioconductor.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,167 @@
rigraph's patch to the revdepx scripts of cynkra/cynkratemplate at e45daecc565a10e0624769f868a680e147d2920c,
applied by .github/workflows/revdep4.yaml: checks Bioconductor reverse dependencies (REVDEPX_BIOC).
See handbook/testing/revdep/README.md.

diff --git a/.github/actions/revdepx/collect.R b/.github/actions/revdepx/collect.R
index 0792c2a..c1e4e6f 100644
--- a/.github/actions/revdepx/collect.R
+++ b/.github/actions/revdepx/collect.R
@@ -42,6 +42,7 @@ source(file.path(
results_dir <- env_chr("RESULTS_DIR")
stopifnot(nzchar(results_dir))
plan <- read_json(env_chr("PLAN", "plan.json"))
+options(revdepx.bioc_packages = unlist(plan$bioc_packages))
retry_dir <- env_chr("RETRY_DIR")
out_dir <- env_chr("OUT_DIR", "revdep")
baseline_out <- env_chr("BASELINE_OUT", "baseline")
@@ -828,6 +829,18 @@ readme <- gsub(
"[\\1](https://cran.r-project.org/package=\\1)",
readme
)
+for (bioc_package in getOption("revdepx.bioc_packages")) {
+ readme <- gsub(
+ sprintf(
+ "[%s](https://cran.r-project.org/package=%s)",
+ bioc_package,
+ bioc_package
+ ),
+ bioc_link(bioc_package),
+ readme,
+ fixed = TRUE
+ )
+}
readme <- gsub("^(#+)(\\s)", "##\\1\\2", readme)

run_id <- env_chr("GITHUB_RUN_ID")
diff --git a/.github/actions/revdepx/plan.R b/.github/actions/revdepx/plan.R
index bb519d8..705f53b 100644
--- a/.github/actions/revdepx/plan.R
+++ b/.github/actions/revdepx/plan.R
@@ -46,6 +46,9 @@
# `broken` to take them from the committed report
# REVDEPX_WHICH - "strong" (default) or "most" (adds Suggests/
# Enhances dependents)
+# REVDEPX_BIOC - which Bioconductor reverse dependencies to check
+# too: "none" (default), "direct" (level 1 only)
+# or "all" (every level walks CRAN and Bioconductor)
# REVDEPX_WORKERS - packages checked concurrently per shard
# (default: 4)
# REVDEPX_R_VERSION - the full R version the *containers* check under,
@@ -113,6 +116,10 @@ which_input <- match.arg(
env_chr("REVDEPX_WHICH", "strong"),
c("strong", "most")
)
+bioc_input <- match.arg(
+ tolower(env_chr("REVDEPX_BIOC", "none")),
+ c("none", "direct", "all")
+)
depth_raw <- tolower(env_chr("REVDEPX_DEPTH", "1"))
depth <- if (depth_raw %in% c("all", "max", "inf", "infinity")) {
Inf
@@ -347,6 +354,10 @@ if (!package %in% rownames(db)) {
cran_version <- unname(db[package, "Version"])
inform("CRAN version: ", cran_version)

+# What may be checked: CRAN alone, or CRAN and Bioconductor. dep_db() keeps
+# CRAN's row for a name both carry, so a CRAN package stays a CRAN check.
+check_db <- if (bioc_input == "none") db else dep_db()
+
# ------------------------------------------------------------- enumeration ---

# Breadth-first over reverse dependencies: level 1 depends on the package
@@ -357,9 +368,12 @@ level_of <- integer()
frontier <- package
level <- 0L
while (level < depth && length(frontier) > 0) {
+ # "direct" adds Bioconductor at level 1 only; deeper levels find CRAN
+ # dependents alone, as without Bioconductor.
+ bioc_level <- bioc_input == "all" || (bioc_input == "direct" && level == 0)
found <- tools::package_dependencies(
frontier,
- db = db,
+ db = if (bioc_level) check_db else db,
which = if (which_input == "most") "most" else "strong",
reverse = TRUE
)
@@ -466,15 +480,23 @@ if (length(packages_input) > 0) {
candidates <- revdeps
}

