Author	SHA1	Message	Date
pat-s	6ed17f3fb1	feat(local): report unclassified and dependency-blocked failures for discovery ... The proposer issue only lists auto-proposable fixes (currently the TBB signatures), so every failure without a signature -- and every group blocked on a dependency build -- was invisible unless someone read the run log. That hid the classifier's blind spots and, with them, which new signatures are worth adding next. Extend the tracker to surface those blind spots and give them the same visibility as the proposals: - add pure `unclassified_summary()` (unknown-signature groups ranked by build count, capped with an explicit dropped count) and `blocked_summary()` helpers - print both sections in proposal-tracking.R and add a `--open-issue` mode that posts/updates a "Unclassified build failures (needs signatures)" Forgejo issue - run the tracker with --open-issue in the weekly crow pipeline (second issue) - cover the new helpers with tests and document the flow in the patches README	2026-07-15 07:34:07 +00:00
pat-s	af481f5129	ci(crow): add weekly patch-proposal + feedback-loop pipeline (#118) ... Adds the scheduled pipeline for the failure-triage proposer/tracker landed in #117 (issue #115, steps 3 + 4). ## `.crow/weekly-patch-proposals.yaml` A single (non-matrix) job -- the classifier groups over all of `single_builds`, so unlike the per-platform `weekly-audit-missing` it runs once globally. Weekly it: 1. `propose-patches.R --open-issue` -- posts/updates a Forgejo tracking issue with the auto-proposable registry entries (human reviews, trial-builds, opens the PR; nothing merges). 2. `proposal-tracking.R` -- logs the feedback-loop metrics (signature hit rate, proposed-vs-merged, retirement candidates). Low blast radius: clones read-only (`REPO_RO_TOKEN`); the only write is the tracking issue via `FORGEJO_TOKEN`. It builds nothing (no B2 keys, no bincraft). Triggers: `cron: weekly-patch-proposals` (register the cron in the crow UI) or manual with `task=weekly-patch-proposals`, matching the `archive-missed-packages` convention. Documented under "Scheduled run" in `local/patches/README.md`. `yamllint` and the other pre-commit hooks pass. Reviewed-on: #118	2026-07-14 15:17:16 +00:00
pat-s	1c297c01bf	feat(local): auto-propose registry patches and track the feedback loop (#117) ... Implements steps 3 + 4 of #115, building on the classifier merged in #116. Now that bincraft **v4.4.3** applies registry `patch`/`makevars`/`configure_args` to the *target* package build (previously deps-only), a trial patched build is a meaningful acceptance gate, so the "propose" half is viable. ## Step 3 — propose, do not apply - **`local/propose-patches.R`** — for each classified, safe fix affecting a package with no current registry entry, emits a pre-filled `registry.json` entry and validates the candidate set against a *temporary* merged registry (the real one is never touched unless asked). - default: print candidates + validation, **take no action** - `--write`: append entries to `registry.json` + the proposals ledger (you commit + open the PR) - `--open-issue`: post/update a Forgejo tracking issue (reuses the weekly-audit `httr2` + `FORGEJO_TOKEN` pattern) - **`local/trial-build-patch.R`** — isolated bincraft build of one package with the registry applied (no upload/archive/metadata; `patchhash` keeps it out of the real cache). Exit 0/1, so it gates a CI step or manual pre-merge check. The human gate stays: nothing merges. Acceptance = `validate-patches.R` passes (checked automatically) **and** the trial build succeeds. Novel source diffs and unknown signatures are never proposed (they carry `auto = FALSE`). ## Step 4 — feedback loop - **`local/proposal-tracking.R`** (read-only) — signature hit rate (builds/pkgs/addressed/open per