build(deps): bump r-lib/actions/setup-r-dependencies from 2.11.4 to 2.13.0

[dependabot]

Bumps r-lib/actions/setup-r-dependencies from 2.11.4 to 2.13.0.

Changelog

Sourced from r-lib/actions/setup-r-dependencies's changelog.

v2.13.0 (2026-08028)

• [setup-r] now retries r-hub.io HTTP failures (#1088, @​nbenn).

• [setup-r] now sets the correct RTOOLS environment variables on aarch64 Windows (@​vjymisal0, #1104).

• [setup-r] keep repositories if they are set by the build. E.g. aarch64 Windows builds now set them (@​jeroen, #1101).

• [setup-r] now retries transient failures when resolving the R version from api.r-hub.io, rather than failing the job on the first timeout or server error (@​nbenn, #1086).

• [setup-r-dependencies] now switches back to classic sudo, if available, on Linux. This fixes installing pak on Ubuntu 26.04 runners (@​jeroen, #1096).

v2.12.1 (2026-06-23)

• [setup-r] now avoids a warning about an url.parse() deprecation (#1074).

• [setup-r-dependencies] now uses quarto-dev/quarto-actions v2.2.0 (@​jdblischak, #1076).

• Examples: test-coverage.yaml now uses codecov/codecov-action v7 (@​shikokuchuo, #1081).

• New example claude-investigate.yaml workflow (@​DavisVaughan, #1084).

v2.12.0 (2026-04-29)

• All node.js actions use node 24 now. Relatedly, all example workflows use recent versions of actions that use node 24.

• [setup-r] now uses use-public-rspm: true by default on Linux and Windows. macOS binaries require further opt-in with use-public-rspm: always.

• It is now possible to require actions to be pinned to a full-length commit SHA in repositories using r-lib/actions (#1070).

• [setup-pandoc][setup-r-dependencies] now default to Pandoc version 3.8.3.

• [setup-r-dependencies] now includes the R architecture in the cache key, so caches for macos-15 (Apple Silicon) and macos-15-intel (Rosetta/x86_64) no longer collide (#1035).

... (truncated)

Commits

• 465b7d8 NEWS for 2.13.0 (#1105)
• d06a540 [setup-r] retry transient r-hub.io request failures (#1088)
• ed9aa85 fix(setup-r): export correct RTOOLS HOME env vars on Windows ARM64 and x64 (#...
• c86f32c setup-r-dependencies: set JAVA_HOME on Windows runners from Java 21 env vars ...
• 2a66450 setup-r-dependencies: switch back to classic sudo on runners with sudo-rs (#1...
• 5cc1f0d Fix minor typo (#1098)
• 33d09fb fix: Remove stray ::group:: (#1103)
• aae88a2 Special-case CRAN mirror for Windows ARM64 (#1101)
• b7484da [setup-r] Support installing RTools without installing R (#1093)
• d3c5be5 Update NEWS for v1.12.1 (#1087)
• Additional commits viewable in compare view

[opencode-agent]

Pull request overview

OpenCode could not approve from deterministic current-head evidence because GitHub Checks have failed.

Findings

1. HIGH Current-head GitHub Checks - Fix failed required checks before approval

• Problem: Failed same-head checks remain for e9402a91cb9ba904d33a415d44e1af4102993514.
• Root cause: The model-unavailable evidence fallback is allowed only when peer GitHub Checks are complete and clean.
• Fix: Read and fix the failed check logs below, then rerun the current-head checks.
• Regression test: Keep the model-unavailable fallback gated on an empty failed-check rollup.

Failed checks:

• CodeQL PR/CodeQL compatibility analysis (python): FAILURE (https://github.com/ContextualWisdomLab/.github/actions/runs/34182952809/job/101943813235)
• CodeQL compatibility analysis (python) check run: failure (https://github.com/ContextualWisdomLab/.github/actions/runs/34182952809/job/101943813235)
• Required Noema Review/noema-review: FAILURE (https://github.com/ContextualWisdomLab/.github/actions/runs/34182950469/job/101927973660)
• noema-review check run: failure (https://github.com/ContextualWisdomLab/.github/actions/runs/34182950469/job/101927973660)

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Workflow: r-package-check.yml"]
  S1 --> I1["GitHub Actions review job"]
  I1 --> R1["Review risk: Workflow: r-package-check.yml"]
  R1 --> V1["actionlint plus required checks"]

Loading

[opencode-agent]

OpenCode Review Overview

• Head SHA: e9402a91cb9ba904d33a415d44e1af4102993514
• Workflow run: 34187701578
• Workflow attempt: 1
• Gate result: REQUEST_CHANGES
• Coverage gate: success
• Model pool: exhausted
• Verdict: REQUEST_CHANGES
• Formal review: build(deps): bump r-lib/actions/setup-r-dependencies from 2.11.4 to 2.13.0 #2013 (review)

[seonghobae]

Exact-head control-loop update for e9402a91cb9ba904d33a415d44e1af4102993514:

• Python Security, SAST, and Security are GREEN.
• CodeQL run 34182952809 is now terminal success; the earlier OpenCode rollup referenced its pre-settlement failed job state.
• Noema job 101927973660 failed at the gateway with HTTP 429 after credential selection, without a source verdict. Because this is a terminal transient provider-communication failure and no newer exact-head Noema job was active, only that failed job was rerun. Replacement job 102002989186 is queued.
• The existing CHANGES_REQUESTED review is not dismissed or treated as approval. Ordinary merge remains blocked until the rerun terminates and current-head review/approval is regenerated.

[seonghobae]

Noema retry result on unchanged exact head e9402a9:

Replacement job 102002989186 also completed failure. The gateway returned HTTP 502 after 442.9s with served_model=google/gemma-4-31b-it; sidecar evidence artifact is 10049950266. This is a second terminal provider-communication failure, not a source verdict.

No additional consumer retry is started. Recovery belongs to the active canonical owner candidate ContextualWisdomLab/contextual-orchestrator#1094, followed by protected merge, immutable release/pin adoption, and an exact-head real Noema replay. #2013 remains Ready but unmergeable while its current CHANGES_REQUESTED review and Noema failure remain.

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