Push the auto/registry-patch-proposals branch over HTTPS with FORGEJO_TOKEN (the
same token already used for the PR API), so no separate write-scoped REPO_RW_TOKEN
secret is needed. Drop it from propose-patches.R, the pipeline, and the docs.
Close the classifier loop (issue #115, step 3): turn the auto-proposable
candidates into an actual PR, gated by a real trial build in our own build-env
images. Model chosen: autonomous PR, PR-first with a CI trial-build gate,
bounded top-N batch per run.
- propose-patches.R: add --limit N (top candidates by failure volume; the rest
defer to the next run) and --open-pr, which writes the entries onto the reused
auto/registry-patch-proposals branch, pushes with REPO_RW_TOKEN, and
opens/updates one PR via the Forgejo API
- add .crow/auto-apply-patches.yaml (single job) to run --open-pr on a cron
- add local/trial-build-registry.R + .crow/trial-build-registry.yaml: the merge
gate. Matrixed over the real OS/IMG build-env images, each platform diffs the
branch registry against main and trial-builds only the entries it adds, in
reg.devxy.io/rpkgs/build-env-*; green only if every new entry builds. The
base-registry read fails loud rather than silently building the whole registry
- add pure entry_applies_to_os()/new_registry_packages() helpers + tests
- document the autonomous-PR + gate flow in local/patches/README.md
The repo uses no pull_request triggers, so the gate runs manually/cron against
the branch; wiring it to the PR needs event: pull_request on the forge.
## Why
Issue #120 (the auto-proposed-patches issue) only lists **auto-proposable** fixes -- currently just the TBB signatures. So a reasonable read of it was "TBB is our only build failure", when in fact three whole categories are simply not shown there:
- **Unclassified failures** -- anything that doesn't match a seeded signature is routed to human triage and never appears (we've only seeded TBB and libuv signatures).
- **Dependency-blocked failures** -- the ~800 RcppParallel dependents (post #121) are still failing; they only show as a log line.
- Human-only signatures (libuv).
These blind spots are exactly where the *next* signatures should come from, so they deserve the same visibility as the proposals.
## What
Extend the feedback-loop tracker to surface the classifier's blind spots:
- **`unclassified_summary()`** -- groups every unknown-signature failure by normalised fingerprint, ranked by build count, capped with an explicit `dropped_groups` count (no silent truncation), each with example packages + platforms. These are the candidates for new `build_signatures()` rules.
- **`blocked_summary()`** -- lists each dependency (e.g. RcppParallel) and how many dependents wait on it.
- `proposal-tracking.R` prints both sections, and a new **`--open-issue`** mode posts/updates a *"Unclassified build failures (needs signatures) (#115)"* Forgejo issue.
- The weekly crow pipeline now runs the tracker with `--open-issue`, so it maintains a second tracking issue alongside the proposals one. Read-only on the DB; the only writes are the two issues.
## Verification
- New tests cover `unclassified_summary` (ranking + both caps) and `blocked_summary`.
- Tracker smoke with a stubbed DB (proposable + blocked + unclassified mix) prints the hit rate, `Blocked on a dependency: RcppParallel: 2 dependent(s)`, and `Unclassified failures ... [2 builds | 2 pkgs] ld: undefined reference ...`.
- Full suite: 95 tests pass; all pre-commit hooks pass (air, prettier, markdownlint, yamllint, validate-patches).
Reviewed-on: #122
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
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
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
## 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
