Speeds up the full rebuild for a new slot, e.g. the upcoming Alpine version.
## Changes
- **Seed pure-R binaries** (`local/seed-pure-r.R`, `local/seed-helpers.R`), opt-in via the new `SEED_FROM` variable on `build-all-versions-install-deps`.
About 74% of the ~84k candidate versions have no compiled code and cost ~20s each to build; their R objects are identical across slots.
Before the build list is computed, each donor candidate is downloaded and verified, then copied server-side:
- donor must be the same OS family and arch;
- DESCRIPTION has `Built` (not a CRAN source fallback) with an empty platform and no `libs/`;
- built by the target's primary R minor;
- bincraft's `tarball_abi_verdict()` calls it portable across every installed minor (unknown means no seed).
Each copy gets the `single_builds` and `abi_flat_safety` rows an upload writes, so build-all skips it and the per-minor indexes keep it.
Re-runs skip existing objects and rewrite rows idempotently.
- **Interleaved shards** in `local/build-all.R` via `shard_slice()`; contiguous alphabetical quarters ranged from 0.1h to 28h.
- **Shared build deadline**: `build-all-versions` sets `BUILD_DEADLINE` from `BUILD_BUDGET_HOURS` (44h, repo timeout 50h); `build-all.R` and `build-newer-r.R` stop cleanly when it passes, so archiving still runs.
- `codename_platform()` replaces the hard-coded codename-to-platform list.
## Testing
- New unit tests for the seed verdict, candidate filter, platform names and deadline; all `local/tests` pass.
- Verdicts checked on real amd64/alpine324 tarballs: R6 2.6.1/2.5.1 and jsonstat seeded, cli refused as compiled.
- `crow lint .crow/` passes.
- The seed has not run against B2/Postgres yet; the first bootstrap run is its end-to-end test.
## Usage
Trigger `build-all-versions` with `target_arch`, `OS`, `OS_VERSION` and `SEED_FROM="alpine324 alpine323"`.
The new Alpine version still needs adding to the `OS_VERSION` options once its image exists.
Reviewed-on: #242
Every `process-cran-updates-redhat-9-arm64` run since bincraft v5.5.1 fails with `there is no package called 'progressr'` (e.g. pipeline 14179).
## Cause
bincraft v5.5.1 dropped `lubridate`, `dplyr`, `purrr`, `data.table`, `gert`, `gh` and `cranlike` from its imports.
The pipelines call some of these directly, and so far got them from the build-env image's site library or the shared `R_LIBS_USER` cache.
The arm64 `redhat:9` image has no `progressr` (and no `bincraft`) under R 4.4.3, and no `RPostgres`, `dplyr` or `purrr` under R 4.5.3.
The amd64 image has all of them, which is why only this slot broke.
## Changes
- `process-updates.yaml`: install `progressr` and `lubridate`, which the inline R calls use (`progressr::handlers`, `$INTERVAL`).
- `build-all-versions*.yaml`: install `purrr` for `packages-to-build.R`.
- `weekly-audit-missing.yaml`: install `data.table` for the audit script.
- `local/packages-to-build.R`: drop the unused `dplyr` and `progressr` `library()` calls.
- `reindex`, `weekly-rebuild-reindex`, `weekly-rebuild-missing`, `backfill-*`, `rebuild-abi-gap`, `repair-unsafe-flat-objects`, `prune-stale-flat-binaries`: install `RPostgres`, because bincraft quietly skips the metadata DB without it and the per-minor index build aborts.
- `prune-stale-flat-binaries.yaml`: reinstall bincraft in the re-index step, since its `/tmp/R-pkgs` library doesn't survive from the prune step.
## Verification
- `crow lint .crow/` passes; `prek` passes on the changed files.
- The image contents were checked by exporting the arm64 and amd64 `build-env-redhat:9` images.
- Not yet run in CI.
Reviewed-on: #238
## Problem
A manual `crow pipeline create` instantiates **every** file in `.crow/`, and a declared variable default is applied even when the run never passed that variable. A gate is therefore only a gate if its default matches nothing.
#155 fixed the three pipelines that had no manual gate at all. It missed that a *permissive default* leaves a pipeline just as exposed. Demonstrated the expensive way: creating a pipeline with only
```
--var weekly_audit_missing=alpine-324-amd64
```
also started `build-all-versions` — because its gate `target_arch` defaults to `amd64`, which matches its own amd64 matrix rows — and `process-updates` across every row, because that gate defaults to `all`. The run was killed before any `Upload package indexes` step produced output and both alpine324 indices were verified unchanged, but `build-all-versions` uploads binaries and rewrites indexes, so the next one might not be caught in time.
