Author	SHA1	Message	Date
pat-s	930a4acd12	fix(ci): install the R packages pipelines use instead of relying on the image ... bincraft v5.5.1 dropped lubridate, dplyr, purrr, data.table and others from its imports, so the pipelines' own calls now depend on whatever the build-env image's site library or the shared R_LIBS_USER cache happens to hold. The arm64 redhat:9 image has no progressr under R 4.4.3, which fails every process-cran-updates-redhat-9-arm64 run since v5.5.1. - Install progressr and lubridate for process-updates, which call them inline. - Install purrr for packages-to-build.R and data.table for the weekly audit. - Drop the unused dplyr and progressr library() calls from packages-to-build.R. - Install RPostgres in every pipeline that talks to the metadata DB, since bincraft silently skips the DB (and the per-minor index aborts) without it. - Reinstall bincraft in the prune re-index step, whose /tmp library does not survive from the prune step.	2026-10-20 08:46:00 +00:00
pat-s	d992a2b636	fix(ci): give each xvfb-run its own display (#230) ... Every `process-cran-updates-ubuntu-2204-arm64` cron run since pipeline 13744 has failed with `xvfb-run: error: Xvfb failed to start` (e.g. 13829). ## Cause The newer-R loop added in #216 runs two `xvfb-run` calls back to back: the R-minor-sensitive `process_cran_updates` pass, then `local/build-newer-r.R`. Without `-a`, `xvfb-run` always uses display `:99`, and on exit it kills its Xvfb without waiting for it. The second call can therefore start while the old server still holds the `:99` lock, so the new Xvfb refuses to start. Only ubuntu-2204-arm64 hits this because it is the only image with a second R minor installed, so the loop body only runs there. ## Change - Default `XVFB_ARGS` to `-a` (`--auto-servernum`) in `process-updates.yaml`, `build-all-versions.yaml` and `weekly-rebuild-missing.yaml`, so each call picks a free display. - The RHEL 10 `xwfb-run` branch still overrides `XVFB_ARGS` with `-c weston`, so it is unchanged. ## Verification `crow lint .crow/` passes. A local repro was not possible (`docker run` hangs on the dev host), so the next ubuntu-2204-arm64 cron run is the real check. Reviewed-on: #230	2026-10-11 12:12:28 +00:00
pat-s	416a2d64d9	chore(alpine): drop the deprecated Alpine 3.22 slot (#213) ... ## Why Alpine 3.22 is deprecated and should be dropped. It was never a published slot to begin with. `local.rpkgs_slots` in `cdn.tf` enumerates eight distros and alpine322 is not one of them, so `UNION_SLOTS` never gated per-minor rewriting for it. The website's `DistroId` union lists the same eight. Every request to the slot therefore fell through to the flat index, which holds R 4.5 builds. ## Evidence The fleet-wide routing verification (pipeline 12591, `verify_routing=all`) measured this end to end. Across all 16 published slots, both architectures, three R minors and both contractual URL forms: **1056 of 1056 install-and-load checks passed.** Every failure in the run was alpine322, identical on amd64 and arm64: ``` amd64/alpine322 R 4.4 via arch|generic|flat: 8 of 11 amd64/alpine322 R 4.6 via arch|generic|flat: 10 of 11 arm64/alpine322 R 4.4 via arch|generic|flat: 8 of 11 arm64/alpine322 R 4.6 via arch|generic|flat: 10 of 11 ``` The tell is that all three forms agree. On a routed slot `arch` and `generic` diverge from `flat`, because that divergence *is* the routing. On alpine322 there is nothing to diverge from. R 4.5 clients were 11 of 11 on every form, because flat happens to be what they need. The data itself is not broken, only unreachable. `alpine322/contrib/4.4/data.table_1.18.6.1.tar.gz` is genuinely `Built: R 4.4.3` and the 4.6 object is `Built: R 4.6.0`. Correct objects, correct per-minor indexes, never served. ## What changed - alpine-322 matrix rows and dropdown options removed from the 12 pipelines that carried them, so `=all` no longer fans out to a slot nobody can reach. - `3.22` removed from the `OS_VERSION` dropdowns in `build-all-versions.yaml` and `repair-built-stamp.yaml`; the latter's default moves to `3.23`. - Stale `3.22` examples updated in `local/packages-to-build.R`. `crow lint .crow/` reports all 18 configs valid. ## Also done