pat-s
55a18fd87d
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## 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
85 lines
2.8 KiB
YAML
85 lines
2.8 KiB
YAML
# Consolidated install-deps for build-all (both arches in one file).
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# Triggered together with build-all-versions; `target_arch` routes the matrix.
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# Variables are declared so the manual-run form exposes them (crow #1165);
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# they are merged with build-all-versions' identical declarations.
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variables:
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target_arch:
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description: "Architecture to build."
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options:
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- amd64
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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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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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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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R_VERSION:
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description: "Primary R version under /opt/R."
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options:
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- 4.5.3
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- 4.4.3
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default: 4.5.3
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when:
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- event: manual
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evaluate: 'target_arch == "${ARCH}"'
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skip_clone: true
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labels:
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platform: linux/${ARCH}
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group: rpkgs-${ARCH}
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matrix:
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include:
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- ARCH: amd64
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- ARCH: arm64
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steps:
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- name: 'Install deps and bincraft'
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image: 'reg.devxy.io/rpkgs/build-env-${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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B2_S3_ACCESS_KEY:
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from_secret: B2_S3_ACCESS_KEY
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B2_S3_SECRET_KEY:
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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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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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- mkdir -p /mnt/cache/pkgcache /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/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")'
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- /opt/R/$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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resources:
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requests:
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memory: 5Gi
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cpu: 1000m
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