signature), proposed-vs-merged (a proposal counts merged once its package is in the registry), and retirement candidates (registry entries whose package no longer fails, i.e. likely fixed upstream). - **`local/proposal-tracking-lib.R`** — the pure metric/ledger helpers. ## Supporting changes - Refactored the classify helpers to expose a pure `build_triage_report()` + a list-returning entry builder; `failing-builds-report.R` now renders from the shared function (no behaviour change). - `validate-patches.R` gains optional `PATCH_DIR`/`REGISTRY_FILE` overrides (backward-compatible) so a candidate registry can be validated in isolation. - Documented the propose/trial-build/tracking workflow in `local/patches/README.md`. ## Verification - 71 unit tests pass (incl. new `test-proposal-tracking-lib.R`) under the Dockerized R 4.5.3 build env. - All pre-commit hooks pass (`air-format`, `validate-patches`, prettier, etc.). - Smoke-tested all three entrypoints end-to-end with a stubbed DB: dry-run, `--write` (produces a registry that passes the canonical validator + a valid ledger, then reverted), and the tracker. Closes #115 Reviewed-on: #117	2026-07-14 15:03:24 +00:00
pat-s	f11ba7172f	feat(local): classify failing binary builds and pre-fill registry suggestions (#116) ... Implements steps 1 + 2 of #115: turn recorded build failures into triaged patch suggestions instead of hand-scraping Crow logs. ## What this adds A **read-only** reporting pipeline over the `single_builds` metadata table. It never writes to the DB or the registry. - `local/failing-builds-classify.R` — pure, DB-free helpers: - `normalise_error()` strips temp paths, version numbers, hex addresses, and the package name so the same root cause collapses to one fingerprint. - `fingerprint_error()` extracts the salient error line and normalises it. - `classify_error()` matches against a seed signature set; unmatched errors are never guessed at. - `propose_registry_entry()` renders a schema-valid `registry.json` entry. - `local/failing-builds-report.R` — entrypoint: queries `single_builds WHERE error_occurred = TRUE AND removed = FALSE`, groups by root cause (signature when classified, fingerprint otherwise), classifies each group, and prints a triaged report. Flags: `--platform`, `--arch`, `--min`, `--json`; `PLATFORM`/`ARCH` env fallbacks. - `local/tests/test-failing-builds-classify.R` — unit tests for the helpers. - `local/patches/README.md` — documents the workflow. ## Seed signatures Each rule carries a fix tier, confidence, and an auto/human-only flag: | Signature | Fix | Disposition | | --- | --- | --- | | `tbb/tbb_stddef.h: No such file` | makevars `-DTBB_INTERFACE_NEW` | auto-proposable | | RcppParallel bundled TBB (musl / new g++) | curated `disable-tbb.patch` | auto-proposable | | system `libuv.so` link leak | force vendored/static lib | **human triage** (novel source diff) | | unmatched | none | **human triage** | ## Guardrails honored - No autonomous novel source diffs: only known env/makevars levers and already-curated package patches are auto-proposable; anything needing a brand-new diff, and any unknown signature, is routed to human triage. - No DB or registry writes; no change to the public `src/contrib` index. - Reuses `single_builds.error_text`; no new failure-capture pipeline. ## Verification - All helper unit tests pass under the Dockerized R 4.5.3 build env. - Pre-commit hooks pass (`air-format`, `validate-patches`, prettier, etc.). - Smoke-tested the full report path with a stubbed DB; generated proposals pass the real `local/validate-patches.R`. Steps 3 (auto-open PRs) and 4 (feedback loop) are intentionally deferred, per the issue's suggestion to validate the signature set first. Closes #115 Reviewed-on: #116	2026-07-14 14:45:25 +00:00