outside this diff The six alpine-322 cron jobs are deleted from the Crow server, since a cron whose matrix row is gone keeps firing against nothing: ``` 5 process-cran-updates-alpine-322-amd64 0 5/8 * * * 6 process-cran-updates-alpine-322-arm64 30 5/8 * * * 68 weekly-audit-missing-alpine-322-amd64 20 0 * * 0 69 weekly-audit-missing-alpine-322-arm64 30 0 * * 0 82 weekly-rebuild-missing-alpine-322-amd64 0 4 * * 0 83 weekly-rebuild-missing-alpine-322-arm64 10 4 * * 0 ``` They are listed here so they can be recreated if this is ever reversed. ## Not done The published objects and indexes under `amd64/alpine322` and `arm64/alpine322` are left in the bucket. Deleting them is a separate decision, and nothing routes to them in the meantime. Reviewed-on: #213	2026-09-11 07:27:03 +00:00
pat-s	50495f5c3b	Revert "fix(ci): split oversized weekly rebuild matrix" ... This reverts commit b75fd2f1c4.	2026-08-14 07:01:56 +00:00
pat-s	b75fd2f1c4	fix(ci): split oversized weekly rebuild matrix	2026-08-14 06:56:41 +00:00
pat-s	132d1d2d3c	docs(ci): clarify parallel manual matrix runs	2026-08-14 06:44:10 +00:00
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	01b8ab43df	fix(rebuild): re-index and purge the CDN after a rebuild (#160) ... ## Problem The rebuild now works — `AATtools 0.0.3` was detected as a source fallback, built, and published: ``` ℹ `upload_single_binary()`: Replacing the CRAN source published for AATtools 0.0.3 … with the binary. ✔ Successfully uploaded package AATtools with tag 0.0.3. ``` But clients still get the source, and will for about a year: ``` $ curl -sI .../src/contrib/AATtools_0.0.3.tar.gz etag: "ea8127d953ca6a2f118ea49441772af6" # CRAN's source MD5 cdn-cache: HIT cdn-cachedat: 08/09/2026 16:43:32 # predates the 18:12 upload ``` Two causes, both specific to a rebuild: 1. **The slot is never re-indexed.** `weekly-rebuild-missing` has no `upload_package_index` step, so the index keeps the old MD5 and — for anything that had been served from source — no `Built` stamp. This one self-heals at the next `process-updates` run. 2. **The tarball URL is never purged.** A normal update publishes new packages at *new* URLs, so `purge_cdn_cache.sh` only needs the five index files. A rebuild replaces an object *in place*, and the zone caches tarballs for `cache_expiration_time = 31919000` (~370 days). This does not self-heal. Nothing about a stale package looks wrong from the outside, which is what makes it worth fixing rather than documenting. ## What this changes **Re-index at the end of a rebuild**, flat and per-minor, mirroring the tail of `process-updates`. The codename is detected from the image's `/etc/os-release` (as `local/packages-to-build.R` already does) rather than adding `OS_ID` to all 18 matrix rows. **Purge the zone afterwards**, via a new `scripts/purge_cdn_zone.sh`. One call to `POST /pullzone/{id}/purgeCache` covers every replaced object, and all three hostnames — `cran.devxy.io`, `cran.allianceswisspass.devxy.io`, `cran.rpkgs.com` — share pull zone `3857050`, confirmed from the `cdn-pullzone` response header. Purging per URL was the alternative and is worse here: ~13.5k rate-limited calls per arch, where a single missed call leaves a package silently stale. The cost of the zone purge is a cold cache for everything else, which is why it stays out of the daily update path — `purge_cdn_cache.sh` is untouched. The purge runs on failure too (`when: status: [success, failure]`): a rebuild that died part-way still replaced objects, and those are exactly the ones a stale edge keeps hiding. ## Verification `crow lint .crow/` reports all ten configs valid; `bash -n` on the new script passes; prek hooks pass. Not yet exercised against Bunny — it needs `BUNNYNET_API_KEY`, which is a CI secret. The failure mode is explicit rather than silent: any status other than 200/204 prints the response body and exits non-zero. Reviewed-on: #160	2026-08-10 06:30:35 +00:00
pat-s	f8e31af75b	fix(ci): make every manual gate default to a value that matches nothing (#158) ... ## 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	2026-08-09 15:31:14 +00:00
