Author	SHA1	Message	Date
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	a4b274f281	fix(ci): bound pkgcache _metadata growth to stop macmini disk-fill (#110) ... ## 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	2026-07-13 09:31:29 +00:00
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	83c761b736	feat(ci): OS/OS_VERSION manual dropdowns + restore lost crow fix (#97) ... ## 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: ${OS}` env vars that break Crow parsing (`unable to parse variable name`) and the unfixed `build-all.R`. This PR re-applies that fix: drop the env additions and derive `platform`/`arch` inside `build-all.R` from the container (bincraft codename → platform mapping + `Sys.info()` arch). ## Notes - `OS_VERSION` options are quoted strings so tags like `8`/`9`/`10` aren't parsed as integers. - Validated: both YAMLs parse, `build-all.R` parses. Reviewed-on: #97	2026-06-18 11:39:11 +00:00
pat-s	0f4330c05c	fix(ci): make build-all self-sufficient on agents without install-deps (#96) ... ## Summary Fixes the recurring `build-all-*` failure on agents where `build-all-versions-install-deps` did **not** run. Both symptoms in the logs — `Parameter 3 does not have length 1` (repeated, in the metadata DB queries) and `argument is of length zero` (system-dependency install) — were the same bug: inside bincraft, `platform` was zero-length. `local/build-all.R` calls `build_binary_package()` without passing `platform`, so bincraft resolves it from the container codename. The primary build step never (re)installed/pinned bincraft and relied on whatever sat in the **per-agent** cache volume; `depends_on` only orders steps, it does not co-locate them on the same agent, so a job landing where install-deps never ran got a stale bincraft that left `platform` empty. ## Changes - **`build-all-versions.yaml`**: pin bincraft `@v4.2.3` in the primary build step (mirroring the R-minor pass and `process-updates.yaml`), so every agent uses a known-good bincraft regardless of where install-deps ran. - Align the R-minor pass `v4.2.2 → v4.2.3`. - Export `OS`/`OS_VERSION`/`ARCH` as runtime env vars — previously only available for `${...}` 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	2026-06-18 11:27:02 +00:00
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	b297f0fbc0	refactor(ci): consolidate build-all-versions workflows into 2 files (#93) ... ## 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	2026-06-16 09:33:13 +00:00
pat-s	a64dea6b23	refactor: separate install-deps workflows for arch	2026-04-11 09:49:44 +02:00
pat-s	9ff676a5cb	chore: don't clean cache	2026-04-10 20:16:05 +02:00
pat-s	270843eaf9	refactor: precompute package list in install-deps step to reduce matrix job memory usage ... 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.	2026-04-10 16:21:33 +02:00
pat-s	e53f11a896	fix: one-time full R-pkgs cache wipe to fix corrupted .so files from previous failed builds	2026-04-10 16:04:49 +02:00
pat-s	858f13140b	fix: clear pak cache before installing bincraft to ensure new version is picked up	2026-04-10 15:02:10 +02:00
pat-s	7bd77a2873	fix: stop wiping entire R-pkgs cache, only clean locks and bincraft now that cache is rebuilt	2026-04-10 00:17:11 +02:00
pat-s	e062c58185	fix: restore pak::sysreqs_db_update() in matrix step and pre-cache it in install-deps	2026-04-10 00:15:23 +02:00
pat-s	18a8f2dc54	fix: install packages-to-build.R deps (RPostgres, s3fs, data.table, future) in install-deps step	2026-04-10 00:07:54 +02:00
pat-s	f3d71a1112	fix: wipe entire R-pkgs cache to rebuild from scratch after corruption from failed installs	2026-04-10 00:01:16 +02:00
pat-s	d5f7ecc0b4	fix: skip dependency upgrades in install-deps step to avoid memory issues	2026-04-09 23:56:46 +02:00
pat-s	272275e868	refactor: move bincraft install to separate pre-matrix pipeline step ... 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.	2026-04-09 23:55:30 +02:00
pat-s	75893a8eda	build rhel10	2026-01-05 17:32:13 +01:00
pat-s	b153d70b92	build alpine 3.23	2025-12-07 00:07:39 +01:00
pat-s	510bff292a	ci: GIT_RO_TOKEN -> REPO_RO_TOKEN	2025-10-17 14:45:07 +02:00
pat-s	bbddf0c12c	refactor: switch to reg.devxy.io	2025-08-31 20:56:59 +02:00
pat-s	5dbfe1127b	reprocess packages without history	2025-07-03 22:45:19 +02:00
pat-s	15eaa91bf7	remove install-deps step for arm64 builds	2025-06-26 23:34:24 +02:00
pat-s	6c499afe1c	fix: use separate yamls for arm and amd	2025-06-18 12:52:41 +02:00
pat-s	1e5042548c	wipe pkgcache dir	2025-06-18 11:25:56 +02:00
pat-s	6b1ae4e555	chore: cleanup workflows	2025-06-17 21:03:49 +02:00
pat-s	cdd823da82	ci: new generic build-all workflow	2025-06-17 09:58:44 +02:00