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build-cran-binaries/.crow/process-updates.yaml
pat-s 1fd8d811e7
 ci(patches): wire patches into all build workflows; pin bincraft v4.3.1 
Pass patches = 'local/patches' to the daily process_cran_updates() calls
(requires bincraft v4.3.1) and the weekly-rebuild build_binary_package() call,
so every CI build path applies the patch registry like build-all/build-one
already do.
Bump the bincraft pin v4.3.0 -> v4.3.1 across all .crow workflows.
2026-06-30 10:46:18 +02:00

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# Consolidated process-updates pipeline (all platforms, both arches).
# One matrix row per OS/arch replaces the former per-platform files.
# Routing is preserved 1:1:
# - cron: each existing `process-cran-updates-<os>-<arch>` cron fires only
# its matching matrix row (via the per-row `cron:` name filter).
# - manual: pick a target from the `process_cran_updates` dropdown
# ("all" = every os/arch).
# Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64).
variables:
process_cran_updates:
description: "Manual run target: a specific <os>-<arch>, or 'all' for every os/arch."
options:
- all
- alpine-322-amd64
- alpine-322-arm64
- alpine-323-amd64
- alpine-323-arm64
- alpine-324-amd64
- alpine-324-arm64
- redhat-8-amd64
- redhat-8-arm64
- redhat-9-amd64
- redhat-9-arm64
- redhat-10-amd64
- redhat-10-arm64
- ubuntu-2204-amd64
- ubuntu-2204-arm64
- ubuntu-2404-amd64
- ubuntu-2404-arm64
- ubuntu-2604-amd64
- ubuntu-2604-arm64
default: all
when:
- event: cron
cron: process-cran-updates-${OS}-${ARCH}
- event: manual
evaluate: 'process_cran_updates == "all" || process_cran_updates == "${OS}-${ARCH}"'
skip_clone: true
labels:
group: rpkgs-${ARCH}
matrix:
include:
- OS: alpine-322
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine322
PROCESS_NEW: "FALSE"
- OS: alpine-322
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine322
PROCESS_NEW: "FALSE"
- OS: alpine-323
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine323
PROCESS_NEW: "FALSE"
- OS: alpine-323
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine323
PROCESS_NEW: "FALSE"
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine324
PROCESS_NEW: "FALSE"
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
OS_ID: alpine324
PROCESS_NEW: "FALSE"
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:8
OS_ID: rhel8
PROCESS_NEW: "TRUE"
- OS: redhat-8
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:8
OS_ID: rhel8
PROCESS_NEW: "TRUE"
- OS: redhat-9
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:9
OS_ID: rhel9
PROCESS_NEW: "TRUE"
- OS: redhat-9
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:9
OS_ID: rhel9
PROCESS_NEW: "TRUE"
- OS: redhat-10
ARCH: amd64
R_VERSION: 4.5.3
IMG: redhat:10
OS_ID: rhel10
PROCESS_NEW: "TRUE"
- OS: redhat-10
ARCH: arm64
R_VERSION: 4.5.3
IMG: redhat:10
OS_ID: rhel10
PROCESS_NEW: "TRUE"
- OS: ubuntu-2204
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
OS_ID: jammy
PROCESS_NEW: "TRUE"
- OS: ubuntu-2204
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
OS_ID: jammy
PROCESS_NEW: "TRUE"
- OS: ubuntu-2404
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:noble
OS_ID: noble
PROCESS_NEW: "TRUE"
- OS: ubuntu-2404
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:noble
OS_ID: noble
PROCESS_NEW: "TRUE"
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.5.3
IMG: ubuntu:resolute
OS_ID: resolute
PROCESS_NEW: "TRUE"
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.5.3
IMG: ubuntu:resolute
OS_ID: resolute
PROCESS_NEW: "TRUE"
steps:
- name: 'Processing Updates'
image: reg.devxy.io/rpkgs/build-env-${IMG}
pull: true
environment:
RED_HAT_DEV_PW:
from_secret: RED_HAT_DEV_PW
B2_S3_ACCESS_KEY:
from_secret: B2_S3_ACCESS_KEY
B2_S3_SECRET_KEY:
from_secret: B2_S3_SECRET_KEY
PGPASS:
from_secret: PGPASS
REPO_RO_TOKEN:
from_secret: REPO_RO_TOKEN
GITHUB_PAT:
from_secret: GITHUB_PAT
# normal env vars
GIT_USER: pat-s
NTFY_SERVER:
from_secret: NTFY_SERVER
NTFY_TOPIC:
from_secret: NTFY_TOPIC
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
R_LIBS_USER: /mnt/cache/R-pkgs
R_VERSION: ${R_VERSION}
CCACHE_DIR: /mnt/cache/ccache
PLATFORM: ${OS}
OS_ID: ${OS_ID}
ARCH: ${ARCH}
NCPUS: 2
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
- /opt/R/$R_VERSION/bin/R -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")'
- /opt/R/$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
- $XVFB $XVFB_ARGS -- /opt/R/$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 = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = ${PROCESS_NEW}, process_removed = TRUE, patches = 'local/patches', r_minor_detection = 'classifier',s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)"
- |
PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2)
for RBIN in /opt/R/[0-9]*/bin/R; do
RV=$(basename "$(dirname "$(dirname "$RBIN")")")
RMINOR=$(echo "$RV" | cut -d. -f1-2)
[ "$RMINOR" = "$PRIMARY_MINOR" ] && continue
echo "=== R-minor-sensitive update pass under R $RV ==="
LIB="/mnt/cache/R-pkgs-$RMINOR"
mkdir -p "$LIB"
R_LIBS_USER="$LIB" "$(dirname "$RBIN")/R" -q -e 'if (!requireNamespace("bincraft", quietly = TRUE) || packageVersion("bincraft") != "4.3.1") pak::pak("git::https://codefloe.com/rpkgs/bincraft.git@v4.3.1")' || true
R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -- "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, patches = 'local/patches', 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
done
- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "${OS_ID}", 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"))'
- |
for RBIN in /opt/R/[0-9]*/bin/R; do
RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
/opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(codename = '${OS_ID}', 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
done
backend_options:
docker:
resources:
requests:
memory: 5Gi
cpu: 3000m
limits:
memory: 18Gi
cpu: 3000m
- name: Purge CDN cache
image: reg.devxy.io/docker.io/library/alpine:3.24
environment:
BUNNYNET_API_KEY:
from_secret: BUNNYNET_API_KEY
SUBDOMAIN1: 'cran.devxy.io'
SUBDOMAIN2: 'cran.allianceswisspass.devxy.io'
SUBDOMAIN3: 'cran.rpkgs.com'
OS_ID: ${OS_ID}
ARCH: ${ARCH}
commands:
- apk add --no-cache -q bash curl
- bash scripts/purge_cdn_cache.sh "$BUNNYNET_API_KEY" "$ARCH" "$OS_ID" "$SUBDOMAIN1" "$SUBDOMAIN2" "$SUBDOMAIN3"
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