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build-cran-binaries/.crow/weekly-rebuild-missing.yaml
pat-s 930a4acd12
 fix(ci): install the R packages pipelines use instead of relying on the image 
bincraft v5.5.1 dropped lubridate, dplyr, purrr, data.table and others from
its imports, so the pipelines' own calls now depend on whatever the build-env
image's site library or the shared R_LIBS_USER cache happens to hold. The arm64
redhat:9 image has no progressr under R 4.4.3, which fails every
process-cran-updates-redhat-9-arm64 run since v5.5.1.

- Install progressr and lubridate for process-updates, which call them inline.
- Install purrr for packages-to-build.R and data.table for the weekly audit.
- Drop the unused dplyr and progressr library() calls from packages-to-build.R.
- Install RPostgres in every pipeline that talks to the metadata DB, since
  bincraft silently skips the DB (and the per-minor index aborts) without it.
- Reinstall bincraft in the prune re-index step, whose /tmp library does not
  survive from the prune step.
2026-10-20 08:46:00 +00:00

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# Consolidated weekly-rebuild-missing pipeline (all platforms, both arches).
# Three matrix rows per OS/arch, one per shard of that slot's rebuild list.
# Routing is preserved 1:1:
# - cron: each existing `weekly-rebuild-missing-<os>-<arch>` cron fires only
# its matching matrix rows (via the per-row `cron:` name filter),
# which is now all three shards of that slot.
# - manual: pick a target from the `weekly_rebuild_missing` dropdown;
# "all" fans out every os/arch and shard as parallel matrix
# workflows, while a single <os>-<arch> runs its three shards.
# Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64).
#
# The shard picks up its own slice and re-derives what is still outstanding
# from the bucket, so a restart resumes rather than replaying; see
# local/rebuild-missing.R.
#
# Re-indexing and the CDN purge deliberately do NOT live here. Three shards
# writing one slot's PACKAGES concurrently would race, so they moved to
# .crow/weekly-rebuild-reindex.yaml, which depends on this pipeline.
variables:
# Gates this pipeline. A manual pipeline creation instantiates every file in
# .crow/, and a declared default is applied even when the run never passed
# this variable, so the default must be a value that matches no matrix row.
weekly_rebuild_missing:
description: "Manual run target: a specific <os>-<arch>, 'all' to run every os/arch in parallel, or 'none' to run nothing."
options:
- none
- all
- 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: none
when:
- event: cron
cron: weekly-rebuild-missing-${OS}-${ARCH}
- event: manual
evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"'
skip_clone: true
labels:
group: rpkgs-${ARCH}
matrix:
include:
- OS: alpine-323
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.23
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: alpine-323
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.23
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: alpine-323
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.23
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: alpine-323
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.23
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: alpine-323
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.23
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: alpine-323
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.23
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:8
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:8
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:8
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: redhat-8
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:8
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: redhat-8
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:8
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: redhat-8
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:8
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: redhat-9
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:9
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: redhat-9
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:9
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: redhat-9
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:9
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: redhat-9
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:9
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: redhat-9
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:9
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: redhat-9
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:9
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: redhat-10
ARCH: amd64
R_VERSION: 4.5.3
IMG: redhat:10
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: redhat-10
ARCH: amd64
R_VERSION: 4.5.3
IMG: redhat:10
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: redhat-10
ARCH: amd64
R_VERSION: 4.5.3
IMG: redhat:10
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: redhat-10
ARCH: arm64
R_VERSION: 4.5.3
IMG: redhat:10
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: redhat-10
ARCH: arm64
R_VERSION: 4.5.3
IMG: redhat:10
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: redhat-10
ARCH: arm64
R_VERSION: 4.5.3
IMG: redhat:10
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: ubuntu-2204
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: ubuntu-2204
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: ubuntu-2204
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: ubuntu-2204
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: ubuntu-2204
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: ubuntu-2204
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: ubuntu-2404
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:noble
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: ubuntu-2404
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:noble
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: ubuntu-2404
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:noble
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: ubuntu-2404
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:noble
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: ubuntu-2404
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:noble
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: ubuntu-2404
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:noble
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
SPLIT_INTO: 3
SPLIT_INDEX: 3
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
SPLIT_INTO: 3
SPLIT_INDEX: 1
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
SPLIT_INTO: 3
SPLIT_INDEX: 2
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
SPLIT_INTO: 3
SPLIT_INDEX: 3
steps:
- name: 'Rebuild missing binaries'
image: reg.devxy.io/rpkgs/build-env-${IMG}
pull: true
environment:
OTEL_R_TRACES_EXPORTER: none
OTEL_R_LOGS_EXPORTER: none
OTEL_R_METRICS_EXPORTER: none
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
FORGEJO_TOKEN:
from_secret: FORGEJO_TOKEN
GIT_USER: pat-s
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
PLATFORM: ${OS}
ARCH: ${ARCH}
NCPUS: 2
SPLIT_INTO: ${SPLIT_INTO}
SPLIT_INDEX: ${SPLIT_INDEX}
# Wall clock after which the shard stops cleanly instead of having to be
# killed. A kill matches neither `success` nor `failure`, so it would skip
# the dependent re-index and leave rebuilt binaries behind a stale edge.
REBUILD_BUDGET_HOURS: 20
commands:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- 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=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS="-a"; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres httr2
- /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")'
- $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1
backend_options:
docker:
resources:
requests:
memory: 5Gi
cpu: 3000m
limits:
memory: 18Gi
cpu: 3000m
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