Author	SHA1	Message	Date
pat-s	4b7dc28cc8	feat(rebuild): shard the weekly rebuild and make each shard resumable (#163) ... ## Problem `weekly-rebuild-missing` runs one job per `<os>-<arch>` and walks that slot's list serially in a single `R -q -e` argument. That was cheap while every source fallback was skipped as "already built". Since bincraft #105/#106/#107 and #159 the gate works, and the lists are large: 8 917 source-served records on `amd64/alpine324`, 15 023 on `amd64/resolute`. Pipeline 10910 (`weekly_rebuild_missing:alpine-324-amd64`) ran for two days, reached `[8692/23885] cholera`, and was killed there. Two failures follow from that shape: - **No parallelism.** The work is embarrassingly parallel across packages; one job does all of it. - **No resumability and no clean stopping point.** The loop ends only by exhausting the list, so the only way to stop it is a kill. A restart re-walks from the first entry, paying a CRAN version resolution and an S3 `HEAD` per package before reaching new work. And a kill matches neither `success` nor `failure`, so the `Purge CDN cache` step never ran: the ~4 600 binaries 10910 did publish stayed hidden behind stale edge copies. ## What this changes **Three shards per slot.** Each of the 18 `OS`/`ARCH` rows gains `SPLIT_INTO`/`SPLIT_INDEX`, mirroring `build-all-versions.yaml`. Cron and manual routing are unchanged: both filters already match on `${OS}-${ARCH}`, so they now match all three shards of a slot. **`local/rebuild-missing.R`** replaces the ~1 500-character inline one-liner. The slice is interleaved rather than contiguous, because the list is alphabetical and cost clusters by name (`Rcpp*`, `Bioc*`, `rstan*`). **Resume by re-deriving state from the bucket.** One `s3_dir_info()` listing gives ETags for the slot; a package is outstanding iff its object's ETag equals CRAN's published `MD5sum`, i.e. it is still byte-identical to CRAN's source. That is `check_s3_root_package()` evaluated in bulk. No progress file, no volume, no DB cursor, and correct when a sibling shard or a `process-updates` run completes something concurrently. It reads ETags rather than the index's `Built` field the way `packages-to-build.R` does, because the index is no longer rewritten until the dependent pipeline runs and so cannot reflect the current run's progress. Unknown always means "already a binary", never "rebuild it": a multipart ETag, an unreadable CRAN index or an empty listing can never mass-schedule work. **A 20 h wall-clock budget** per shard. It exits 0, so the re-index and purge always fire and the remainder is picked up next run with no bookkeeping. **`.crow/weekly-rebuild-reindex.yaml`** takes over re-indexing and the purge, with `depends_on: [weekly-rebuild-missing]` and `runs_on: [success, failure]`. Three shards writing one slot's `PACKAGES` concurrently would race: `update_PACKAGES()` lists the live bucket, so an early lister that uploads last publishes an index missing its siblings' work. ## Verification `crow lint .crow/` passes on all 11 pipelines. `prek run` passes. 19 assertions in `local/tests/test-rebuild-missing.R`, 0 failures, covering the partition (disjoint, covering, deterministic, short lists, out-of-range index) and the outstanding filter (source ETag kept, binary ETag dropped, absent object kept, multipart and missing-from-CRAN treated as built). One of those tests caught a real bug before it shipped: an empty ETag table indexed to zero length rather than to `NA`, which recycled the result away and reported "nothing to build" — the dangerous direction. Fixed with an explicit `lookup()`. The filter run against the live `amd64/alpine324` index, using its `MD5sum` column as the ETag (established to match the objects): ``` index packages: 24343 outstanding (filter): 8950 no Built stamp: 8917 filter vs no-Built agreement: 8917 of 8917 outstanding but stamped Built: 33 (version drift vs CRAN) shard sizes: 2984/2983/2983 (sum 8950, unique 8950) ``` It reproduces the source-served set exactly. The extra 33 are packages whose slot version differs from CRAN's current one, so no object exists at the CRAN version key: correctly outstanding. ## Notes for review - The 20 h budget is a chosen default, exposed as `REBUILD_BUDGET_HOURS` in the pipeline. - `depends_on` is file-level, not row-level, so on a full cron run no slot is re-indexed until the slowest of all 54 jobs finishes. The budget bounds that at roughly a day. - An explicit cancel still skips the re-index. Recovery is to trigger `weekly-rebuild-reindex` on its own. - The purge runs on every re-index row rather than one designated slot: a cron fires only its own slot's row, so gating on a named slot would leave every other slot unpurged. - Out of scope: `build-all-versions` still cannot rebuild source fallbacks, because `local/build-all.R:113-122` drops every version with any `single_builds` row, which is precisely the source-fallback set. Design: `specs/2026-08-12-shard-weekly-rebuild-design.md` Reviewed-on: #163	2026-08-12 08:30:29 +00:00
