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	736564a4ff	fix: prevent renovate bumps for fixed matrix assignments	2026-07-24 11:18:28 +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
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	2ad22cfc6a	chore: renovate ignore docker/	2025-02-10 09:27:11 +01:00
automation-bot	f5ba3229a9	chore: Configure Renovate (#6) ... Welcome to [Renovate](https://github.com/renovatebot/renovate)! This is an onboarding PR to help you understand and configure settings before regular Pull Requests begin. 🚦 To activate Renovate, merge this Pull Request. To disable Renovate, simply close this Pull Request unmerged. --- ### Detected Package Files * `docker/Dockerfile-ubi9` (dockerfile) * `docker/Dockerfile.rhel8` (dockerfile) * `.woodpecker/build.yaml` (woodpecker) * `.woodpecker/images.yaml` (woodpecker) ### Configuration Summary Based on the default config's presets, Renovate will: - Start dependency updates only once this onboarding PR is merged - Enable Renovate Dependency Dashboard creation. - Use semantic commit type `fix` for dependencies and `chore` for all others if semantic commits are in use. - Ignore `node_modules`, `bower_components`, `vendor` and various test/tests directories. - Group known monorepo packages together. - Use curated list of recommended non-monorepo package groupings. - Apply crowd-sourced package replacement rules. - Apply crowd-sourced workarounds for known problems with packages. - Run lock file maintenance (updates) early Monday mornings. - Schedule automerge daily. - Schedule for weekends. - Enable Renovate Dependency Dashboard creation. - Use semantic commit type `fix` for dependencies and `chore` for all others if semantic commits are in use. - Ignore `node_modules`, `bower_components`, `vendor` and various test/tests directories. - Group known monorepo packages together. - Use curated list of recommended non-monorepo package groupings. - Apply crowd-sourced package replacement rules. - Apply crowd-sourced workarounds for known problems with packages. - Run lock file maintenance (updates) early Monday mornings. - Schedule automerge daily. - Schedule for weekends. - Run Renovate on following schedule: every weekend 🔡 Do you want to change how Renovate upgrades your dependencies? Add your custom config to `renovate.json` in this branch. Renovate will update the Pull Request description the next time it runs. --- ### What to Expect It looks like your repository dependencies are already up-to-date and no Pull Requests will be necessary right away. --- ❓ Got questions? Check out Renovate's [Docs](https://docs.renovatebot.com/), particularly the Getting Started section. If you need any further assistance then you can also [request help here](https://github.com/renovatebot/renovate/discussions). --- This PR has been generated by [Renovate Bot](https://github.com/renovatebot/renovate). <!--renovate-config-hash:5194d01a36db041d33badf95c91bbd2577f7875d668ecaa620d459efdda0b7ef--> Reviewed-on: devxy/arm64-r-binaries#6 Co-authored-by: automation-bot <no-reply@devxy.io> Co-committed-by: automation-bot <no-reply@devxy.io>	2024-07-29 21:21:39 +00:00