## 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
## Problem
The scheduled `--open-issue` run (issue #120) posted **800+** proposed entries, all `rcppparallel-bundled-tbb` on `ubuntu-2604`, each pre-filling `RcppParallel/disable-tbb.patch` for an unrelated package (`ACEsimFit`, `AovBay`, `AdaptGauss`, ...).
Root cause: those packages fail on ubuntu-2604 only because their **RcppParallel dependency** does not build there. bincraft records RcppParallel's TBB error text against each dependent, so every one of them matches the `rcppparallel-bundled-tbb` signature. Proposing a RcppParallel source patch for `ACEsimFit` is not just noise -- it is **broken**: the diff targets RcppParallel's `Makevars.in`, so it cannot apply to a dependent's source.
## Fix
Add an optional `applies_to` field that pins a package-specific fix to the package it targets:
- A signature whose fix is a curated per-package source patch (`rcppparallel-bundled-tbb` -> `RcppParallel`) is only ever proposed **for that package**.
- Other packages matching the signature are downstream failures, reported as **"blocked on `<dependency>`"** and never proposed a bogus entry. Fix the dependency once and the whole cascade clears.
Generic levers (the `tbb-stddef-removed` makevars fix) are unaffected -- they carry no `applies_to`, so they still apply to any matching package.
## Changes
- gate proposal generation in `build_triage_report()` on `applies_to`; add a `blocked_on` field to group records
- surface blocked groups in both `failing-builds-report.R` and `propose-patches.R` instead of the misleading "already registered" note
- document `applies_to` in the signature-table header
## Verification
- New tests: RcppParallel dependents are blocked (no `proposed_entries`, `blocked_on = "RcppParallel"`), while RcppParallel *itself* is still proposed when it is the failing package.
- Reproduced the avalanche end-to-end with a stubbed DB: 5 dependents now report "Blocked on RcppParallel: 5 package(s) fail because RcppParallel does not build" and **zero** candidates are emitted; a genuine `tbb-stddef` proposal in the same run is unaffected.
- Full suite: 84 tests pass; all pre-commit hooks pass.
Refs #120.
Note: the underlying build problem (RcppParallel failing on ubuntu-2604 despite its registry entry) is real and separate -- this PR stops the classifier from spamming broken per-dependent proposals about it.
Reviewed-on: #121
## Problem
A live `propose-patches.R --open-issue` run aborted with:
```
Patch registry validation FAILED:
- ambiguous duplicate entries: hmmTMB|ubuntu-2604|*, imt|ubuntu-2604|*, refundBayes|ubuntu-2604|*
Error: Candidate registry failed validation; not writing or proposing.
```
Root cause: a package whose failing builds match **more than one** auto-proposable signature (e.g. some logs hit `tbb-stddef-removed`, others `rcppparallel-bundled-tbb`) landed in two separate signature groups, so the proposer emitted two candidate entries with the same `package|platforms|versions` key. The validator's ambiguous-duplicate check then failed the whole candidate set, aborting the run — so even the unambiguous candidates (e.g. `vacalibration`) never got proposed.
## Fix
Add a pure, tested `dedupe_candidates()` that:
- keeps a package's candidate only when it maps to a **single** signature (collapsing an accidental repeat under the same signature), and
- routes a package that maps to **multiple** signatures (conflicting fix tiers -- makevars vs source patch) to **human triage** instead of guessing between them.
The proposer prints the skipped ambiguous packages and proceeds with the clean candidates, so one ambiguous package no longer blocks the rest. This matches the issue #115 guardrail: don't auto-pick when the fix is ambiguous.
## Verification
- New unit tests in `test-proposal-tracking-lib.R` cover the single-signature, multi-signature (conflict), duplicate-under-one-signature, and empty cases.
- Reproduced the original failure end-to-end with a stubbed DB (`hmmTMB` ambiguous + `vacalibration` clean): `hmmTMB` is now listed under "Ambiguous -> human triage", `vacalibration` is proposed, and the candidate registry validates (`Patch registry OK`).
