Author	SHA1	Message	Date
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	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	b46472b59e	fix(ci): pass Backblaze B2 credentials to process_unarchived_pkgs ... The function defaults to Hetzner S3 with HETZNER_S3_*_K3S env vars that are not set in these workflows, so paws failed with "No compatible credentials provided". Pass the B2 endpoint/region/bucket and B2_S3_* secrets explicitly, matching the other S3 calls. Also use set_codename(NULL) for the build-all-versions codename so it matches the S3 repo path.	2026-06-21 10:55:22 +02:00
pat-s	f9bc72d5ab	chore: bump bincraft to 4.2.3	2026-06-18 09:43:05 +02:00
pat-s	1cd86b65e1	feat(build): skip already-built package versions on workflow restart (#91) ... ## Summary When a `build-all-*` workflow is restarted, the build job re-reads the static `pkgs_to_build.rds` that the install-deps step produced once, so it cycles over every package an interrupted run already built. This adds a DB-based skip filter so a restart only processes what is genuinely left. - At job start, `build-all.R` queries the `single_builds` metadata table for `(name, tag)` already built successfully (`error_occurred = FALSE`) on this `platform`/`arch`, and drops those pairs from the chunk before the build loop. It logs how many it skipped. - One indexed query, one round trip, run before the pak forks — no extra S3 listing and no new Python/s3fs memory pressure (`RPostgres`/`DBI` are already used in the container). - Errored versions are intentionally **not** skipped, so transient failures still get retried on restart. ## Dependency Correctness depends on a `error_occurred = FALSE` row meaning the binary is actually published. That guarantee is added in rpkgs/bincraft#56 (success row written only after a confirmed S3 upload). This PR should land together with / after a bincraft release including that fix. Reviewed-on: #91	2026-06-16 07:27:20 +00:00
pat-s	f51617018d	ci: bump bincraft to 4.2.1 and scope multi-R loops to versioned R dirs ... - Pin bincraft v4.2.0 -> v4.2.1 (per-minor archive.rds/index fix) across the process-updates, weekly-rebuild and archive workflows. - Restrict the per-R-minor build and index loops to /opt/R/[0-9]* so the `current` symlink dir is not treated as a distinct minor (avoids double- building a minor and writing a bogus contrib/current/ index slot).	2026-06-14 13:02:47 +02:00
pat-s	d558e27c11	feat: R-minor-sensitive binary builds (full + iterative) (#84) ... ## Summary Builds R-minor-sensitive CRAN packages once per installed R minor version (into per-minor S3 slots `…/contrib/<x.y>/`) and everything else once into the generic slot, driven by bincraft 4.2.0's ABI classifier. Both the full and iterative pipelines are covered. ## What's in here **Detection / precompute** - `local/r-minor-helpers.R` — pure `classify_from_metadata()` (NeedsCompilation / risky `LinkingTo`) + `parse_build_args()`, with unit tests. - `local/packages-to-build.R` — adds a per-package `r_minor_sensitive` flag: cheap CRAN-metadata rules first, source download + `bincraft::needs_per_minor_recompile()` only for the ambiguous compiled subset (fail-safe to sensitive). Classified once per package, applied to all versions. **Full build** - `local/build-all.R` — passes the per-row `is_r_minor_sensitive` flag; new `--sensitive-only` mode builds just the risky subset. - `.crow/build-all-versions-{amd64,arm64}.yaml` — install-deps persists the sensitive subset; build step runs a sensitive-only pass under each non-primary `/opt/R/*` minor; new step uploads the generic index plus a per-minor index for each minor. **Iterative build** - All 14 `.crow/process-updates-*.yaml` — primary pass uses `r_minor_detection = 'classifier'`; a sensitive-only multi-R pass builds risky updates under each other minor; per-minor index upload added. **Tooling / housekeeping** - Pins bincraft `v4.1.1` → `v4.2.0` across all workflows; removes the superseded standalone `build-r-minor-sensitive-packages.yaml`. - Adds prek/pre-commit hooks (prettier, markdownlint, editorconfig-checker, yamllint, air) and applies them repo-wide; excludes the verbatim GPL `LICENSE.md` and auxiliary shell scripts. - Design + implementation docs under `docs/superpowers/`. ## Requires before merge - A `v4.2.0` git tag must be pushed on the bincraft repo (codefloe.com/rpkgs/bincraft) — the workflow install steps pin `@v4.2.0`. The full-build install-deps clones `main`, so it is unaffected. Reviewed-on: #84	2026-06-14 08:04:40 +00:00
automation-bot	f28ccaf008	chore(deps): update reg.devxy.io/rpkgs/build-env-alpine docker tag to v3.24	2026-06-14 00:33:22 +00:00
automation-bot	d018f31376	chore(deps): update dependency bincraft to v4.2.0	2026-06-14 00:32:46 +00:00