-dropped <- setdiff(candidates, rownames(db))
+dropped <- setdiff(candidates, rownames(check_db))
if (length(dropped) > 0) {
- inform("Not on CRAN, dropped: ", paste(dropped, collapse = ", "))
+ inform(
+ if (bioc_input == "none") "Not on CRAN" else "Not on CRAN or Bioconductor",
+ ", dropped: ",
+ paste(dropped, collapse = ", ")
+ )
}
-packages <- intersect(candidates, rownames(db))
+packages <- intersect(candidates, rownames(check_db))
if (length(packages) == 0) {
plan_nothing("no packages left to check")
}
-their_version <- setNames(unname(db[packages, "Version"]), packages)
+their_version <- setNames(unname(check_db[packages, "Version"]), packages)
+bioc_packages <- sort(setdiff(packages, rownames(db)))
+if (length(bioc_packages) > 0) {
+ inform(length(bioc_packages), " of them from Bioconductor")
+}

# ------------------------------------------------------------------ weights --

@@ -1192,6 +1214,8 @@ plan <- list(
ref = env_chr("GITHUB_REF_NAME"),
which = which_input,
depth = depth_raw,
+ bioc = bioc_input,
+ bioc_packages = as.list(bioc_packages),
levels = as.list(level_counts),
selection = selection,
part = part,
diff --git a/.github/actions/revdepx/shard.R b/.github/actions/revdepx/shard.R
index 1460e84..6ac1c95 100644
--- a/.github/actions/revdepx/shard.R
+++ b/.github/actions/revdepx/shard.R
@@ -606,12 +606,14 @@ src_dir <- file.path(work, "src")
dir.create(src_dir, showWarnings = FALSE)
sources <- list()
for (name in runnable) {
+ # The plan names the Bioconductor revdeps it admitted under REVDEPX_BIOC.
+ repos <- if (name %in% unlist(plan$bioc_packages)) bioc_repos() else cran_repo()
tarball <- tryCatch(
{
hit <- utils::download.packages(
name,
destdir = src_dir,
- repos = cran_repo(),
+ repos = repos,
type = "source",
quiet = TRUE
)
diff --git a/.github/actions/revdepx/util.R b/.github/actions/revdepx/util.R
index 69d954f..9379269 100644
--- a/.github/actions/revdepx/util.R
+++ b/.github/actions/revdepx/util.R
@@ -104,11 +104,19 @@ this_run_link <- function(text = env_chr("GITHUB_RUN_ID", "local")) {
}

# A revdep, linked to its CRAN page -- the one page about it that is reachable
-# from a job summary, and the one that names its maintainer.
+# from a job summary, and the one that names its maintainer -- or to its
+# Bioconductor page for the names in option `revdepx.bioc_packages`.
cran_link <- function(package) {
+ if (package %in% getOption("revdepx.bioc_packages")) {
+ return(bioc_link(package))
+ }
sprintf("[%s](https://cran.r-project.org/package=%s)", package, package)
}

+bioc_link <- function(package) {
+ sprintf("[%s](https://bioconductor.org/packages/%s)", package, package)
+}
+
# ------------------------------------------------------------------- JSON ----

write_json <- function(x, path) {
70 changes: 54 additions & 16 deletions .github/workflows/revdep4.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,14 @@
# so history from the sibling's live runs still serves as baselines and
# timings.
#
# Every kit action is pinned to one kit commit, and the jobs that run
# plan.R, shard.R or collect.R apply .github/revdepx/bioconductor.patch to
# the scripts first: it checks Bioconductor reverse dependencies too
# (REVDEPX_BIOC, the `bioconductor` input). The patch is read from the
# workflow's own commit, so a `ref` that lacks it still gets it. Moving the
# pin means re-cutting the patch; handbook/testing/revdep/ says what a run
# covers.
#
# Results land in artifacts:
# revdepx-report the merged report -- fetch with
# `gh run download <run-id> --name revdepx-report`
Expand Down Expand Up @@ -100,6 +108,14 @@ on:
- strong
- most
default: strong
bioconductor:
description: "Bioconductor reverse dependencies to check beside CRAN's: all (at every level, like CRAN's), direct (level 1 only) or none"
type: choice
options:
- all
- direct
- none
default: all
depth:
description: "Levels of reverse dependencies: 1 = direct, 2 = also revdeps of revdeps, ..., 'all' = the full transitive closure"
type: string
Expand Down Expand Up @@ -176,6 +192,7 @@ env:
REVDEPX_PACKAGES: ${{ inputs.packages || '' }}
REVDEPX_WHICH: ${{ inputs.which || 'strong' }}
REVDEPX_DEPTH: ${{ inputs.depth || '1' }}
REVDEPX_BIOC: ${{ inputs.bioconductor || 'all' }}
REVDEPX_RETRY_RUN: ${{ inputs.retry-run || '' }}
REVDEPX_PART: ${{ inputs.part || '' }}
REVDEPX_R_VERSION_INPUT: ${{ inputs.r-version || '4.6.1' }}
Expand Down Expand Up @@ -254,20 +271,27 @@ jobs:
steps:
# The scripts are served with the kit's actions, not copied into the repository.
- name: Locate the revdep scripts
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@main
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@e45daecc565a10e0624769f868a680e147d2920c