- Full suite: 78 tests pass; all pre-commit hooks pass.
Reviewed-on: #119
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
## 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
## Problem
The arm64 `build-all` pipeline fills the macmini (gaia) host disk despite an 8h prune.
Root cause is not images or job volumes: it is the persistent dep-cache volume, specifically `pkgcache/R/pkgcache/_metadata`, which grew to ~165 GB.
`{pkgcache}` mints a new content hash for the "patched" binaries repo on every PACKAGES change, so each per-package build writes a fresh ~70 MB `pkgs-<hash>.rds` (+ `patched-<hash>/`) that is never evicted (2407 snapshots observed).
When the disk hits 100% OrbStack stops and the on-host prune can no longer connect to the daemon, so it never self-heals.
## Change (Workstream A of the disk-fill fix)
- Add `trim_pkgcache_metadata()` to `local/r-minor-helpers.R`: keeps the newest `keep` (default 20) `patched-*`/`pkgs-*.rds` entries under `_metadata`, deleting only entries older than `min_age_secs` (default 600s) so it never races the up-to-4 concurrent split-jobs sharing the volume.
Preserves `pkg/` downloads and the stable CRAN/BioC/INLA repo dirs.
No-op when `R_PKG_CACHE_DIR` is empty (amd64) or `_metadata` is absent (first run).
- Call it every 25 packages inside the build loop in `local/build-all.R`.
- Add a defensive start-of-run cleanup of `_metadata/patched-*` + `pkgs-*.rds` to the two workflows that mount the persistent volume (`build-all-versions.yaml`, `build-all-versions-install-deps.yaml`).
Only these paths are touched; `process-updates.yaml`/`weekly-rebuild-missing.yaml` (no persistent volume) are unchanged.
Follow-ups (separate workstreams): on-host self-healing prune watcher + OrbStack disk cap (ansible), and Prometheus/Grafana alerting (k8s-talos).
Upstream: bincraft patched-repo hash churn is the true source fix.
New unit tests (6) for the helper; full suite 24/24 green.
Reviewed-on: #110
## Motivation
Build jobs were cycling through hundreds of packages that were only ever printed as `Skipping … due to previous build error recorded in metadata DB`, wasting wall-clock on per-package preparation before dropping each one.
## Cause
The prefilter query in `local/build-all.R` selected only successfully-built versions (`error_occurred = FALSE`) into `built`, so line 112 removed only those from the chunk.
Every previously-errored version stayed in the work list and was walked one-by-one, each hitting the internal skip in `build_binary_package()`.
This also explains the misleading `Skipped 0 already-built package versions` line for alphabetical chunks whose leading packages only have error records.
## Changes
- `local/build-all.R`: drop the `AND error_occurred = FALSE` clause so `built` holds every version already attempted (built or errored) for this platform/arch; the existing filter then removes all of them up front.
- Rename the log line to `already-attempted` so the reported count reflects successes and errors.
- Update the surrounding comment to explain why errored versions are excluded.
## Behaviour change
Previously-errored versions are now dropped before the build loop instead of being iterated and individually skipped.
No package that would otherwise build is affected, `build_binary_package()` already skipped these internally.
Retrying errored versions is out of scope and would need a separate opt-in flag on both the prefilter and the in-loop skip.
Reviewed-on: #113
## 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
## Summary
Stop hardcoding the bincraft version. Every `.crow` workflow and the build-one image pinned `@vX.Y.Z` (and a `packageVersion() != "X.Y.Z"` guard), so each bincraft release meant editing the version in ~8 places — and it was easy to miss one (the Dockerfile lagged at v4.2.1; v4.4.1 shipped without the empty-env fix because of exactly this churn).
## Change
New `local/install-bincraft.R` resolves the **latest release tag dynamically**:
- `git ls-remote --tags` on the public repo (no token),
- keep `vX.Y.Z` tags, pick the highest version (filtered/sorted in R for portability, not via git `--sort`/refspec which behaved inconsistently under `system2()`),
- `pak::pak("git::…@<latest>")` — idempotent on the git ref, so re-runs keep the package unless a newer tag exists.
