ci: migrate R-CMD-check to the org reusable workflow - #31
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All changes have been used in FireSenseTesting for some time; time to merge
Firesense_LCC_flammability downloads from ftp.maps.canada.ca (LCC) and cwfis.cfs.nrcan.gc.ca (fire polygons) at build time. R-CMD-check runners routinely can't reach these, failing the vignette build with "Failed to connect to ... port 443". Probe both servers up front and skip the live download/analysis chunks when either is unreachable, degrading to documentation-only (same as the existing macOS/archive path). Adds curl to Suggests for the reachability probe. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Replaces this repo's hand-rolled matrix with a thin caller, so third-party action versions, system dependencies, caching and the check itself are maintained in one place instead of 17. Bumping actions/checkout there now updates every repo at once. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012DVjmY3im9Xak7tXLSMGCa
This was referenced Aug 31, 2026
The org concurrency budget is shared across every PredictiveEcology repo and is the binding constraint on getting work through. These legs added R versions below the default matrix; testing older R is explicitly not worth the runner contention it causes. oldrel-N is relative, so the default matrix's floor still rises on its own with each R release -- no standing commitment to any particular old version. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012DVjmY3im9Xak7tXLSMGCa
This reverts commit 654d7ab.
NLMR is not referenced anywhere in this package -- not in DESCRIPTION, R/,
vignettes/, tests/ or man/. Its only appearances were the two CI workflows,
which installed it from GitHub on every leg:
NLMR=?ignore
post-install: pak::pkg_install("ropensci/NLMR")
That is the same dead weight the PE CI standards call out from SpaDES, where
ropensci/NLMR and s-u/fastshp were installed on every pkgdown build while
being referenced nowhere -- the slowest step and the largest failure surface.
Removed from both R-CMD-check.yaml and test-coverage.yaml (this PR migrates
only the former, but the install was equally unused in the latter, and "remove
it entirely" means both).
Also sync extra-packages to the current Suggests:
- drop cowplot: promoted to Imports in 7b5afe5, so it now installs as a hard
dependency and does not belong in extra-packages.
- add curl: a real Suggests, and the LCC vignette's reachability probe is
gated on requireNamespace("curl") -- without it the probe silently degrades
to "skip" rather than testing anything.
Both files parse as valid YAML.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01T3NTQTNStSLZ3mA3CsLcon
The `dependencies: '"hard"'` setting plus 16 hand-listed Suggests worked around a pak solver bug: an inconsistent Matrix entry (R>=4.7 from /src/contrib/4.7.0/Recommended coexisting with R>=4.4 from the main /src/contrib path) that only surfaced when Suggests was traversed transitively. Hard-deps-only resolved, and the Suggests were re-added by hand. That failure depended on CRAN's metadata layout at a point in time. Retested in #37 (branched from this one, so the only variable was resolution mode): `dependencies: '"all"'` with no extra-packages list came back 12/12 green -- every platform, every R version including devel, and the nosuggests leg. The metadata that caused it has moved on. - R-CMD-check.yaml: '"hard"' -> '"all"', extra-packages list removed (16 entries, which duplicated DESCRIPTION's Suggests exactly). any::rcmdcheck is supplied by the reusable workflow. - test-coverage.yaml: same change. Its comment deferred to R-CMD-check.yaml for a rationale this migration would have deleted, and its mirrored-Suggests note no longer applied. This removes the drift class that bit earlier today: the list had gone stale against DESCRIPTION (cowplot promoted to Imports in 7b5afe5 and still listed; curl a Suggests and missing, which silently degraded the LCC vignette's reachability probe to "skip"). There is now nothing to keep in sync. The workaround is documented in-place, so if a pak resolve error naming Matrix ever returns, the fix is recorded rather than rediscovered. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01T3NTQTNStSLZ3mA3CsLcon
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Replaces this repo's hand-rolled matrix with a thin caller on
PredictiveEcology/actions/.github/workflows/R-CMD-check.yaml@main.157 → 37 lines. Across both workflows touched here: +38 / −181.
Why
Third-party action versions, system dependencies, caching and the check itself were maintained separately in 17 repos. This repo was on
actions/checkout@v4; the org spread was v2/v4/v5/v6/v7. Node 20 deprecation warnings are the current symptom. Consolidated, bumping it once inactionsupdates every repo.Customizations preserved
oldrel-2on both OSes, viaextra-config(the org default matrix is 8 legs; these two are deliberate back-compat coverage). The hand-rolled pandoc retries, library cache and dependency retry are now the reusable workflow's job.dependencies: "hard"dropped — DESCRIPTION is now the single source of truthThe old workflow set
dependencies: '"hard"'and then hand-listed 16 Suggests inextra-packages, to work around a pak solver bug:That depended on CRAN's metadata layout at a moment in time, so it was retested in #37 — branched from this PR so resolution mode was the only variable. 12/12 green: every platform, every R version including devel, plus the
nosuggestsleg.So
'"all"'now installs Suggests straight fromDESCRIPTIONand theextra-packageslist is gone. The workaround is documented in-place, with the symptom to watch for, so it can be reapplied rather than rediscovered if CRAN's metadata regresses.This also removes a live drift class. The hand-maintained list had already gone stale against
DESCRIPTION:cowplotwas still listed after being promoted to Imports in 7b5afe5, andcurlwas missing despite being a Suggests — andcurlis load-bearing, since the LCC vignette's reachability probe is gated onrequireNamespace("curl")and silently degrades to "skip" without it. There is now nothing to keep in sync.Applied to
test-coverage.yamltoo. It set'"hard"'independently, with a comment deferring toR-CMD-check.yamlfor a rationale this PR deletes — so leaving it would have kept the workaround alive pointing at a missing explanation.NLMR removed, not migrated
An earlier revision carried
NLMR=?ignoreand thepak::pkg_install("ropensci/NLMR")post-install across, on the grounds of preserving existing behaviour. That was wrong: NLMR is not referenced anywhere in this package — not inDESCRIPTION,R/,vignettes/,tests/orman/. Its only appearances were the two workflows installing it from GitHub on every leg.This is the dead weight the PE CI standards call out from SpaDES, where
ropensci/NLMRands-u/fastshpwere installed on every pkgdown build while referenced nowhere — the slowest step and the largest failure surface. Removed from both workflows.Dropped deliberately
The bespoke
Restore R library cachestep —setup-r-dependenciescaching replaces it. Worth watching the first run if that cache was load-bearing.Note on the earlier red
The failures on this PR before 2026-09-01 were not caused by the migration. They were
Deriv 4.3.0failing to compile on R 4.4.x (fixed in #36 by droppingggpubr) and the LCC vignette's ~2.7 GB of build-time downloads truncating (fixed in #35 by using pre-cropped fixtures). Both are ondevelopmentand merged in here, so current runs test the migration itself. It went 12/12 green before the"hard"change above.New coverage worth knowing about: the org workflow adds a
release, nosuggestsleg (_R_CHECK_DEPENDS_ONLY_=true) this repo did not have. It passes — the package checks clean without its Suggests.Depends on PredictiveEcology/actions#27 (per-leg
extra-env).🤖 Generated with Claude Code
https://claude.ai/code/session_012DVjmY3im9Xak7tXLSMGCa