- name: Check out the ref under test
uses: actions/checkout@v6
with:
ref: ${{ inputs.ref || github.ref }}

- name: Patch the revdep scripts for Bioconductor
run: |
git fetch --quiet --depth 1 origin "${GITHUB_SHA}"
git show FETCH_HEAD:.github/revdepx/bioconductor.patch |
patch --batch --forward -p4 -d "${REVDEPX_DIR}"
shell: bash

# The same resolution runs in the base and build jobs: the three run in
# parallel and each needs the answer before any of them could publish
# it. It is one cached HTTPS call; determinism within a run is what
# matters, and the alias moves at most once every few months.
- name: Resolve the R version
id: resolve
uses: cynkra/cynkratemplate/.github/actions/revdepx-resolve-r-version@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-resolve-r-version@e45daecc565a10e0624769f868a680e147d2920c
with:
input: ${{ env.REVDEPX_R_VERSION_INPUT }}

Expand Down Expand Up @@ -322,7 +346,7 @@ jobs:
steps:
# The scripts are served with the kit's actions, not copied into the repository.
- name: Locate the revdep scripts
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@main
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@e45daecc565a10e0624769f868a680e147d2920c

- name: Check out the ref under test
uses: actions/checkout@v6
Expand All @@ -331,7 +355,7 @@ jobs:

# Same resolution as in the plan job; see the comment there.
- name: Resolve the R version
uses: cynkra/cynkratemplate/.github/actions/revdepx-resolve-r-version@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-resolve-r-version@e45daecc565a10e0624769f868a680e147d2920c
with:
input: ${{ env.REVDEPX_R_VERSION_INPUT }}

Expand Down Expand Up @@ -400,7 +424,7 @@ jobs:
# container's R (the pinned oldrel), and a binary built by the runner's
# newer R would not.
- name: Build the binary in the base container
uses: cynkra/cynkratemplate/.github/actions/revdepx-build-binary@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-build-binary@e45daecc565a10e0624769f868a680e147d2920c
with:
base-image: ${{ needs.base.outputs.image }}
- name: Upload the package binary
Expand Down Expand Up @@ -445,7 +469,7 @@ jobs:
steps:
# The scripts are served with the kit's actions, not copied into the repository.
- name: Locate the revdep scripts
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@main
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@e45daecc565a10e0624769f868a680e147d2920c

- name: Check out the ref under test
uses: actions/checkout@v6
Expand Down Expand Up @@ -474,7 +498,7 @@ jobs:
# this job lands in one accounted place. The commit step below
# measures against that one disk before copying anything large.
- name: Make room for docker on the one disk
uses: cynkra/cynkratemplate/.github/actions/revdepx-docker-room@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-docker-room@e45daecc565a10e0624769f868a680e147d2920c
# The universe build downloads every dependency once; saving the pak
# cache under the plan's hash hands the next build a warm start even
# when the image itself cannot be reused.
Expand All @@ -499,7 +523,7 @@ jobs:

