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	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	75893a8eda	build rhel10	2026-01-05 17:32:13 +01:00