Before:
| pipeline | gate | default | fired on an unrelated manual run |
| --- | --- | --- | --- |
| `build-all-versions` | `target_arch` | `amd64` | amd64 rows — builds and uploads |
| `build-all-versions-install-deps` | `target_arch` | `amd64` | amd64 rows |
| `weekly-rebuild-missing` | `weekly_rebuild_missing` | `all` | every row |
| `weekly-audit-missing` | `weekly_audit_missing` | `all` | every row |
| `process-updates` | `process_cran_updates` | `all` | every row |
| `repair-built-stamp` | `repair_built_stamp` | `arm64` | arm64 rows |
`archive-missed-packages` was the one that behaved, because its gate variable is never declared and so matches nothing. That is the property this restores everywhere.
## What this changes
Each of the six gets a `none` option on its gate variable and defaults to it, so a manual run has to name its target explicitly. The reason is recorded next to the default, where someone would go to change it.
`none` is used rather than dropping the default so the expression always has a defined value to compare, instead of relying on undefined-variable semantics.
Cron triggers are untouched — they match on the `cron:` name, not the variable.
## Verification
`crow lint .crow/` reports all ten configs valid. Auditing every pipeline that accepts a manual event:
```
archive-missed-packages.yaml: gate=task default=<none>
auto-apply-patches.yaml: gate=auto_apply_patches default='false'
build-all-versions-install-deps.yaml gate=target_arch default=none
build-all-versions.yaml: gate=target_arch default=none
process-updates.yaml: gate=process_cran_updates default=none
repair-built-stamp.yaml: gate=repair_built_stamp default=none
trial-build-registry.yaml: gate=trial_build_registry default='false'
weekly-audit-missing.yaml: gate=weekly_audit_missing default=none
weekly-patch-proposals.yaml: gate=weekly_patch_proposals default='false'
weekly-rebuild-missing.yaml: gate=weekly_rebuild_missing default=none
```
Every gate now defaults to something that matches no matrix row.
Reviewed-on: #158
`bincraft` dropped pak in favour of uvr (5.0.x, "Dependencies and their system requirements are now installed with `uvr` instead of pak during `build_binary_package()`"), so the pipelines, helper scripts and images in this repo move with it.
## Approach
uvr is project-scoped in a way pak is not: `uvr add` refuses to run outside a project and always installs into `.uvr/library/`, and only `uvr sync` honours `--library`. So there is no one-line `pak::pak(...)` equivalent. `local/uvr-install.sh` encapsulates the dance — bootstrap a pinned uvr, mint a throwaway project under `TMPDIR`, `uvr add --no-install`, then `uvr sync --library <target>`. Keeping the project outside the checkout also keeps `uvr init`'s `.Rprofile` from hijacking `.libPaths()` for every other R call in the pipeline.
This matches what bincraft itself does (`uvr sync --install-system-deps --library <lib>`), and bincraft requires `uvr` on `PATH`, which the bootstrap provides: every pipeline that calls `bincraft::` runs `install-bincraft.R` (and therefore the bootstrap) first.
## Changes
| File | Change |
| --- | --- |
| `local/uvr-install.sh` | **New.** The single replacement for `pak::pak(...)`. Bootstraps uvr `v0.4.4`, resolves the R interpreter from `UVR_R_BIN`/`R_VERSION`/`PATH`, pins the manifest to that R's exact version, and syncs into `UVR_TARGET_LIB`/`R_LIBS_USER`. |
| `local/install-bincraft.R` | Installs `forgejo::codefloe.com/rpkgs/bincraft@<tag>` instead of a `git::` URL; keeps the `git ls-remote` tag resolution. Exports `UVR_R_BIN`/`UVR_TARGET_LIB` from `R.home()`/`.libPaths()[1]` so the per-R-minor passes target their own R and library. |
| `.crow/auto-apply-patches.yaml`, `.crow/weekly-patch-proposals.yaml`, `.crow/weekly-audit-missing.yaml`, `.crow/weekly-rebuild-missing.yaml`, `.crow/build-all-versions-install-deps.yaml` | `pak::pak(...)` → `UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh ...`. The explicit `UVR_R_BIN` matters in `build-all-versions-install-deps.yaml`, which has no `R_VERSION` in its step environment. |
| `.crow/build-all-versions.yaml`, `.crow/process-updates.yaml`, `.crow/weekly-rebuild-missing.yaml` | `R_PKG_CACHE_DIR` → `UVR_CACHE_DIR` + `UVR_PACKAGES_DIR` on the same `/mnt/cache` volume, preserving the amd64-off/arm64-on split. Drops the `rm -rf .../pkgcache/_metadata/...` cleanup. |
