build(deps): bump r-lib/actions/setup-r-dependencies from 2.11.4 to 2.13.0 by dependabot[bot] · Pull Request #2013 · ContextualWisdomLab/.github

dependabot · 2026-09-07T13:36:23Z

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"]

opencode-agent · 2026-09-08T06:22:16Z

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 · 2026-09-08T09:08:44Z

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 · 2026-09-08T10:01:50Z

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.

Bumps [r-lib/actions/setup-r-dependencies](https://github.com/r-lib/actions) from 2.11.4 to 2.13.0. - [Release notes](https://github.com/r-lib/actions/releases) - [Changelog](https://github.com/r-lib/actions/blob/v2-branch/NEWS.md) - [Commits](r-lib/actions@6f6e5bc...465b7d8) --- updated-dependencies: - dependency-name: r-lib/actions/setup-r-dependencies dependency-version: 2.13.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

coderabbitai · 2026-09-10T05:16:08Z

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dependabot Bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Sep 7, 2026

dependabot Bot requested a review from seonghobae as a code owner September 7, 2026 13:36

dependabot Bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Sep 7, 2026

seonghobae added maintenance priority: low labels Sep 8, 2026 — with ChatGPT Codex Connector

dependabot Bot force-pushed the dependabot/github_actions/main/r-lib/actions/setup-r-dependencies-2.13.0 branch from 4be39b4 to e9402a9 Compare September 8, 2026 03:16

opencode-agent Bot requested changes Sep 8, 2026

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seonghobae mentioned this pull request Sep 9, 2026

fix(scheduler): retire a dispatch status its own check run superseded #2061

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dependabot Bot force-pushed the dependabot/github_actions/main/r-lib/actions/setup-r-dependencies-2.13.0 branch from e9402a9 to 5c9bd51 Compare September 10, 2026 05:16

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build(deps): bump r-lib/actions/setup-r-dependencies from 2.11.4 to 2.13.0 - #2013

build(deps): bump r-lib/actions/setup-r-dependencies from 2.11.4 to 2.13.0#2013
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v2.13.0 (2026-08028)

v2.12.1 (2026-06-23)

v2.12.0 (2026-04-29)

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Pull request overview

Findings

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

Changed-File Evidence Map

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OpenCode Review Overview

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dependabot Bot commented on behalf of github Sep 7, 2026 •

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`v2.13.0` (2026-08028)

`v2.12.1` (2026-06-23)

`v2.12.0` (2026-04-29)