Update to R 4.6 - #44
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Agent-Logs-Url: https://github.com/d-morrison/qwt/sessions/5ccdb166-ec38-4409-b536-3e091bd66504 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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Pull request overview
This PR updates the repository’s required and CI-provisioned R version to 4.6, aligning the package DESCRIPTION minimum R dependency with GitHub Actions and related automation environments.
Changes:
- Raise the package minimum R version in
DESCRIPTIONtoR (>= 4.6.0). - Pin
r-lib/actions/setup-r@v2tor-version: '4.6'across the relevant GitHub Actions workflows. - Pin the spellcheck workflow container from
rocker/verse:latesttorocker/verse:4.6.
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
DESCRIPTION |
Raises the declared minimum supported R version to 4.6.0. |
.github/workflows/publish.yml |
Pins CI R version to 4.6 for publish workflow. |
.github/workflows/preview.yml |
Pins CI R version to 4.6 for preview builds. |
.github/workflows/check-bibliography-dois.yml |
Pins CI R version to 4.6 for DOI checks. |
.github/workflows/lint-project.yaml |
Pins CI R version to 4.6 for linting. |
.github/workflows/copilot-setup-steps.yml |
Pins Copilot agent environment R version to 4.6. |
.github/workflows/check-spelling.yaml |
Pins the spellcheck container image to an R 4.6-based tag. |
Comments suppressed due to low confidence (1)
.github/workflows/check-bibliography-dois.yml:26
setup-r-dependenciesis pinned to@HEAD, which makes this workflow non-reproducible and can break unexpectedly. Since this PR is pinning the R toolchain, it would be more consistent to pin this action to a stable tag (e.g.,@v2) or a specific commit SHA as well.
with:
r-version: '4.6'
use-public-rspm: true
- uses: r-lib/actions/setup-r-dependencies@HEAD
with:
…oesn't exist) Agent-Logs-Url: https://github.com/d-morrison/qwt/sessions/9d60643e-a1bc-4376-adae-a3476be2a26f Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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Fixed in e1ba4cc. The |
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not needed yet |
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d-morrison
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Aug 8, 2026
Phase 2 of the qwt -> gha migration (#116). All three blockers are now closed (gha#43/#44/#45), so these can move to thin callers of the reusable workflows: - summary.yml -> Morrison-Lab/gha/.github/workflows/summary.yml@v1 (unchanged since the v1 freeze per gha's README Versioning section; the reusable version already has the nonce-based prompt-injection hardening and blank-response guard qwt's own copy had grown). - claude.yml -> .../claude.yml@v2 (picked up a real fix since the v1 freeze, per gha's README). The reusable workflow now owns branch setup + draft-PR opening for issue triggers, posting Claude's prose reply, review dispatch on "@claude review", and the late-comment dedup/rescue machinery that gha originally ported FROM this repo's own #73/#90/#95. - claude-code-review.yml -> .../claude-code-review.yml@v2 (same v2 rationale). Draft/fork/Dependabot/self-edit skip logic is now handled inside the reusable workflow; this caller only supplies the qwt-specific Quarto/R/build-hygiene/CI review guidance and the ready-to-paste "@claude address review comments" draft convention via prompt-addendum. Deviates from the issue's literal checklist in two places, per gha's current README (written after the issue was filed): - claude.yml/claude-code-review.yml pin @v2, not @v1 -- @v2 has fixes @v1 lacks (gha#182). - Secrets are passed explicitly rather than via `secrets: inherit`: GitHub only inherits secrets into a same-owner reusable workflow, and Morrison-Lab/gha is a different owner than d-morrison/qwt. Behavior change: claude.yml now defaults mark-ready-for-review: true, so an issue-triggered draft PR is taken out of draft once Claude commits code (previously always left as a draft). Net: -835/+115 lines across the three files; qwt's hand-rolled dedup/branch/PR/review-dispatch logic is now upstream in gha.
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Pins R to 4.6 across all GitHub Actions workflows and raises the minimum R requirement in
DESCRIPTION.Changes
DESCRIPTION–Depends: R (>= 4.1.0)→R (>= 4.6.0)publish.yml,preview.yml,check-bibliography-dois.yml,lint-project.yaml– addr-version: '4.6'tor-lib/actions/setup-r@v2(previously unversioned)copilot-setup-steps.yml–r-version: 'release'→r-version: '4.6'check-spelling.yaml– kept asrocker/verse:latest(Rocker does not publish a4.6short-form tag)