pat-s	04059f20e3	fix(patches): add rstan entry to skip removed tbb_stddef.h (#114) ... ## Motivation `rstan` fails to compile when it is pulled in as a transitive dependency (e.g. of `ctsem`), aborting the dependency install: ``` /mnt/cache/R-pkgs/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: tbb/tbb_stddef.h: No such file or directory 9 | #include <tbb/tbb_stddef.h> ``` StanHeaders' `init_threadpool_tbb.hpp` unconditionally includes the legacy `<tbb/tbb_stddef.h>` to detect the TBB version, but that header was removed in oneTBB 2021+, which is the TBB that StanHeaders now bundles. ## Fix Add an `rstan` entry to `local/patches/registry.json` that pre-defines `TBB_INTERFACE_NEW` via `CPPFLAGS`. The header's own guard skips the removed include when that macro is already defined and selects the modern `tbb/global_control.h` + `tbb/task_arena.h` path that the bundled oneTBB actually provides: ```cpp #ifndef TBB_INTERFACE_NEW #include <tbb/tbb_stddef.h> // removed in oneTBB 2021+ #if TBB_VERSION_MAJOR >= 2020 #define TBB_INTERFACE_NEW #endif #endif #ifdef TBB_INTERFACE_NEW #include <tbb/global_control.h> // taken when we pre-define the macro #include <tbb/task_arena.h> ``` This is a makevars-tier override (no source diff), applied through bincraft's `R_MAKEVARS_USER`, so `CPPFLAGS` stays additive and does not clobber rstan's own `PKG_CPPFLAGS`. `-I/usr/local/include` is kept because the override replaces the default `CPPFLAGS`. ## Files changed - `local/patches/registry.json`: add the `rstan` entry (`versions: "*"`, `platforms: ["*"]`, `makevars.CPPFLAGS = "-DTBB_INTERFACE_NEW -I/usr/local/include"`). ## Behaviour change When bincraft resolves `rstan` (direct or transitive) it builds a patched binary with `TBB_INTERFACE_NEW` defined, so `rstan` (and dependents such as `ctsem`) compile against the bundled oneTBB. The scope is `["*"]` because the failure is bound to StanHeaders' bundled TBB version, not the OS or toolchain. Reviewed-on: #114	2026-07-14 13:52:17 +00:00
pat-s	36d3bc8604	fix(patches): force fs to build vendored static libuv (#111) ... ## Problem The `fs` 2.1.0 binary links **system libuv** (`readelf -d fs.so` shows `NEEDED libuv.so.1`). fs's `configure` prefers system libuv whenever `pkg-config` resolves it, and our build images ship `libuv-devel` (installed as a pak build-time system requirement), so the resulting binary is dynamically linked against `libuv.so.1`. That binary fails to load on any consumer machine without runtime libuv: ```text unable to load shared object '.../fs/libs/fs.so': libuv.so.1: cannot open shared object file: No such file or directory ``` `install.packages()`/renv do **not** install `SystemRequirements` (only `pak` does, and only inside the build container), so most consumers hit this. Older fs 1.6.x always vendored libuv, so only the 2.x binaries regressed. Reproduced in a clean `reg.devxy.io/r/r-alma:4.5-9`. ## Fix Add `local/patches/fs/force-vendored-libuv.patch`, registered for all platforms. It short-circuits `configure` to `cp -f src/Makevars.vendor src/Makevars; exit 0` before the pkg-config detection, forcing the bundled static libuv build (`tools/libuv-v1.52.0.tar.gz`, built via cmake). An env/pkg-config override (`PKG_CONFIG_LIBDIR`) was tried first but the rebuilt binary still linked `libuv.so.1` (the registry `env` tier does not reach fs's configure step), so a source patch is used instead. ## Verification Built end-to-end inside the real `build-env-redhat:9` image (system libuv present): - patch fires (`Building static libuv (bincraft: forced vendored)`), - cmake compiles the vendored libuv, - resulting `fs.so` has **no `libuv.so.1`** in `NEEDED` (only libR, libstdc++, libm, libgcc_s, libc). `Rscript local/validate-patches.R` passes (2 entries). cmake confirmed present in the build-env images. ## Follow-up (not in this PR) - Rebuild `fs 2.1.0` on every affected platform (rhel8/9/10, ubuntu jammy/noble, alpine 3.22/3.23; amd64 + arm64) and purge the CDN binary paths. - CDN delivery gap: `purge_cdn_cache.sh` only purges `PACKAGES*`, never package binaries, so rebuilt binaries stay masked until their `.tar.gz` path is purged. Reviewed-on: #111	2026-07-07 18:12:36 +00:00