All call sites now invoke the helper instead of a pinned version:
- `.crow/build-all-versions.yaml` (primary + per-minor pass)
- `.crow/build-all-versions-install-deps.yaml`
- `.crow/process-updates.yaml` (primary + per-minor pass)
- `.crow/weekly-rebuild-missing.yaml`
- `.crow/archive-missed-packages.yaml`
- `docker/build-one.Dockerfile` (ships the helper into the image; `ensure_bincraft` sources it)
## Effect
Tag a new bincraft release → the next CI run / `just rebuild` picks it up automatically. No more pin edits, and no more "forgot to bump the Dockerfile" drift.
## Verified
- Resolver returns the current latest tag (`v4.4.2`) via `git ls-remote` + R-side version sort.
- All five workflow YAMLs parse; helper R parses; air/editorconfig clean.
Note: this tracks the latest **tag**, so cutting a release is still the deliberate gate — CI won't pick up un-tagged main.
Reviewed-on: #107
## 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
## 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
## Summary
Two changes:
1. **`OS`/`OS_VERSION` manual-run dropdowns** — give these form variables explicit `options:` lists (like `target_arch` and `R_VERSION`), so the manual-run form shows dropdowns instead of free-text, in both `build-all-versions.yaml` and `build-all-versions-install-deps.yaml`. Crow form variables are independent (no cascading), so the operator still has to pick a coherent `OS` + `OS_VERSION` combination (e.g. `redhat` + `9`, not `alpine` + `jammy`).
2. **Repairs `main`** — the crow fix from PR #96 (`bc2f6f1`) was lost when that PR was squashed (only the first commit was captured). As a result `main` currently carries the `OS: ${OS}` env vars that break Crow parsing (`unable to parse variable name`) and the unfixed `build-all.R`. This PR re-applies that fix: drop the env additions and derive `platform`/`arch` inside `build-all.R` from the container (bincraft codename → platform mapping + `Sys.info()` arch).
## Notes
- `OS_VERSION` options are quoted strings so tags like `8`/`9`/`10` aren't parsed as integers.
- Validated: both YAMLs parse, `build-all.R` parses.
Reviewed-on: #97
## Summary
`build-all.R` reads three snapshot files from `/mnt/cache/packages/` that the `build-all-versions-install-deps` step precomputes: `pkgs_to_build.rds`, `r_minor_sensitive_pkgs.rds`, and `s3_cache.rds`.
That cache volume is **per-agent**, so a build job scheduled on a different (fresh) agent than the one that ran install-deps finds the snapshot absent and dies at `readRDS` (`cannot open compressed file '/mnt/cache/packages/pkgs_to_build.rds'`).
This adds a conditional guard at the top of `build-all.R`: when any of the three files is missing, it sources `local/packages-to-build.R` (which has all needed creds via `PGPASS` / `B2_S3_*` env, already present in the build step) and writes the derived `.rds` files — exactly mirroring the install-deps command.
- The first build job on a fresh agent repopulates the shared cache, so subsequent jobs on that agent reuse it.
- Concurrent jobs that also miss simply redo the work (accepted tradeoff vs. slow shared storage like NFS).
- Saves use a temp-file + atomic `file.rename`, so a concurrent reader never sees a half-written `.rds`.
Reviewed-on: #95
## Summary
When a `build-all-*` workflow is restarted, the build job re-reads the static `pkgs_to_build.rds` that the install-deps step produced once, so it cycles over every package an interrupted run already built. This adds a DB-based skip filter so a restart only processes what is genuinely left.
- At job start, `build-all.R` queries the `single_builds` metadata table for `(name, tag)` already built successfully (`error_occurred = FALSE`) on this `platform`/`arch`, and drops those pairs from the chunk before the build loop. It logs how many it skipped.
- One indexed query, one round trip, run before the pak forks — no extra S3 listing and no new Python/s3fs memory pressure (`RPostgres`/`DBI` are already used in the container).
