ci: fix R CMD check — rebuild stringfish against installed RcppParallel by seonghobae · Pull Request #212 · ContextualWisdomLab/aFIPC

seonghobae · 2026-08-04T07:30:23Z

R CMD check fails on every PR: installing the package dies loading stringfish —

unable to load shared object '.../stringfish/libs/stringfish.so':
undefined symbol: _ZN3tbb8internal25concurrent_vector_base_v316internal_grow_byEmmPFvPvPKvmES4_

Prebuilt CRAN/RSPM binaries that link RcppParallel's TBB predate its oneTBB migration, which removed the legacy tbb::internal symbols. Same org-wide skew as ContextualWisdomLab/kaefa#77, where fixing only stringfish immediately surfaced the identical failure in qs2.

Fix: one step after setup-r-dependencies that rebuilds every installed package LinkingTo RcppParallel from source (tools::dependsOnPkgs("RcppParallel", dependencies = "LinkingTo")), so they all link the RcppParallel actually installed. Marked for removal once CRAN/RSPM binaries re-sync.

🤖 Generated with Claude Code

Summary by CodeRabbit

개선 사항
- R 환경 설정 과정에서 관련 패키지가 소스에서 안정적으로 빌드되도록 절차를 강화했습니다.
- 병렬 처리 기능과 연동된 의존 패키지의 설치 및 재빌드 안정성이 향상되었습니다.
- 패키지 설치 과정에서 발생할 수 있는 환경별 호환성 문제를 줄였습니다.

coderabbitai · 2026-08-04T07:30:33Z

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: 1f35fb57-0262-414f-a609-dddfcc97b693

📥 Commits

Reviewing files that changed from the base of the PR and between 35e4498 and d810009.

📒 Files selected for processing (1)

.github/workflows/r.yml

📝 Walkthrough

Walkthrough

R 패키지 의존성 설치 전에 RcppParallel과 stringfish를 CRAN 소스에서 빌드합니다. RcppParallel에 LinkingTo로 의존하는 패키지를 조회하고 소스에서 재설치합니다.

Changes

R 소스 의존성 설정

Layer / File(s)	Summary
소스 설치 및 LinkingTo 재빌드 `.github/workflows/r.yml`	의존성 설치 전에 `RcppParallel`과 `stringfish`를 소스에서 설치합니다. `tools::dependsOnPkgs`로 `RcppParallel`의 `LinkingTo` 의존 패키지를 조회하고 해당 패키지를 소스에서 재설치합니다.

Estimated code review effort: 2 (Simple) | ~10 minutes

Merge Risk: ⚪ Minimal · up to d8100

This localized CI change rebuilds affected packages against the installed RcppParallel version; no actionable merge-blocking risk remains after normal checks and review.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
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.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	제목은 설치된 RcppParallel에 맞춰 stringfish를 재빌드하는 핵심 변경과 R CMD check 수정 목적을 명확히 설명합니다.

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

Create stacked PR
Commit on current branch

🧪 Generate unit tests (beta)

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

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… skew)

… load it); fold long line

…s config)

…or source URLs); rebuild RcppParallel first

seonghobae · 2026-08-07T15:04:50Z

@opencode-agent review-only request for exact current head d8100098f56f6b55ba1f4a0ee524925306b95e95. Please inspect the one-file RcppParallel/oneTBB ABI repair, including the source-build ordering and whether rebuilding every installed LinkingTo consumer is the narrowest reliable fix. Exact-head R CMD check, Security Audit, Code Quality, SAST Semgrep, and Security Scan are successful and CodeRabbit commit status is success. Do not mutate the branch, change ready state, merge, or bypass protection; submit only a formal current-head verdict.

seonghobae · 2026-08-14T12:51:32Z

@opencode-agent review-only request for exact current head d8100098f56f6b55ba1f4a0ee524925306b95e95.

All exact-head repository checks are complete and successful: R CMD check, Code Quality, Security Audit, Security Scan, SAST Semgrep, Strix, and the required-workflow checks. CodeRabbit reports no actionable findings and minimal merge risk. Please inspect only the one-file RcppParallel/oneTBB ABI workaround, verify the source-build ordering and bounded scope, and submit a formal current-head APPROVE or REQUEST_CHANGES review. Do not modify the branch, alter ready state, merge, or bypass protection.

seonghobae · 2026-08-14T13:27:37Z

@cwl-noema-review @opencode-agent exact-head review request for d8100098f56f6b55ba1f4a0ee524925306b95e95. Review only: inspect the one-file ABI rebuild workflow against the completed successful exact-head R CMD, quality, security, SAST, and Strix evidence; submit a formal APPROVE or REQUEST_CHANGES decision. Do not modify the branch, merge, dismiss findings, or weaken protection.

ci: rebuild stringfish from source (RcppParallel oneTBB ABI skew)

23efd34

seonghobae enabled auto-merge August 4, 2026 07:34

seonghobae added 4 commits August 4, 2026 16:35

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

e5790d2

… skew)

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

02a366b

… load it); fold long line

ci: pass explicit repos (R_PROFILE_USER=/dev/null blanks setup-r repo…

1da25b7

…s config)

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

d810009

…or source URLs); rebuild RcppParallel first

seonghobae mentioned this pull request Aug 7, 2026

ci: build qs2/stringfish from source (RcppParallel 6.2.0 oneTBB ABI break) #211

Closed

seonghobae marked this pull request as draft August 14, 2026 07:59

auto-merge was automatically disabled August 14, 2026 07:59
Pull request was converted to draft

seonghobae marked this pull request as ready for review August 14, 2026 07:59

seonghobae enabled auto-merge (squash) August 14, 2026 08:00

seonghobae marked this pull request as draft August 14, 2026 12:52

auto-merge was automatically disabled August 14, 2026 12:52
Pull request was converted to draft

seonghobae marked this pull request as ready for review August 14, 2026 12:52

seonghobae enabled auto-merge (squash) August 14, 2026 12:52

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ci: fix R CMD check — rebuild stringfish against installed RcppParallel - #212

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