pat-s	ee15c50f53	refactor: migrate package installation from pak to uvr (#147) ... `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	2026-07-31 12:19:26 +00:00
pat-s	61e1c0188d	chore: adjust weekly audit runs	2026-07-20 19:09:50 +02:00
pat-s	1ad7a6bfe9	chore: resolve latest bincraft release dynamically (no hardcoded pins) (#107) ... ## 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	2026-07-01 08:10:02 +00:00
pat-s	b4ec6291a9	chore: bump bincraft to 4.4.2	2026-06-30 16:09:44 +02:00
pat-s	d496029a79	chore: bump bincraft to 4.4.1	2026-06-30 15:51:07 +02:00
pat-s	b93d1ef6bd	chore: silence otelsdk warnings across build paths (#105) ... ## 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	2026-06-30 12:41:32 +00:00
pat-s	00db47398d	chore: 4.4.0 instead of 4.3.1	2026-06-30 14:07:22 +02:00
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
pat-s	f9bc72d5ab	chore: bump bincraft to 4.2.3	2026-06-18 09:43:05 +02:00
pat-s	4c67703f52	refactor(ci): route workflows by agent group label instead of named agent (#94) ... ## 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	2026-06-17 16:26:04 +00:00
pat-s	dc92bd6a2c	fix(ci): restore cron triggers via per-row cron name filter ... The matrix consolidation routed cron events through `evaluate: 'CI_PIPELINE_CRON == "..."'`, but CI_PIPELINE_CRON is not exposed to the when.evaluate constraint context, so no matrix row ever matched and the scheduled process-updates / weekly runs stopped firing. Switch back to the first-class `cron:` name filter (still parameterized per matrix row) which the server matches directly against the fired cron.	2026-06-17 11:03:12 +02:00
pat-s	4406a8735b	refactor(ci): consolidate per-platform crow workflows into 3 matrix files (#92) ... ## Summary Collapse **44** per-platform crow pipeline files into **3** matrix-driven files (one per family), using `matrix.include` + the crow #1165 declarative manual `variables:` block: | Family | Before | After | |---|---|---| | process-updates | 14 | `process-updates.yaml` | | weekly-audit-missing | 16 | `weekly-audit-missing.yaml` | | weekly-rebuild-missing | 14 | `weekly-rebuild-missing.yaml` | - **One file per family** (not split by arch). Arch placement is via the agent label as a matrix var (`artemis`=amd64, `gaia`=arm64) for process-updates and weekly-rebuild; weekly-audit keeps its arch-`nodeSelector` placement (no agent label). - **Matrix axis is named `OS`** (e.g. `redhat-9`) per request, with per-row `R_VERSION`, image tag, codename, and `process_new` (FALSE for alpine). - **Runs preserved 1:1:** - *Cron*: each existing `<family>-<os>-<arch>` cron still fires only its matching matrix row via `CI_PIPELINE_CRON`. Server-side cron entries unchanged. - *Manual*: a #1165 dropdown variable (`process_cran_updates` / `weekly_audit_missing` / `weekly_rebuild_missing`) selects a single `<os>-<arch>` or `all`. weekly-rebuild defaults to `all`, matching its former bare `event: manual` trigger. ## Behavior deltas (intentional, flagged) To fit one file per family the backend was unified: - The amd64-only `node.kubernetes.io/instance-type: AX42` nodeSelector pin is **dropped**; placement now relies on the `artemis`/`gaia` agents. - **process-updates arm64** jobs now share the same `backend_options` as amd64 (resource requests/limits + tolerations) — they previously had none, so they gain an 18Gi memory limit. Tell me if arm64 should stay uncapped. ## Validation required before merge Relies on crow interpolating matrix variables inside `when.evaluate`, `labels.agent`, and `commands`. Interpolation in image/env/commands is standard crow; the novel bit is `when.evaluate`. The manual dropdown routing exercises the same interpolation as the cron routing, so on this branch: 1. Trigger manually with the dropdown = `redhat-9-amd64` -> confirm only that one job runs (image `build-env-redhat:9`, R 4.4.3, agent artemis). 2. Trigger with `all` -> confirm all os/arch jobs schedule. Crons only fire on the default branch, so no collision while unmerged. Fallback if `${...}` doesn't interpolate in `when`: a runtime `case "$CI_PIPELINE_CRON" in ...` guard, same files otherwise. Reviewed-on: #92	2026-06-16 09:33:06 +00:00

Renamed from .crow/weekly-rebuild-missing-alpine-322-arm64.yaml (Previous history)