ci: fix mac/windows R-CMD-check — rebuild stringfish against installed RcppParallel by seonghobae · Pull Request #77 · ContextualWisdomLab/kaefa

seonghobae · 2026-08-04T04:57:45Z

All non-ubuntu R-CMD-check jobs — and on some snapshots the ubuntu jobs, test-fast, and test-suite — fail on every PR: loading kaefa dies because prebuilt CRAN/RSPM binaries that link RcppParallel's TBB were built before its oneTBB migration, which removed the legacy tbb::internal/tbb::task symbols:

stringfish.so: Symbol not found: __ZN3tbb8internal12NFS_AllocateEmmPv          (macOS)
stringfish.so: undefined symbol: _ZN3tbb8internal25concurrent_vector_base_...  (ubuntu)
qs2.so:        Symbol not found: __ZN3tbb4task13note_affinityEt                (macOS, after fixing stringfish)

It's upstream binary skew, not a code regression — develop last ran green 2026-07-13.

Fix: one step after setup-r-dependencies in each of the three workflows that rebuilds every installed package LinkingTo RcppParallel from source (tools::dependsOnPkgs("RcppParallel", dependencies = "LinkingTo")), so they all link the RcppParallel actually installed. Package-agnostic on purpose — the first attempt patched only stringfish and qs2 promptly failed the same way. Marked for removal once CRAN/RSPM binaries re-sync.

🤖 Generated with Claude Code

Summary by CodeRabbit

테스트
- 다양한 환경에서 패키지 설치와 빌드 검증이 보다 안정적으로 수행되도록 자동화된 검사 절차를 개선했습니다.
- 관련 패키지를 소스에서 다시 빌드하는 검증 단계를 추가해 호환성 문제를 조기에 확인할 수 있습니다.

…B ABI skew)

coderabbitai · 2026-08-04T04:58:06Z

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: c8aa5b0d-8c24-435b-8a54-90099f4c4d68

📥 Commits

Reviewing files that changed from the base of the PR and between 5128d48 and 810dfa0.

📒 Files selected for processing (3)

.github/workflows/R-CMD-check.yaml
.github/workflows/test-fast.yaml
.github/workflows/test-suite.yaml

📝 Walkthrough

Walkthrough

R-CMD-check, test-fast, test-suite 워크플로에 RcppParallel과 stringfish의 소스 설치 단계를 추가했습니다. RcppParallel에 LinkingTo로 의존하는 패키지도 탐지하여 소스에서 재빌드합니다.

Changes

CI 의존성 소스 빌드

Layer / File(s)	Summary
소스 패키지 설치 `.github/workflows/R-CMD-check.yaml`, `.github/workflows/test-fast.yaml`, `.github/workflows/test-suite.yaml`	세 워크플로가 일반 의존성 설정 전에 `RcppParallel`과 `stringfish`를 CRAN 소스에서 설치합니다.
`LinkingTo` 패키지 재빌드 `.github/workflows/R-CMD-check.yaml`, `.github/workflows/test-fast.yaml`, `.github/workflows/test-suite.yaml`	세 워크플로가 `RcppParallel`에 `LinkingTo`로 의존하는 패키지를 검색하고 소스에서 재설치합니다.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Possibly related PRs

ContextualWisdomLab/kaefa#30: R-CMD-check.yaml 워크플로의 기존 의존성 설정을 추가로 변경합니다.

Suggested reviewers: copilot

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	제목은 RcppParallel에 맞춘 stringfish 재빌드와 CI 수정이라는 주요 변경 사항을 구체적으로 설명합니다.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

Create PR with unit tests
Commit unit tests in branch ci/rebuild-stringfish-abi

_{Comment @coderabbitai help to get the list of available commands.}

… skew)

… load it); fold long line

…or source URLs); rebuild RcppParallel first

seonghobae · 2026-08-07T21:25:49Z

@coderabbitai review

coderabbitai · 2026-08-07T21:25:54Z

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seonghobae · 2026-08-07T21:30:46Z

@opencode-agent

seonghobae · 2026-08-07T21:31:46Z

@cwl-noema-review

seonghobae · 2026-08-07T21:34:36Z

@coderabbitai review

coderabbitai · 2026-08-07T21:34:42Z

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opencode-agent · 2026-08-07T22:08:25Z

Queued @cwl-noema-review for PR #77 at head fbba747eaf1399613c7faf5b9332d3f5a1b557a3. Central exact-name Actions artifacts are the durable dispatch ledger; existing review workflows remain authoritative for the final verdict and failure evidence.

opencode-agent · 2026-08-08T09:24:55Z

Queued @cwl-noema-review for PR #77 at head 810dfa0466b920cabc617f9be6817ab46d2e3b00. Central exact-name Actions artifacts are the durable dispatch ledger; existing review workflows remain authoritative for the final verdict and failure evidence.

opencode-agent

Pull request overview

OpenCode cannot approve yet because required coverage evidence did not pass.

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

Problem: The required coverage-evidence job result was failure, so OpenCode cannot establish approval sufficiency for this head.
Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.
Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports success with required evidence or explicit no-source not-applicable evidence.
Regression test: Keep the approval branch checking needs.coverage-evidence.result == success before posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present.
Result: REQUEST_CHANGES
Reason: coverage-evidence result was failure, so required test/docstring evidence was not proven for current head 810dfa0466b920cabc617f9be6817ab46d2e3b00.
Head SHA: 810dfa0466b920cabc617f9be6817ab46d2e3b00
Workflow run: 31541299973
Workflow attempt: 1

Coverage evidence

Coverage evidence job did not run or did not publish coverage evidence.

