build-cran-binaries/.crow/backfill-flat-safety.yaml
pat-s f3984f337d
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fix(ci): authenticate uvr's GitHub resolution in the index workflows (#204)
## Why

The post-backfill re-index (12257) reported failure. Five slots could not write their indexes:

```
WARN Failed to fetch git Remote pat-s/cranlike@s3 (GitHub API error: 403 Forbidden);
     falling back to registry resolution
! Attempt 1/3 to update PACKAGES failed (unused argument (built = built)). Retrying in 5s...
Error: Failed to update PACKAGES after 3 attempts.
       Last error: unused argument (built = built)
```

uvr resolves bincraft's dependencies through the GitHub API, including the `pat-s/cranlike@s3` fork. Unauthenticated, that is rate limited. uvr does not fail on the 403 — it **warns and falls back to the registry copy of cranlike**, which has no `built` parameter, so `update_PACKAGES(built = ...)` dies three retries later.

Affected: alpine323, rhel8, rhel9, rhel10, noble. The remaining 13 slots resolved the fork fine and indexed correctly, which is what makes this insidious: the same pipeline passes or fails on identical input depending on the rate-limit window.

`build-all-versions.yaml` and `rebuild-abi-gap.yaml` already pass `GITHUB_PAT`, which is why they were never affected.

## What changed

Adds the `GITHUB_PAT` secret to `reindex.yaml`, `weekly-rebuild-reindex.yaml` and `backfill-flat-safety.yaml`, with a comment recording why its absence is quiet rather than loud.

`crow lint` passes on all three.

## Context

The re-index itself did what it was meant to. Drops per per-minor index fell from ~1800-2200 to:

```
4.4: avg 129    4.5: avg 172    4.6: avg 145
```

so the per-object safety verdicts recovered roughly 93% of the coverage while still dropping every object that genuinely cannot load. This PR is about the five slots that never got to apply it.

Reviewed-on: #204
2026-09-05 15:59:16 +00:00

186 lines
5.4 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-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: 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-${ARCH}
matrix:
include:
- OS: alpine-322
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.22
- OS: alpine-322
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.22
- OS: alpine-323
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.23
- OS: alpine-323
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.23
- OS: alpine-324
ARCH: amd64
R_VERSION: 4.5.3
IMG: alpine:3.24
- OS: alpine-324
ARCH: arm64
R_VERSION: 4.5.3
IMG: alpine:3.24
- OS: redhat-8
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:8
- OS: redhat-8
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:8
- OS: redhat-9
ARCH: amd64
R_VERSION: 4.4.3
IMG: redhat:9
- OS: redhat-9
ARCH: arm64
R_VERSION: 4.4.3
IMG: redhat:9
- OS: redhat-10
ARCH: amd64
R_VERSION: 4.5.3
IMG: redhat:10
- OS: redhat-10
ARCH: arm64
R_VERSION: 4.5.3
IMG: redhat:10
- OS: ubuntu-2204
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
- OS: ubuntu-2204
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:jammy
- OS: ubuntu-2404
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:noble
- OS: ubuntu-2404
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:noble
- OS: ubuntu-2604
ARCH: amd64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
- OS: ubuntu-2604
ARCH: arm64
R_VERSION: 4.4.3
IMG: ubuntu:resolute
steps:
- name: 'Inspect flat objects and record safety'
image: reg.devxy.io/rpkgs/build-env-${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
# uvr resolves bincraft's dependencies through the GitHub API, including
# the pat-s/cranlike@s3 fork. Unauthenticated it is rate limited, and the
# failure is not loud: uvr warns, falls back to the registry copy of
# cranlike, and the index write then dies on `unused argument (built =
# built)` because upstream has no such parameter. Intermittent by nature,
# since it depends on the rate-limit window.
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