- name: Build the universe image
id: build-universe
uses: cynkra/cynkratemplate/.github/actions/revdepx-build-universe@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-build-universe@e45daecc565a10e0624769f868a680e147d2920c
with:
base-image: ${{ needs.base.outputs.image }}
# Everything here is written and UPLOADED before the commit below
Expand All @@ -510,7 +534,7 @@ jobs:
# starts, or they do not exist.
- name: Record the state before the commit
id: precommit
uses: cynkra/cynkratemplate/.github/actions/revdepx-record-precommit@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-record-precommit@e45daecc565a10e0624769f868a680e147d2920c
- name: Publish the pre-commit state (survives a dying runner)
uses: actions/upload-artifact@v6
with:
Expand All @@ -533,7 +557,7 @@ jobs:
# already takes.
- name: Commit and push the universe image
id: publish
uses: cynkra/cynkratemplate/.github/actions/revdepx-publish-universe@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-publish-universe@e45daecc565a10e0624769f868a680e147d2920c
- name: Upload the universe image artifact (registry fallback only)
uses: actions/upload-artifact@v6
if: steps.publish.outputs.saved == 'true'
Expand Down Expand Up @@ -641,13 +665,20 @@ jobs:
steps:
# The scripts are served with the kit's actions, not copied into the repository.
- name: Locate the revdep scripts
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@main
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@e45daecc565a10e0624769f868a680e147d2920c

- name: Check out the ref under test
uses: actions/checkout@v6
with:
ref: ${{ inputs.ref || github.ref }}

- name: Patch the revdep scripts for Bioconductor
run: |
git fetch --quiet --depth 1 origin "${GITHUB_SHA}"
git show FETCH_HEAD:.github/revdepx/bioconductor.patch |
patch --batch --forward -p4 -d "${REVDEPX_DIR}"
shell: bash

# The host runs only the driver: R with jsonlite and rcmdcheck to
# parse, compare and account. Everything a check needs -- TeX, pandoc,
# qpdf, the dependency library -- lives in the image. This is the whole
Expand Down Expand Up @@ -709,7 +740,7 @@ jobs:
# and put that data-root under RUNNER_TEMP beside the checks' work
# directories, so everything heavy is in one accounted place.
- name: Make room for docker on the one disk
uses: cynkra/cynkratemplate/.github/actions/revdepx-docker-room@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-docker-room@e45daecc565a10e0624769f868a680e147d2920c

# Both driver phases need these and neither can name them itself: the
# `runner` context does not reach the job's `env`, so they are set once
Expand All @@ -719,7 +750,7 @@ jobs:
# `NOT_CRAN=true` into `$GITHUB_ENV`, and a later write is what
# reliably overrides an earlier one.
- name: Point the driver at this runner's directories
uses: cynkra/cynkratemplate/.github/actions/revdepx-driver-env@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-driver-env@e45daecc565a10e0624769f868a680e147d2920c
with:
not-cran-input: ${{ env.REVDEPX_NOT_CRAN }}
# Emit machine state while the work runs: a reclaimed runner never
Expand All @@ -739,7 +770,7 @@ jobs:
# universe job died -- build a shard-local image from the base), and
# extract its library index for the driver's dependency screen.
- name: Prepare the check image
uses: cynkra/cynkratemplate/.github/actions/revdepx-check-image@main
uses: cynkra/cynkratemplate/.github/actions/revdepx-check-image@e45daecc565a10e0624769f868a680e147d2920c
with:
universe-image: ${{ needs.universe.outputs.image }}
revdepx-base-image: ${{ needs.base.outputs.image }}
Expand Down Expand Up @@ -875,13 +906,20 @@ jobs:
steps:
# The scripts are served with the kit's actions, not copied into the repository.
- name: Locate the revdep scripts
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@main
uses: cynkra/cynkratemplate/.github/actions/revdep-scripts@e45daecc565a10e0624769f868a680e147d2920c

- name: Check out the ref under test
uses: actions/checkout@v6
with:
ref: ${{ inputs.ref || github.ref }}

- name: Patch the revdep scripts for Bioconductor
run: |
git fetch --quiet --depth 1 origin "${GITHUB_SHA}"
git show FETCH_HEAD:.github/revdepx/bioconductor.patch |
patch --batch --forward -p4 -d "${REVDEPX_DIR}"
shell: bash

- name: Set up R
uses: r-lib/actions/setup-r@v2
with:
Expand Down Expand Up @@ -969,7 +1007,7 @@ jobs:
&& vars.REVDEPX_COMMIT_REPORT != 'false'
&& steps.collect.outputs.compared != '0'
continue-on-error: true
uses: cynkra/cynkratemplate/.github/actions/revdep-commit-report@main
uses: cynkra/cynkratemplate/.github/actions/revdep-commit-report@e45daecc565a10e0624769f868a680e147d2920c
with:
ref: ${{ inputs.ref }}
workflow: revdep4
Expand Down
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