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Workflow (3 files)"]
  S1 --> I1["GitHub Actions review job"]
  I1 --> R1["Review risk: Workflow (3 files)"]
  R1 --> V1["actionlint plus required checks"]

opencode-agent · 2026-08-11T22:58:43Z

OpenCode Review Overview

Head SHA: 810dfa0466b920cabc617f9be6817ab46d2e3b00
Workflow run: 31541299973
Workflow attempt: 1
Gate result: REQUEST_CHANGES (approval step)

Pull request overview

OpenCode cannot approve yet because required coverage evidence did not pass.

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

Problem: The required coverage-evidence job result was failure, so OpenCode cannot establish approval sufficiency for this head.
Root cause: Automated approval is only valid when the same-head coverage-evidence job proves supported repository test suites passed and configured docstring gates passed or were advisory, or reports not applicable because no supported source files or package manifests exist. Missing, failed, skipped, unavailable, or unsupported-tooling test evidence is a blocker.
Fix: Install or configure the repository test/docstring evidence tooling when source files or package manifests exist, rerun the current-head coverage-evidence job, and approve only after it reports success with required evidence or explicit no-source not-applicable evidence.
Regression test: Keep the approval branch checking needs.coverage-evidence.result == success before posting APPROVE, and publish REQUEST_CHANGES when coverage-evidence blocker states such as cancelled, skipped, failed, unsupported-tooling, or below-100 evidence are present.
Result: REQUEST_CHANGES
Reason: coverage-evidence result was failure, so required test/docstring evidence was not proven for current head 810dfa0466b920cabc617f9be6817ab46d2e3b00.
Head SHA: 810dfa0466b920cabc617f9be6817ab46d2e3b00
Workflow run: 31541299973
Workflow attempt: 1

Coverage evidence

Coverage evidence job did not run or did not publish coverage evidence.

Changed-File Evidence Map

flowchart LR
  PR["PR changed files"] --> Evidence["OpenCode bounded evidence"]
  Evidence --> S1["Workflow (3 files)"]
  S1 --> I1["GitHub Actions review job"]
  I1 --> R1["Review risk: Workflow (3 files)"]
  R1 --> V1["actionlint plus required checks"]

ci: rebuild stringfish from source on mac/windows (RcppParallel oneTB…

d55a2b5

…B ABI skew)

seonghobae added 3 commits August 4, 2026 16:29

ci: rebuild stringfish on all platforms (Linux hit too)

31d8d8b

ci: rebuild stringfish before install in test-fast

e7b7f3d

ci: rebuild stringfish before install in test-suite

21755e0

seonghobae mentioned this pull request Aug 4, 2026

ci: fix R CMD check — rebuild stringfish against installed RcppParallel ContextualWisdomLab/aFIPC#212

Open

seonghobae enabled auto-merge August 4, 2026 07:33

seonghobae added 9 commits August 4, 2026 16:35

ci: rebuild all RcppParallel-linked packages (qs2 hit the same oneTBB…

0446de9

… skew)

ci: rebuild all RcppParallel-linked packages (qs2 hit the same oneTBB…

648e948

… skew)

ci: rebuild all RcppParallel-linked packages (qs2 hit the same oneTBB…

34ef00f

… skew)

ci: source-build stringfish before dep setup (SimDesign source builds…

b944368

… load it); fold long line

ci: source-build stringfish before dep setup (SimDesign source builds…

46012b7

… load it); fold long line

ci: source-build stringfish before dep setup (SimDesign source builds…

4acfcf0

… load it); fold long line

ci: real source rebuilds via CRAN cloud (RSPM serves linux binaries f…

d75e72c

…or source URLs); rebuild RcppParallel first

ci: real source rebuilds via CRAN cloud (RSPM serves linux binaries f…

28e8442

…or source URLs); rebuild RcppParallel first

ci: real source rebuilds via CRAN cloud (RSPM serves linux binaries f…

fbba747

…or source URLs); rebuild RcppParallel first

This was referenced Aug 7, 2026

ci(test-suite): rebuild stringfish from source to fix P3M TBB ABI drift #71

Closed

ci: pin R workflows to jammy to fix the noble stringfish TBB ABI failure #72

Closed

ci: build qs2/stringfish from source (RcppParallel 6.2.0 oneTBB ABI break) #76

Closed

seonghobae mentioned this pull request Aug 7, 2026

docs(agents): code-owner gates disabled org-wide until multiple maintainers exist #73

Closed

Merge branch 'develop' into ci/rebuild-stringfish-abi

810dfa0

opencode-agent Bot requested changes Aug 11, 2026

View reviewed changes

opencode-agent Bot disabled auto-merge August 11, 2026 22:59

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ci: fix mac/windows R-CMD-check — rebuild stringfish against installed RcppParallel - #77

ci: fix mac/windows R-CMD-check — rebuild stringfish against installed RcppParallel#77
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Pull request overview

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

Coverage evidence

Changed-File Evidence Map

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opencode-agent Bot commented Aug 11, 2026

OpenCode Review Overview

Pull request overview

Review outcome

1. HIGH .github/workflows/opencode-review.yml:1 - Coverage evidence did not prove required test/docstring evidence

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Changed-File Evidence Map

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