build-cran-binaries/.crow/backfill-flat-safety.yaml
pat-s c61d951875
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fix(repair-built-stamp): patch the published PACKAGES.rds once bincraft drops cranlike (#236)
Follow-up to https://codefloe.com/rpkgs/bincraft/pulls/228 (bincraft#33), which drops the cranlike and desc forks.

## Why

After that change, `upload_package_index()` no longer keeps a `PACKAGES.db`.
It reuses the records of the slot's published `PACKAGES.rds`, as long as each tarball is still listed with the same ETag.
`local/repair-built-stamp.R` patched `PACKAGES.db`, so it would stop having any effect.

## Changes

- `local/repair-built-stamp.R` now patches `Built` in each slot's `PACKAGES.rds` and then re-emits the index.
  - Only the slot's own rows are patched: the generic slot's rows without a `Path`, or a per-minor slot's rows whose `Path` is its minor.
  - A missing stamp is not counted as broken, since bincraft clears it on purpose for source fallbacks.
  - With a bincraft release that still loads cranlike, the script patches `PACKAGES.db` as before, so merge order does not matter.
  - `bincraft::built_stamp()` was never exported, so the script failed at that line before this change; it now calls `bincraft:::built_stamp()`.
- The `GITHUB_PAT` comments in `reindex`, `weekly-rebuild-reindex` and `backfill-flat-safety` now give the current reason: bincraft reads DESCRIPTIONs from raw.githubusercontent.com.
- The README section on index files describes `upload_package_index()` instead of the forks.

## Testing

Tested against a moto S3 bucket, with bincraft installed from the bincraft#228 branch:

- A slot was indexed, then 3 of its 5 `Built` stamps were set to `R 4.5.0; NA; ...`.
- The dry run reported 5 entries, 3 broken.
- `--apply` rewrote the 3 stamps, and the re-emit logged `Index records: 5 reused, 0 read, 0 unreadable.`
- The published `PACKAGES` then had a valid stamp on all 5 records.
- With the released bincraft, which still loads cranlike, the script chose `PACKAGES.db`.

The stale `PACKAGES.db` objects in the slots can be deleted once a bincraft release with #228 is in use.

Reviewed-on: #236
2026-10-18 11:55:21 +00:00

175 lines
5.1 KiB
YAML

# Record, per flat-slot object, whether it loads under every supported R minor.
#
# `union_index_records()` keeps a carried flat record when that object is
# recorded safe and drops it otherwise. Objects uploaded before that record
# existed have no verdict, so they are dropped: a full re-index removed roughly
# 2000 records per per-minor index (16398 across the 4.4 indexes, 20076 across
# 4.5, 15532 across 4.6), each one resolving to CRAN source for clients the
# routing serves correctly.
#
# This inspects what is already in the bucket and writes the verdict, which is
# what restores that coverage. Decided by symbols rather than heuristics: a
# binary fails at dyn.load() under minor M exactly when it references a symbol M
# does not export, and the volatile set is derived by diffing the R builds in
# the image.
#
# Re-running is cheap; recorded objects are skipped.
#
# crow pipeline create devxy/build-cran-binaries --var flat_safety=all
variables:
# A manual pipeline creation instantiates every file in .crow/, so the default
# must match no matrix row.
flat_safety:
description: "Inspect target: a specific <os>-<arch>, 'all' for every slot, or 'none'."
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
FLAT_SAFETY_LIMIT:
description: 'Inspect at most this many objects per slot (0 = no limit).'
default: '0'
when:
- event: manual
evaluate: 'flat_safety == "all" || flat_safety == "${OS}-${ARCH}"'
skip_clone: true
labels:
group: rpkgs-${ARCH}
matrix:
include:
- OS: alpine-323
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.23
- OS: alpine-323
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.23
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:8
- OS: redhat-8
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:8
- OS: redhat-9
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:9
- OS: redhat-9
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:9
- OS: redhat-10
ARCH: amd64
R_VERSION: 4.5.3
IMG: redhat:10
- OS: redhat-10
ARCH: arm64
R_VERSION: 4.5.3
IMG: redhat:10
- OS: ubuntu-2204
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
- OS: ubuntu-2204
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
- OS: ubuntu-2404
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:noble
- OS: ubuntu-2404
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:noble
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
steps:
- name: 'Inspect flat objects and record safety'
image: reg.devxy.io/rpkgs/build-env-${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
# bincraft reads the DESCRIPTION of every new or replaced tarball from
# the CRAN mirror on raw.githubusercontent.com, and authenticates with
# this token when it is set. A slot whose published index cannot be read
# is re-read in full, ~25k requests, which the anonymous rate limit would
# cut short.
GITHUB_PAT:
from_secret: GITHUB_PAT
GIT_USER: pat-s
R_LIBS_USER: /tmp/R-pkgs
FLAT_SAFETY_ARCH: ${ARCH}
FLAT_SAFETY_LIMIT: ${FLAT_SAFETY_LIMIT}
commands:
- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
- mkdir -p /tmp/R-pkgs
- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
- |
set -eu
LIMIT=""
if [ "$$FLAT_SAFETY_LIMIT" != "0" ]; then
LIMIT="$$FLAT_SAFETY_LIMIT"
fi
# The codename comes from the image's /etc/os-release, exactly as the
# re-index step derives it, so it cannot drift from the matrix.
CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e 'cat(bincraft::set_codename(NULL))')
echo "slot: $$FLAT_SAFETY_ARCH/$$CODENAME"
/opt/R/$R_VERSION/bin/Rscript local/backfill-flat-safety.R \
"$$FLAT_SAFETY_ARCH" "$$CODENAME" $$LIMIT
backend_options:
docker:
resources:
requests:
memory: 4Gi
cpu: 1000m