| `local/r-minor-helpers.R`, `local/build-all.R`, `local/tests/test-trim-pkgcache.R` | Removes `trim_pkgcache_metadata()`, its every-25-packages call and its tests. uvr's cache does not mint a fresh ~70 MB snapshot per `PACKAGES` change. |
| `.crow/build-all-versions-install-deps.yaml` | Drops `pak::sysreqs_db_update()`; uvr resolves sysreqs from its vendored `r-system-requirements` rules via `--install-system-deps`. |
| `docker/Containerfile-shiny-app` | Bootstraps uvr and drives both dependency installs through one uvr project with `UVR_LIBRARY` pointed at the image's R library. |
| `docker/build-one.Dockerfile` | Ships `uvr-install.sh` at `/work/local/` so `install-bincraft.R` finds it. |
| `docker/reprex/alpine.sh` | Replaces `pak::local_install_deps()` with DESCRIPTION parsing + `uvr add`. |
| `local/test-package-loading.R` | Installs via the helper instead of `pak::pkg_install()`. |
| `README.md` | Documents uvr for sysreq inference, archived-version installs and cache clearing. |
| `renovate.json` | Tracks the `UVR_PIN` in `uvr-install.sh` via `github-releases`. |
## Behaviour notes
- **`weekly-audit-missing` still takes bincraft from the default branch**, not the latest release tag, matching what the `git::` pak call did. Called out in a comment rather than silently changed.
- **The uvr pin is repo-wide.** bincraft resolves `uvr` from `PATH` and pins no version of its own, so `UVR_PIN` in `uvr-install.sh` governs the whole pipeline.
- **Persistent caches now also benefit bincraft**, which reads `UVR_CACHE_DIR`/`UVR_PACKAGES_DIR` from the inherited pipeline environment.
- **`uvr sync` will not prune the shared library.** Pruning is disabled whenever `--library` is passed (`do_prune = prune && library_override.is_none()`), so `/mnt/cache/R-pkgs` keeps bincraft and its dependencies. The wipe-on-ABI-mismatch path is *not* similarly guarded, which is why the helper pins the manifest to the active R's exact version.
- **`plans/` and `specs/` are untouched** — they are dated records of decisions made in June 2026 and describe bincraft's then-pak-based internals; rewriting them would misstate history.
## Verification
`shellcheck`, all pre-commit hooks (on this commit's file range) and the `local/tests/` suite (100 assertions) pass.
Not yet exercised in CI: the build-env images do not ship `uvr`, so the per-step `curl install.sh` bootstrap is untested against a real image. Worth a manual `build-all-versions-install-deps` run before merging.
Reviewed-on: #147
## 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
## 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
Silences the recurring `OpenTelemetry error: there is no package called 'otelsdk'` warnings during builds.
## Root cause
The `build-env-*` images configure an OTel exporter (traces/logs/metrics), but `otelsdk` (the R OTel SDK backend) isn't installed. pak's `otel` instrumentation therefore tries to load `otelsdk` on every run and logs the error, falling back to a no-op.
`OTEL_SDK_DISABLED=true` (already set in `build-one.Dockerfile`) does **not** help — the R `otel` package ignores it and gates purely on `OTEL_R_<SIGNAL>_EXPORTER` (then the standard `OTEL_<SIGNAL>_EXPORTER`). When that resolves to a real exporter (`otlp`/`http`/…) with no SDK present, you get the error.
## Fix
Set `OTEL_R_TRACES_EXPORTER`, `OTEL_R_LOGS_EXPORTER`, and `OTEL_R_METRICS_EXPORTER` to `none` so the R otel providers are clean no-ops:
- `docker/build-one.Dockerfile` — exported alongside the existing OTel var.
- `.crow/process-updates.yaml`, `weekly-rebuild-missing.yaml`, `build-all-versions.yaml`, `build-all-versions-install-deps.yaml` — added to each step's `environment` block.
Using the R-specific variables (not the standard `OTEL_*_EXPORTER`) keeps OTel intact for any non-R tooling in the images.
Reviewed-on: #105
## 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: ${OS}` env vars that break Crow parsing (`unable to parse variable name`) and the unfixed `build-all.R`. This PR re-applies that fix: drop the env additions and derive `platform`/`arch` inside `build-all.R` from the container (bincraft codename → platform mapping + `Sys.info()` arch).
