pat-s
d558e27c11
## 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- Pins bincraft `v4.1.1` → `v4.2.0` across all workflows; removes the superseded standalone `build-r-minor-sensitive-packages.yaml`.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
105 lines
6.2 KiB
YAML
105 lines
6.2 KiB
YAML
when:
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- event: [cron]
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cron: process-cran-updates-alpine-322-amd64
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- event: manual
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evaluate: 'process_cran_updates == "all"'
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- event: manual
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evaluate: 'process_cran_updates == "alpine-322-amd64"'
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skip_clone: true
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labels:
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agent: artemis
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steps:
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- name: 'Processing Updates'
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image: reg.devxy.io/rpkgs/build-env-alpine:3.24
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pull: true
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environment:
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RED_HAT_DEV_PW:
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from_secret: RED_HAT_DEV_PW
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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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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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# normal env vars
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GIT_USER: pat-s
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NTFY_SERVER:
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from_secret: NTFY_SERVER
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NTFY_TOPIC:
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from_secret: NTFY_TOPIC
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NTFY_AUTH: TRUE
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NTFY_PASSWORD:
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from_secret: ntfy_token
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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: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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R_VERSION: 4.5.3
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CCACHE_DIR: /mnt/cache/ccache
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PLATFORM: alpine-322
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ARCH: amd64
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NCPUS: 2
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STRATEGY: sequential
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INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3)
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# volumes:
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# - amd64-binaries-r-dep-cache-alpine-322:/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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- rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/R-pkgs/pkgcache /mnt/cache/pkgcache/R/pkgcache
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- /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.2.0") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.2.0")'
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- /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# 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
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- xvfb-run /opt/R/$R_VERSION/bin/R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'alpine-322', process_updated = TRUE, process_new = FALSE, process_removed = TRUE, r_minor_detection = 'classifier', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)"
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- |
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PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2)
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for RBIN in /opt/R/*/bin/R; do
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RV=$(basename "$(dirname "$(dirname "$RBIN")")")
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RMINOR=$(echo "$RV" | cut -d. -f1-2)
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[ "$RMINOR" = "$PRIMARY_MINOR" ] && continue
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echo "=== R-minor-sensitive update pass under R $RV ==="
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xvfb-run "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = 'alpine-322', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true
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done
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- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "alpine322", 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"))'
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- |
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for RBIN in /opt/R/*/bin/R; do
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RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
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"$(dirname "$RBIN")/R" -q -e "library(bincraft); upload_package_index(codename = 'alpine322', r_minor = '$RMINOR', 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'))" || true
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done
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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: 5Gi
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cpu: 3000m
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limits:
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memory: 18Gi
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cpu: 3000m
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nodeSelector:
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kubernetes.io/arch: amd64
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node.kubernetes.io/instance-type: AX42
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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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- name: Purge CDN cache
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image: reg.devxy.io/docker.io/library/alpine:3.24
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environment:
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BUNNYNET_API_KEY:
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from_secret: BUNNYNET_API_KEY
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SUBDOMAIN1: 'cran.devxy.io'
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SUBDOMAIN2: 'cran.allianceswisspass.devxy.io'
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SUBDOMAIN3: 'cran.rpkgs.com'
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OS_ID: alpine322
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ARCH: amd64
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commands:
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- apk add --no-cache -q bash curl
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- bash scripts/purge_cdn_cache.sh "$BUNNYNET_API_KEY" "$ARCH" "$OS_ID" "$SUBDOMAIN1" "$SUBDOMAIN2" "$SUBDOMAIN3"
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