- Errored versions are intentionally **not** skipped, so transient failures still get retried on restart.
## Dependency
Correctness depends on a `error_occurred = FALSE` row meaning the binary is actually published. That guarantee is added in rpkgs/bincraft#56 (success row written only after a confirmed S3 upload). This PR should land together with / after a bincraft release including that fix.
Reviewed-on: #91
A package's ABI sensitivity is the same across R minors, so for a non-sensitive
package the per-minor loop only ran `ensure_bincraft` (a ~14s bincraft/cranlike
install per minor) before build-one.R classified and skipped it. The primary
pass now writes a .r_minor_sensitive sentinel when it builds a sensitive
package, and the wrapper gates the whole per-minor loop (installs included) on
that file — non-sensitive rebuilds no longer touch other minors' libraries.
- Dockerfile: install bincraft into each R minor, run a primary pass plus a
sensitive-only pass under every other /opt/R/[0-9]* minor (deduped by minor),
probe/skip xvfb, set GIT_TERMINAL_PROMPT=0; extra-minor failures are non-fatal.
- build-one.R: add --sensitive-only mode, log + shallow-clone the ABI classify
step, and clear cranlike's stale ./PACKAGES.db before each index refresh
(workaround for the "table packages already exists" bug; pending cranlike fix).
## Summary
Adds a local `just rebuild` recipe to (re)build specific versions of a single package on a given OS/arch, dispatching to a remote buildx builder (the build runs there, not locally).
- `just rebuild <os> <tag> <arch> <package> <version>...` → `docker buildx build --builder <artemis|gaia> --platform linux/<arch> …` (amd64→artemis, arm64→gaia; names + `R_VERSION` env-overridable).
- `docker/build-one.Dockerfile` runs `build-one.R` as a secret-mounted `RUN`, built `--no-cache --output type=cacheonly` (pure side-effect: the S3 upload; no image kept).
- `local/build-one.R` auto-classifies each version via the ABI classifier (risky → per-minor slot `contrib/<x.y>/`, else generic), force-rebuilds + uploads + stores metadata, then refreshes the touched slot's `PACKAGES` index.
## Prerequisites
- buildx builders named `artemis` (amd64) and `gaia` (arm64) registered (`docker buildx create --name artemis ssh://…`).
- Exported secrets: `B2_S3_ACCESS_KEY`, `B2_S3_SECRET_KEY`, `PGPASS` (`GITHUB_PAT` optional).
- bincraft `v4.2.0` tag must exist (the build installs `@v4.2.0` and uses its classifier + per-minor index API).
Reviewed-on: #87
## Summary
Builds R-minor-sensitive CRAN packages once per installed R minor version (into per-minor S3 slots `…/contrib/<x.y>/`) and everything else once into the generic slot, driven by bincraft 4.2.0's ABI classifier. Both the full and iterative pipelines are covered.
## What's in here
**Detection / precompute**
- `local/r-minor-helpers.R` — pure `classify_from_metadata()` (NeedsCompilation / risky `LinkingTo`) + `parse_build_args()`, with unit tests.
- `local/packages-to-build.R` — adds a per-package `r_minor_sensitive` flag: cheap CRAN-metadata rules first, source download + `bincraft::needs_per_minor_recompile()` only for the ambiguous compiled subset (fail-safe to sensitive). Classified once per package, applied to all versions.
**Full build**
- `local/build-all.R` — passes the per-row `is_r_minor_sensitive` flag; new `--sensitive-only` mode builds just the risky subset.
- `.crow/build-all-versions-{amd64,arm64}.yaml` — install-deps persists the sensitive subset; build step runs a sensitive-only pass under each non-primary `/opt/R/*` minor; new step uploads the generic index plus a per-minor index for each minor.
**Iterative build**
- All 14 `.crow/process-updates-*.yaml` — primary pass uses `r_minor_detection = 'classifier'`; a sensitive-only multi-R pass builds risky updates under each other minor; per-minor index upload added.
