pat-s
ee15c50f53
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`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
63 lines
2.4 KiB
YAML
63 lines
2.4 KiB
YAML
# ### Required extra vars
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# # ARCH (amd64)
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# # OS (alpine)
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# # OS_VERSION (3.22)
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# # R_VERSION (4.5)
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# # when:
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# # - event: manual
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# # evaluate: 'task == "build-all-arm64"'
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# # - event: manual
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# # evaluate: 'task == "build-all-amd64"'
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# skip_clone: true
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# labels:
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# platform: linux/amd64
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# backend: kubernetes
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# steps:
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# - name: 'Install common R deps'
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# image: "reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}"
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# pull: true
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# environment:
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# REPO_RO_TOKEN:
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# from_secret: REPO_RO_TOKEN
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# GITHUB_PAT:
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# from_secret: GITHUB_PAT
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# HETZNER_S3_ACCESS_KEY_K3S:
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# from_secret: HETZNER_S3_ACCESS_KEY_K3S
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# HETZNER_S3_SECRET_KEY_K3S:
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# from_secret: HETZNER_S3_SECRET_KEY_K3S
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# # normal env vars
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# GIT_USER: pat-s
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# # set the location of uvr's caches, which persist the R package dependencies needed to install the packages themselves
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# # UVR_CACHE_DIR: /mnt/cache/uvr/cache
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# # UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
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# R_LIBS_USER: /mnt/cache/R-pkgs
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# CCACHE_DIR: /mnt/cache/ccache
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# volumes:
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# - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
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# commands:
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# - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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# - mkdir -p /mnt/cache/R-pkgs
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# - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/uvr
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# - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh forgejo::codefloe.com/rpkgs/bincraft
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# - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
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# # - /opt/R/$R_VERSION/bin/R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine322', 'amd64'); saveRDS(pkgs, '/mnt/cache/pkgs_amd64.rds')"
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# - /opt/R/$R_VERSION/bin/R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine323', 'arm64'); saveRDS(pkgs, '/mnt/cache/pkgs_arm64.rds')"
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# backend_options:
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# kubernetes:
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# resources:
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# requests:
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# memory: 1000Mi
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# cpu: 1000m
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# limits:
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# memory: 4500Mi
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# cpu: 8000m
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# nodeSelector:
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# kubernetes.io/arch: ${ARCH}
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# tolerations:
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# - key: 'CI'
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# operator: 'Equal'
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# value: 'true'
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# effect: 'NoSchedule'
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