refactor: migrate package installation from pak to uvr (#147)
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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
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7 changed files with 326 additions and 245 deletions
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@ -45,7 +45,7 @@ steps:
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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-*
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- /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))'
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- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
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- /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-pr --limit $PATCH_LIMIT
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backend_options:
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kubernetes:
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@ -10,22 +10,22 @@ variables:
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- arm64
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default: amd64
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OS:
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description: "Base OS image name."
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description: 'Base OS image name.'
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options:
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- alpine
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- redhat
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- ubuntu
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default: alpine
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OS_VERSION:
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description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
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description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
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options:
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- "3.24"
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- "8"
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- "9"
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- "10"
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- "jammy"
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- "noble"
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default: "3.24"
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- '3.24'
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- '8'
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- '9'
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- '10'
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- 'jammy'
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- 'noble'
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default: '3.24'
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R_VERSION:
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description: 'Primary R version under /opt/R.'
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options:
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@ -66,23 +66,24 @@ steps:
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from_secret: B2_S3_SECRET_KEY
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PGPASS:
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from_secret: PGPASS
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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# Keep uvr's downloads and extracted-package entries on the persistent
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# volume instead of the container-local ~/.uvr default.
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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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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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# one-time full wipe to fix corrupted .so files from previous failed builds
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# - rm -rf /mnt/cache/R-pkgs
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# Clear churny pkgcache metadata left by a prior crashed run (the "patched"
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# repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
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# Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs.
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- rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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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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# Pin the same bincraft version the build steps use, so the precomputed
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# snapshot and the per-agent library stay consistent across the pipeline.
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- /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); source("local/install-bincraft.R"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
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- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
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- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite
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- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
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- /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))"
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backend_options:
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docker:
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@ -11,25 +11,25 @@ variables:
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- arm64
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default: amd64
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OS:
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description: "Base OS image name."
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description: 'Base OS image name.'
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options:
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- alpine
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- redhat
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- ubuntu
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default: alpine
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OS_VERSION:
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description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)."
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description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).'
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options:
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- "3.22"
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- "3.23"
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- "3.24"
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- "8"
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- "9"
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- "10"
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- "jammy"
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- "noble"
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- "resolute"
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default: "3.24"
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- '3.22'
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- '3.23'
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- '3.24'
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- '8'
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- '9'
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- '10'
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- 'jammy'
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- 'noble'
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- 'resolute'
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default: '3.24'
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R_VERSION:
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description: 'Primary R version under /opt/R.'
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options:
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@ -47,38 +47,49 @@ labels:
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platform: linux/${ARCH}
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group: rpkgs-${ARCH}
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# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local
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# ~/.uvr defaults; amd64 deliberately does not persist them (as with the
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# pkgcache dir it replaces), arm64 does.
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matrix:
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include:
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- ARCH: amd64
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R_PKG_CACHE_DIR: ''
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 1
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- ARCH: amd64
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R_PKG_CACHE_DIR: ''
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 2
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- ARCH: amd64
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R_PKG_CACHE_DIR: ''
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 3
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- ARCH: amd64
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R_PKG_CACHE_DIR: ''
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UVR_CACHE_DIR: ''
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UVR_PACKAGES_DIR: ''
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SPLIT_INTO: 4
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SPLIT_INDEX: 4
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- ARCH: arm64
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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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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SPLIT_INTO: 4
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SPLIT_INDEX: 1
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- ARCH: arm64
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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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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SPLIT_INTO: 4
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SPLIT_INDEX: 2
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- ARCH: arm64
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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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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SPLIT_INTO: 4
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SPLIT_INDEX: 3
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- ARCH: arm64
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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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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SPLIT_INTO: 4
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SPLIT_INDEX: 4
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from_secret: GITHUB_PAT
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# normal env vars
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: ${R_PKG_CACHE_DIR}
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# set the location of uvr's caches, which persist the R package
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# dependencies needed to install the packages themselves
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UVR_CACHE_DIR: ${UVR_CACHE_DIR}
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UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR}
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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NCPUS: 2
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@ -116,12 +129,7 @@ steps:
|
|||
- ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache
|
||||
commands:
|
||||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
||||
# Clear churny pkgcache metadata left by a prior crashed run (the "patched"
|
||||
# repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*).
|
||||
# Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs. Within-run
|
||||
# growth is bounded separately by trim_pkgcache_metadata() in build-all.R.
|
||||
- rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# The primary pass must not rely on build-all-versions-install-deps having
|
||||
# run on *this* agent: depends_on only orders the steps, but the cache
|
||||
# volume is per-agent, so a job landing on an agent where install-deps did
|
||||
|
|
|
|||
|
|
@ -49,109 +49,109 @@ matrix:
|
|||
R_VERSION: 4.5.3
|
||||
IMG: alpine:3.22
|
||||
OS_ID: alpine322
|
||||
PROCESS_NEW: "FALSE"
|
||||
PROCESS_NEW: 'FALSE'
|
||||
- OS: alpine-322
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: alpine:3.23
|
||||
OS_ID: alpine322
|
||||
PROCESS_NEW: "FALSE"
|
||||
PROCESS_NEW: 'FALSE'
|
||||
- OS: alpine-323
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: alpine:3.23
|
||||
OS_ID: alpine323
|
||||
PROCESS_NEW: "FALSE"
|
||||
PROCESS_NEW: 'FALSE'
|
||||
- OS: alpine-323
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: alpine:3.23
|
||||
OS_ID: alpine323
|
||||
PROCESS_NEW: "FALSE"
|
||||
PROCESS_NEW: 'FALSE'
|
||||
- OS: alpine-324
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: alpine:3.24
|
||||
OS_ID: alpine324
|
||||
PROCESS_NEW: "FALSE"
|
||||
PROCESS_NEW: 'FALSE'
|
||||
- OS: alpine-324
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: alpine:3.24
|
||||
OS_ID: alpine324
|
||||
PROCESS_NEW: "FALSE"
|
||||
PROCESS_NEW: 'FALSE'
|
||||
- OS: redhat-8
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: redhat:8
|
||||
OS_ID: rhel8
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: redhat-8
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: redhat:8
|
||||
OS_ID: rhel8
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: redhat-9
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: redhat:9
|
||||
OS_ID: rhel9
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: redhat-9
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: redhat:9
|
||||
OS_ID: rhel9
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: redhat-10
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: redhat:10
|
||||
OS_ID: rhel10
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: redhat-10
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: redhat:10
|
||||
OS_ID: rhel10
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: ubuntu-2204
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: ubuntu:jammy
|
||||
OS_ID: jammy
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: ubuntu-2204
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: ubuntu:jammy
|
||||
OS_ID: jammy
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: ubuntu-2404
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: ubuntu:noble
|
||||
OS_ID: noble
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: ubuntu-2404
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.4.3
|
||||
IMG: ubuntu:noble
|
||||
OS_ID: noble
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: ubuntu-2604
|
||||
ARCH: amd64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: ubuntu:resolute
|
||||
OS_ID: resolute
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
- OS: ubuntu-2604
|
||||
ARCH: arm64
|
||||
R_VERSION: 4.5.3
|
||||
IMG: ubuntu:resolute
|
||||
OS_ID: resolute
|
||||
PROCESS_NEW: "TRUE"
|
||||
PROCESS_NEW: 'TRUE'
|
||||
|
||||
steps:
|
||||
- name: 'Processing Updates'
|
||||
|
|
@ -182,8 +182,10 @@ steps:
|
|||
NTFY_AUTH: TRUE
|
||||
NTFY_PASSWORD:
|
||||
from_secret: ntfy_token
|
||||
# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
# set the location of uvr's caches, which persist the R package
|
||||
# dependencies needed to install the packages themselves
|
||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
R_VERSION: ${R_VERSION}
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
|
|
@ -194,10 +196,10 @@ steps:
|
|||
INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3)
|
||||
commands:
|
||||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/R-pkgs/pkgcache /mnt/cache/pkgcache/R/pkgcache
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft
|
||||
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
# rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run
|
||||
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
|
||||
# options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
|
||||
|
|
|
|||
|
|
@ -142,7 +142,8 @@ steps:
|
|||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
||||
- mkdir -p /mnt/cache/packages /mnt/cache/R-pkgs
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("git::https://codefloe.com/rpkgs/bincraft.git", "httr2", "jsonlite"))'
|
||||
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
||||
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")'
|
||||
backend_options:
|
||||
docker:
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ steps:
|
|||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
||||
- mkdir -p /mnt/cache/R-pkgs
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))'
|
||||
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite
|
||||
- /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-issue
|
||||
- /opt/R/$R_VERSION/bin/Rscript local/proposal-tracking.R --open-issue
|
||||
backend_options:
|
||||
|
|
|
|||
|
|
@ -141,7 +141,8 @@ steps:
|
|||
FORGEJO_TOKEN:
|
||||
from_secret: FORGEJO_TOKEN
|
||||
GIT_USER: pat-s
|
||||
R_PKG_CACHE_DIR: /mnt/cache/pkgcache
|
||||
UVR_CACHE_DIR: /mnt/cache/uvr/cache
|
||||
UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
|
||||
R_LIBS_USER: /mnt/cache/R-pkgs
|
||||
R_VERSION: ${R_VERSION}
|
||||
CCACHE_DIR: /mnt/cache/ccache
|
||||
|
|
@ -150,12 +151,12 @@ steps:
|
|||
NCPUS: 2
|
||||
commands:
|
||||
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
|
||||
- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
- mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
|
||||
- rm -rf /mnt/cache/R-pkgs/00LOCK-*
|
||||
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
|
||||
- XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")'
|
||||
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2
|
||||
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
|
||||
- $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1
|
||||
backend_options:
|
||||
|
|
|
|||
Loading…
Reference in a new issue