feat: extra-env input on R-CMD-check and test-coverage - #26
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Blocks the migration of most remaining packages onto these workflows. A survey of the 17 repos still carrying their own R-CMD-check.yaml found per-package env this workflow cannot enumerate and had no way to accept: OMP_THREAD_LIMIT (quickPlot), R_KEEP_PKG_SOURCE (climateData, fpCompare), R_PKG_INSTALL_RETRIES (SpaDES.shiny), _R_CHECK_THINGS_IN_OTHER_DIRS_ (Require). Without this input those packages could not migrate without silently dropping settings, and "silently dropped" is the failure mode this repo keeps having to dig out of. Newline-separated KEY=VALUE, blank lines and #-comments ignored, applied before setup-r-deps so it reaches dependency resolution and not just the check. A line that is not KEY=VALUE fails the step rather than being skipped. Also refreshes the GOOGLEDRIVE_AUTH secret description, which still advertised service-account keys as accepted after #24 made them a hard failure. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012DVjmY3im9Xak7tXLSMGCa
eliotmcintire
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Aug 31, 2026
The workflow-level extra-env from #26 is static, so it cannot express env that varies across the matrix. Require gates its slow tests on exactly one leg (R_REQUIRE_RUN_LONG_CI, driven by a runLong flag) specifically so its 11-job matrix does not camp on GHA's concurrency cap. That made Require the one repo that could not migrate onto this workflow at all. An extra-config leg may now carry its own `extra-env`, applied after the workflow-level block so a leg can override it. Generic rather than Require-shaped: any caller can vary env per leg. Claude-Session: https://claude.ai/code/session_012DVjmY3im9Xak7tXLSMGCa Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Unblocks the migration of the remaining packages onto the org workflows.
Why
Surveying the 17 repos still carrying their own
R-CMD-check.yamlturned up per-package env that these workflows cannot enumerate and had no way to accept:OMP_THREAD_LIMIT: 4R_KEEP_PKG_SOURCER_PKG_INSTALL_RETRIES_R_CHECK_THINGS_IN_OTHER_DIRS_(Ubuntu)Without an escape hatch, migrating those repos means silently dropping settings — and "silently dropped" is the failure mode this repo keeps having to dig out of.
What
Newline-separated
KEY=VALUE; blank lines and#-comments ignored. Applied immediately after checkout and beforesetup-r-deps, so it reaches dependency resolution rather than only the check step. A line that is notKEY=VALUEfails the step rather than being quietly skipped.Added to both
R-CMD-check.yamlandtest-coverage.yaml, since several of these vars affect test behaviour and so matter undercovrtoo.Carried along
The
GOOGLEDRIVE_AUTHsecret description still advertised service-account keys as accepted, which #24 made a hard failure. Refreshed in both workflows.Not covered
Requirealso gatesR_REQUIRE_RUN_LONG_CIon arunLong: trueflag on one matrix leg.extra-configcan add the leg, but the workflow does not propagate arbitrary matrix keys into env, soRequirestill needs work beyond this. It is the last repo I would migrate.🤖 Generated with Claude Code
https://claude.ai/code/session_012DVjmY3im9Xak7tXLSMGCa