## Notes
- `OS_VERSION` options are quoted strings so tags like `8`/`9`/`10` aren't parsed as integers.
- Validated: both YAMLs parse, `build-all.R` parses.
Reviewed-on: #97
## Summary
Fixes the recurring `build-all-*` failure on agents where `build-all-versions-install-deps` did **not** run.
Both symptoms in the logs — `Parameter 3 does not have length 1` (repeated, in the metadata DB queries) and `argument is of length zero` (system-dependency install) — were the same bug: inside bincraft, `platform` was zero-length. `local/build-all.R` calls `build_binary_package()` without passing `platform`, so bincraft resolves it from the container codename. The primary build step never (re)installed/pinned bincraft and relied on whatever sat in the **per-agent** cache volume; `depends_on` only orders steps, it does not co-locate them on the same agent, so a job landing where install-deps never ran got a stale bincraft that left `platform` empty.
## Changes
- **`build-all-versions.yaml`**: pin bincraft `@v4.2.3` in the primary build step (mirroring the R-minor pass and `process-updates.yaml`), so every agent uses a known-good bincraft regardless of where install-deps ran.
- Align the R-minor pass `v4.2.2 → v4.2.3`.
- Export `OS`/`OS_VERSION`/`ARCH` as runtime env vars — previously only available for `${...}` interpolation, so `build-all.R`'s already-built dedup query matched platform `"-"` and skipped nothing.
- Fix the unarchive call: pass the codename via `bincraft::set_codename(NULL)` instead of the malformed `paste(OS, OS_VERSION)` (`"alpine 3.24"`), matching `archive-missed-packages.yaml`.
- **`build-all-versions-install-deps.yaml`**: pin install-deps to `@v4.2.3` (was installing HEAD), so the precomputed snapshot and per-agent library stay consistent pipeline-wide.
Reviewed-on: #96
## Summary
- Switch crow workflow placement from a per-agent label (`agent: ${AGENT}`) to a group label (`group: rpkgs-${ARCH}`), so jobs target the `rpkgs-amd64` / `rpkgs-arm64` agent pools instead of a single named agent (`artemis`/`gaia`).
- Remove the now-unused `AGENT` matrix variable from all build/process/weekly workflows.
- Update header comments to reflect group-based placement.
Agents opt into a pool via `CROW_AGENT_LABELS="group=rpkgs-<arch>"`. The group name derives from each matrix row's `ARCH`, so adding or replacing agents no longer requires touching the workflow files.
Reviewed-on: #94
## Summary
Consolidate the four `build-all-versions*` files into two, mirroring the matrix approach used for the process-updates / weekly families:
| Before | After |
|---|---|
| `build-all-versions-amd64.yaml` + `build-all-versions-arm64.yaml` | `build-all-versions.yaml` |
| `build-all-versions-install-deps-amd64.yaml` + `-arm64.yaml` | `build-all-versions-install-deps.yaml` |
`ARCH` becomes a matrix axis carrying the per-arch differences: `agent` (artemis/gaia), `BACKEND` (kubernetes/docker), and `R_PKG_CACHE_DIR`. Build-all keeps its `SPLIT_INDEX` parallelism, so its matrix is ARCH x SPLIT = 8 rows; only the rows matching the selected arch run.
**Invocation unchanged.** Routing uses the existing task selector `task == "build-all-${ARCH}"`, so `--var task=build-all-amd64 ...` still runs exactly the amd64 rows. `OS` / `OS_VERSION` / `R_VERSION` / `K8S_INSTANCE_TYPE` are still passed via `--var`. (You can drop `--var ARCH=...` now — arch comes from the matrix/task.)
**No cron.** These pipelines are manual-only, so there are no scheduled runs to affect.
## Validation before merge
Same matrix-interpolation-in-`when`/`labels` mechanism validated for #92, plus it now relies on per-row `agent`/`BACKEND` selecting the right execution backend (kubernetes for amd64, docker for arm64). Before merge, on this branch trigger a small `task=build-all-arm64` run and confirm it lands on the gaia/docker backend (and amd64 on artemis/kubernetes). Originals are in git history for rollback.
Note: `archive-missed-packages.yaml` was already a single consolidated matrix file (cron + manual) and is left untouched.
Reviewed-on: #93
Move packages-to-build.R execution to the single install-deps step and save results as RDS. Matrix jobs read the precomputed list instead of loading the massive CRAN archive/release databases, freeing memory for fork/system calls.
Adds build-all-versions-install-deps pipeline that runs once before the matrix builds, cleaning stale locks and installing bincraft to the shared cache without contention.