pat-s	2f732457d2	feat(edge): route PACKAGES requests to the per-R-minor slot (#152) ... ## Problem `install.packages("curl")` fails in `reg.devxy.io/r/r-alpine:4.5-3.24` with "package 'curl' is not available for this version of R", on both arches. `curl` is not missing from the repo: it is in `…/latest/src/contrib/4.5/` and `…/4.6/`, the per-minor slots that base R cannot address. The image's repo URL resolves to `…/latest/src/contrib`, whose index does not list it. On `amd64/alpine324` that is 2 886 packages invisible to `install.packages()` (23 on `amd64/noble`) — what issue #63 records as "missing binaries". Two further findings while investigating: - The middleware only ever rewrote the bare `cran.rpkgs.com/src/contrib/…` form, and that form was broken for every Linux client on a stock R user agent: `ALPINE_REGEX`/`UBUNTU_REGEX`/`RHEL_REGEX` need a Posit-style UA that carries the distro, so stock R fell through to `extractOs()` and got redirected to `/amd64/linux-musl/latest/…`, a slot that does not exist. - `PACKAGES*` is served `cdn-cache: BYPASS` (bincraft uploads it `no-store`), so the middleware sees every index request and no purge is needed for routing changes to take effect. ## What this changes **`edge/rpkgs-router.ts`** — the middleware, now a reviewed file in this repo rather than dashboard state. It routes `PACKAGES`, `PACKAGES.gz` and `PACKAGES.rds` into `…/src/contrib/<x.y>/` for slots listed in `UNION_SLOTS`, and nothing else. Tarballs are deliberately left alone. R keeps the `contriburl` it *asked for*, not the one the redirect served it, so every tarball URL is resolved against the flat directory and the union index steers the per-minor ones with a `Path: <x.y>` field. Rewriting a tarball request here would send flat-slot packages into a directory that does not hold them. Also in the script: the phantom `linux-gnu`/`linux-musl` fallback is gone (an unidentifiable distro goes to CRAN, as an unparseable UA already did), and every redirect carries `Cache-Control: no-store` since its target depends on the User-Agent. The macOS branches are unchanged. **`cdn.tf`** — `bunnynet_compute_script.rpkgs_router` with `content = file("edge/rpkgs-router.ts")`, the `UNION_SLOTS` variable, and `middleware_script` pointing at the resource instead of the literal `29277`. `UNION_SLOTS` is empty, so merging and applying this changes no client's behaviour. A slot is added only once bincraft has republished its per-minor index as a union (rpkgs/bincraft#97); routing to a raw per-minor index would hide every package it does not carry. Rolling back is a variable edit, not a deploy. **`specs/`, `plans/`** — the design and the implementation plan, including the two approaches that were rejected (edge-side merge, moving the minor up the path) and why. ## Verification `just edge-test` runs 13 routing cases against the SDK's local server, so what is tested is the artifact that gets deployed; pass-through cases proxy to the real origin. All pass. End to end, with the middleware in front of a locally built union index for `amd64/alpine324` (31 507 records), inside the runtime image: ``` curl: 7.1.0 -> …/latest/src/contrib/4.5 -> curl_7.1.0.tar.gz 717 725 B jsonlite: 2.0.0 -> …/latest/src/contrib -> jsonlite_2.0.0.tar.gz 1 055 849 B ``` `tofu validate` passes. `tofu plan` has not been run: no `BUNNYNET_API_KEY` available in this environment. ## Before applying The script pre-dates this configuration, so it must be adopted, not created: ```sh tofu import bunnynet_compute_script.rpkgs_router 29277 tofu plan ``` The plan should show an in-place `content` update and no replacement of the pull zone. Without the import, tofu creates a second script and repoints the zone at it. Note that `name = "rpkgs-router"` will rename the existing script on apply. ## Not fixed here `install.packages("curl")` on `alpine324` will now *resolve*, then fail to build: that slot's tarballs are byte-identical CRAN **source** tarballs (no `Meta/`, no `Built:` in DESCRIPTION) which the index nevertheless stamps `Built: R 4.5.3; …-linux-musl`. Sampled: `amd64/alpine324` 3/12 binary, `arm64/alpine324` 13/30, `amd64/noble` 12/12, `amd64/alpine323` 17/20. That slot needs a rebuild, tracked separately. Reviewed-on: #152	2026-08-07 14:12:22 +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