Author	SHA1	Message	Date
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)