pat-s	4425904eeb	feat(ci): archive missed packages for redhat-10 and alpine323 (#75) ... ## Summary `archive-missed-packages.yaml`'s matrix was last touched when redhat-9 and alpine322 were the newest targets. redhat-10 and alpine323 builds are now wired up across `process-updates-*` and `weekly-rebuild-missing-*` workflows, but the daily archive sweep wasn't catching them — so missed-archive packages on those platforms accumulate untouched. Adds the 4 missing entries: - `redhat-10` × `{amd64, arm64}` - `alpine323` × `{amd64, arm64}` Reviewed-on: #75	2026-06-08 08:30:38 +00:00
pat-s	2ba6ab28f7	chore: bump to bincraft 4.1.1	2026-05-31 09:30:02 +02:00
pat-s	b1bed68898	refactor(ci): skip bincraft reinstall when image already has it (#72) ... ## Summary bincraft is baked into the build-env images, but every workflow still unconditionally calls `pak::pak("git::.../bincraft.git")` (~30–60s per job). Pin bincraft to a specific tag (currently `v4.0.2`) and guard the install on a version check. ``` - /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.0.2") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.0.2")' ``` - Image matches the pin → skip install entirely. - Image is missing bincraft or has a different version → install the pinned tag (covers both broken bakes and intentional version bumps). - Renovate customManager keeps the pin and the version-check string in sync whenever bincraft cuts a new tag (uses `git-tags` datasource against the bincraft repo). Touches 43 `.crow` YAMLs + `renovate.json`. Reviewed-on: #72	2026-05-28 12:37:58 +00:00
pat-s	8c5362b7ab	refactor: R_VERSION syntax	2026-05-27 22:36:09 +02:00
pat-s	6faa3772d1	refactor(ci): use multi-R-version images across workflows (#70) ... ## Summary - Switches all 64 `.crow/*.yaml` workflows, the `Justfile`, and the commented-out `build-all-versions-install-deps.yaml` template to the new multi-R-version container images. - Each image tag drops `-${R_VERSION}` (e.g. `build-env-alpine:3.22-4.5` → `build-env-alpine:3.22`); workflows pick an R version by calling `/opt/R/${R_VERSION}/bin/R` explicitly. - Pattern-1 workflows (hard-coded image tag) gain a single `R_VERSION:` env var per file. - Pattern-2 workflows (`build-all-versions-*`, matrix-driven) continue to receive `R_VERSION` via `crow pipeline create --var`. ## Platform → R_VERSION mapping | Platform | Image | R_VERSION | | --- | --- | --- | | alpine 3.22 / 3.23 | `build-env-alpine:3.{22,23}` | 4.5.3 | | ubuntu jammy / noble | `build-env-ubuntu:{jammy,noble}` | 4.4.3 | | redhat 8 / 9 | `build-env-redhat:{8,9}` | 4.4.3 | | redhat 10 | `build-env-redhat:10` | 4.5.3 | The `alpine-321` audit-only workflows fall back to `build-env-alpine:3.23` since no 3.21 image exists in the new scheme; the audits only query S3/CRAN, so the container OS does not affect correctness. ## Bug fixes folded in 1. All six `weekly-audit-missing-alpine-*.yaml` files were pinned to `alpine:3.23-4.5` regardless of platform. Now each one points at its own alpine image. 2. All fourteen `update-package-index-*.yaml` files were pinned to `build-env-ubuntu:noble-4.4` (or `noble-4.5` for `redhat-10-amd64`) regardless of platform. Now each one uses its own platform's image. 3. `process-updates-ubuntu-2404-{amd64,arm64}.yaml` had `R_VERSION` of `4.4` (no patch) baked into the tag. Aligned to `4.4.3`, matching the audit and rebuild counterparts. ## Smoke targets (post-merge) One workflow per shape, ready to dry-run: - `process-updates-alpine-322-amd64.yaml` - `weekly-rebuild-missing-redhat-9-amd64.yaml` - `weekly-audit-missing-ubuntu-2204-amd64.yaml` - `update-package-index-redhat-10-amd64.yaml` - `archive-missed-packages.yaml` - `build-all-versions-amd64.yaml` (with its install-deps predecessor) - `build-r-minor-sensitive-packages.yaml` ## Follow-ups (out of scope, surfaced during review) - `process-updates-redhat-10-{amd64,arm64}.yaml` set `codename = "rhel9"` in their `upload_package_index(...)` calls. Pre-existing bug — should be `"rhel10"`. The `update-package-index-redhat-10-*` counterparts already use `"rhel10"` correctly. - `update-package-index-redhat-8-amd64.yaml` is missing the `packageVersion("bincraft")` diagnostic line that every sibling file has. Pre-existing asymmetry between amd64 and arm64. ## Spec & plan - Spec: `docs/superpowers/specs/2026-05-25-multi-r-version-images-design.md` - Plan: `docs/superpowers/plans/2026-05-25-multi-r-version-images.md` Reviewed-on: #70	2026-05-26 08:51:27 +00:00
pat-s	e959d9743f	refactor: migrate to backblaze	2026-03-22 00:32:03 +01:00
automation-bot	a3b3d37fe3	chore(deps): update reg.devxy.io/rpkgs/build-env-alpine docker tag	2026-03-20 00:03:02 +00:00
pat-s	1def662598	refactor: update build-env image names	2025-12-13 10:53:39 +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	80fb794cd6	archive refinement	2025-06-28 22:29:00 +02:00
pat-s	c8ff16cbac	add archived-missed-pkgs workflow	2025-06-28 22:03:05 +02:00