**Tooling / housekeeping**
- Pins bincraft `v4.1.1` → `v4.2.0` across all workflows; removes the superseded standalone `build-r-minor-sensitive-packages.yaml`.
- Adds prek/pre-commit hooks (prettier, markdownlint, editorconfig-checker, yamllint, air) and applies them repo-wide; excludes the verbatim GPL `LICENSE.md` and auxiliary shell scripts.
- Design + implementation docs under `docs/superpowers/`.
## Requires before merge
- A `v4.2.0` git tag must be pushed on the bincraft repo (codefloe.com/rpkgs/bincraft) — the workflow install steps pin `@v4.2.0`. The full-build install-deps clones `main`, so it is unaffected.
Reviewed-on: #84
## Summary
`local/build-all.R` had a 75-name hardcoded `exclude <- c(...)` vector that had drifted from `local/excluded-packages.json` — `RcmdrPlugin.ROC` was in the R vector but missing from the JSON.
`.crow/weekly-rebuild-missing-*.yaml` already reads the JSON via `jsonlite::fromJSON(...)[["package"]]`. This brings `build-all.R` in line with that pattern.
Changes:
- **`local/excluded-packages.json`**: add the missing `RcmdrPlugin.ROC` entry (reason `"hang"`, matching siblings).
- **`local/build-all.R`**: replace the 16-line hardcoded vector with one `jsonlite::fromJSON(...)` call.
- **`.crow/build-all-versions-install-deps-{amd,arm}64.yaml`**: add `jsonlite` to the install-deps `pak::pak()` list so it's available in `/mnt/cache/R-pkgs` for the build step.
- **`.crow/build-all-versions-arm64.yaml`**: drop the dead base64-encoded `SKIP_PKGS` docs comment that nobody was passing as a `--var` anyway; replace with a one-line pointer to the JSON.
Reviewed-on: #79
## Summary
Both helpers still point at the old Hetzner storage:
- `Justfile` — all 3 recipes (`build-all`, `build-single`, `process-updates`) hit `hel1.your-objectstorage.com` / bucket `devxy-r-package-binaries-hel1` using `HETZNER_S3_*_K3S` env vars.
- `local/manual-package-index-update.R` — same endpoint + bucket, hardcoded into `s3fs::s3_dir_ls()` / `s3_file_delete()` calls.
Storage moved to Backblaze (`s3.eu-central-003.backblazeb2.com` / `devxy-rpkgs-binaries`) a while back, so running either of these today would write to the wrong bucket or fail outright.
No callers reference them in-tree, deleting outright. A one-off rebuild can just call `bincraft::upload_package_index()` directly with current Backblaze settings.
Reviewed-on: #77
s3fs uses reticulate/Python which significantly increases R process memory.
When pak tries to fork R to install package dependencies, the enlarged
process can't be duplicated within the container memory limit.
Now the install-deps step saves the S3 file listing as s3_cache.rds,
and the build step reads it with readRDS() — no s3fs loading needed.
- Load bincraft eagerly via library() to avoid lazy-load memory spike
- Do bulk S3 listing upfront and pass as s3_package_cache to avoid
per-package S3 calls that accumulate memory and trigger fork failures
- Consolidate amd64/arm64 exclude lists into single script
- Much easier to read and maintain than a YAML-embedded one-liner
The precompute script was constructing S3 paths as "redhat10" while
bincraft uses "rhel10" as the codename. This mismatch caused the
precompute to find no existing packages in S3, producing ~77K false
positive package versions that all get skipped at build time.
Now uses bincraft::set_codename() to ensure path alignment.
Also fixes nrow() vs length() in install-deps summary message.
packages-to-build.R now saves the full (Package, Version) data.table
so the build step can pass specific tags to build_binary_package(),
eliminating redundant per-package tag discovery and S3 checks.
Also reduces archive versions from 9 to 4 (+ 1 release = 5 total).
The S3 credentials, endpoint, and bucket name were still pointing to the old Hetzner storage after the Backblaze migration, causing silent build failures.