pat-s	e59590e2d6	fix: RcppParallel disable-TBB source patch (env var was a no-op) (#106) ... ## Summary Fixes the RcppParallel patch, which was a **no-op** and left the build hanging. The previous registry entry set `env: { RCPP_PARALLEL_USE_TBB: "0" }`. But `RCPP_PARALLEL_USE_TBB` is a **compile-time `-D` flag** in RcppParallel's Makevars — it is never read from the environment. So the override did nothing: `USE_TBB=Linux` (hardcoded from `uname`) still triggered the **bundled Intel TBB build**, which hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604). The `Applying patch …` log only meant the env was set, not that it had any effect. ## Fix Replace the env entry with a **source patch** (`local/patches/RcppParallel/disable-tbb.patch`) on `src/Makevars.in` that, on Linux: - leaves `USE_TBB` unset → the whole bundled-TBB build/link path is skipped (no hang), and - forces `PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=0` → the sources compile the **TinyThread** backend (needed because `RcppParallel.h` otherwise auto-defaults TBB on for glibc Linux). ## Verification In a Linux container, applying the patch and running `R CMD INSTALL RcppParallel`: ``` bundled_TBB_build=0 # bundled TBB build never runs * DONE (RcppParallel) # installs via TinyThread ``` ## Note bincraft's `apply_source_patch` shells out to `patch`. If a build-env image lacks the `patch` tool (common on Alpine), the patch will report "did not apply cleanly" and fall back to an unpatched (hanging) build. If that happens, the follow-up is to switch bincraft's patch application to `git apply` (git is always present) — happy to do that if needed. Reviewed-on: #106	2026-06-30 13:27:01 +00:00
pat-s	55a18fd87d	feat: patch registry + wiring for per-package patching (#103) ... ## Summary Adds the curated **patch registry** and wiring that drives bincraft's new package-patching mechanism (see bincraft PR `feat/package-patching`). Lets specific packages be patched (env/configure/Makevars overrides or source diffs) before pak installs them — including as transitive dependencies — so compiler-/OS-specific failures like RcppParallel's bundled TBB stop cascading. ## What's included - `local/patches/registry.json` — initial entry: RcppParallel with `RCPP_PARALLEL_USE_TBB=0` for alpine / ubuntu-2604, plus `local/patches/README.md` schema docs. - `local/validate-patches.R` — validates schema, referenced patch files, and ambiguous overlaps; clean failure + exit 1 (no stacktrace). - `.pre-commit-config.yaml` — a `validate-patches` hook (re-runs when the registry or the validator changes). - `local/build-one.R` / `local/build-all.R` — pass `patches = "local/patches"` to `bincraft::build_binary_package()`. - `specs/2026-06-30-package-patching-design.md` and `plans/2026-06-30-package-patching-implementation.md`. ## ⚠️ Merge ordering (blocker) This PR adds a `patches = ...` argument to `build_binary_package()` calls. The `.crow/*.yaml` workflows currently pin bincraft **v4.2.3**, which does not accept that argument — CI will error with `unused argument (patches=...)` until: 1. bincraft **v4.3.0** is released (PR `feat/package-patching`), and 2. the pin is bumped in `.crow/build-all-versions-install-deps.yaml`, `.crow/build-all-versions.yaml`, and `.crow/process-updates.yaml`. The `.crow` pin bump will be added to this PR once bincraft v4.3.0 is tagged. Do not merge before then. Reviewed-on: #103	2026-06-30 08:50:19 +00:00