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build-cran-binaries/docs/superpowers/specs/2026-04-11-weekly-missing-binaries-design.md

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Weekly Missing Binaries Audit & Rebuild

Goal

A weekly CI workflow that identifies CRAN packages whose latest release version has no binary available, reports them in Forgejo issues grouped by OS family and arch, and rebuilds those that have no prior build failure recorded in the database.

Architecture Overview

Two independent workflow sets, each with one file per platform/arch combo (14 files each), plus a shared R script and an excluded-packages config file.

weekly-audit-missing-*-*.yaml (14 files)
        │
        ▼
local/weekly-missing-binaries-audit.R
        │
        ├── Updates Forgejo issues (3 issues, one per OS family)
        └── Writes RDS files to /mnt/cache/packages/

weekly-rebuild-missing-*-*.yaml (14 files)
        │
        ▼
  Reads RDS, builds missing packages via bincraft::build_binary_package()

The audit and build workflows are fully independent. Either can be triggered on its own via cron or manually.

Platforms

All current platform/arch combinations:

Platform Arch Image Codename
ubuntu-2204 amd64 reg.devxy.io/rpkgs/build-env-ubuntu:jammy-4.4.3 jammy
ubuntu-2204 arm64 reg.devxy.io/rpkgs/build-env-ubuntu:jammy-4.4.3 jammy
ubuntu-2404 amd64 reg.devxy.io/rpkgs/build-env-ubuntu:noble-4.4.3 noble
ubuntu-2404 arm64 reg.devxy.io/rpkgs/build-env-ubuntu:noble-4.4.3 noble
alpine-321 amd64 reg.devxy.io/rpkgs/build-env-alpine:3.21-4.5 alpine321
alpine-321 arm64 reg.devxy.io/rpkgs/build-env-alpine:3.21-4.5 alpine321
alpine-322 amd64 reg.devxy.io/rpkgs/build-env-alpine:3.22-4.5 alpine322
alpine-322 arm64 reg.devxy.io/rpkgs/build-env-alpine:3.22-4.5 alpine322
alpine-323 amd64 reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5 alpine323
alpine-323 arm64 reg.devxy.io/rpkgs/build-env-alpine:3.23-4.5 alpine323
redhat-8 amd64 reg.devxy.io/rpkgs/build-env-redhat:8-4.4.3 rhel8
redhat-8 arm64 reg.devxy.io/rpkgs/build-env-redhat:8-4.4.3 rhel8
redhat-9 amd64 reg.devxy.io/rpkgs/build-env-redhat:9-4.4.3 rhel9
redhat-9 arm64 reg.devxy.io/rpkgs/build-env-redhat:9-4.4.3 rhel9

Component 1: Excluded Packages Config

File: local/excluded-packages.json

A JSON array of objects with package and reason fields:

[
  {"package": "RInno", "reason": "windows-only"},
  {"package": "KeyboardSimulator", "reason": "windows-only"},
  {"package": "doBy", "reason": "hang"},
  {"package": "frailtypack", "reason": "hang"},
  ...
]

This file is the single source of truth for packages that should be skipped. Both the audit script and rebuild workflows read from it.

The existing build-all-versions-*.yaml workflows retain their inline lists for now (migration is out of scope).

Component 2: Audit R Script

File: local/weekly-missing-binaries-audit.R

Environment variables consumed:

  • PLATFORM — e.g. ubuntu-2204, alpine-321, redhat-9
  • ARCH — amd64 or arm64
  • B2_S3_ACCESS_KEY, B2_S3_SECRET_KEY — S3 credentials
  • PGPASS — PostgreSQL password
  • FORGEJO_TOKEN — API token for issue updates

The workflow commands (not the R script) also use:

  • REPO_RO_TOKEN — for git clone in the workflow commands

Logic:

  1. Parse PLATFORM to derive OS family (Ubuntu, Alpine, Red Hat) and S3 codename (e.g. ubuntu-2204 -> jammy, redhat-9 -> rhel9).
  2. Fetch CRAN release packages via tools::CRAN_package_db() — extract Package and Version.
  3. List S3 tarballs at devxy-rpkgs-binaries/{arch}/{codename}/latest/src/contrib/ and parse {name}_{version}.tar.gz.
  4. Find packages where the CRAN release version is missing from S3.
  5. Read local/excluded-packages.json and remove those packages from the missing list.
  6. Query the single_builds DB table: for each missing package+version+platform+arch, check if error_occurred = TRUE. Split into:
    • Rebuildable: missing, not excluded, no prior failure for this version
    • Known failures: missing, not excluded, but has a recorded failure for this version
  7. Write the rebuildable package list (names only) to /mnt/cache/packages/weekly_rebuild_{platform}_{arch}.rds.
  8. Update the Forgejo issue for this OS family.

Issue update logic:

  • Issue title: Missing package binaries for latest version (<OS family>) where OS family is Ubuntu, Alpine, or Red Hat.
  • Search for existing open issue via GET /api/v1/repos/devxy/build-cran-binaries/issues?type=issues&state=open&q=<url-encoded title>. Match by exact title.
  • If found, read the existing body, replace the section for this platform/arch, and PATCH the issue.
  • If not found, POST a new issue with just this platform/arch section.

Issue body format:

_Last updated: 2026-04-11_

## ubuntu-2204

### amd64 (12 missing, 8 to rebuild)
- ggplot2 (3.5.2)
- dplyr (1.1.5)
- ...

#### Known build failures
- somepkg (1.0.0)

### arm64 (5 missing, 5 to rebuild)
- ...

## ubuntu-2404

### amd64 (3 missing, 3 to rebuild)
- ...

### arm64 (0 missing)
All binaries available.

---

## Excluded packages
doBy (hang), frailtypack (hang), RInno (windows-only), ...

Each audit workflow run updates only its own platform/arch section within the issue. The "Excluded packages" section and "Last updated" timestamp are rewritten on every run.

Section replacement strategy: The script parses the existing issue body as markdown, finds the ## {platform} + ### {arch} section, replaces it, and writes back the full body. If the section doesn't exist yet, it's appended under the correct ## {platform} header (or a new one is created).

Component 3: Audit Workflows

Files: 14 files, named weekly-audit-missing-{platform}-{arch}.yaml

Example: .crow/weekly-audit-missing-ubuntu-2204-amd64.yaml

Trigger:

when:
  - event: cron
    cron: weekly-audit-missing-ubuntu-2204-amd64
  - event: manual
    evaluate: 'task == "weekly-audit-missing-ubuntu-2204-amd64"'

Step: Lightweight — clones repo, installs bincraft + dependencies, runs the audit R script.

Container: Uses the platform-appropriate build image (needed for correct platform identification), but with minimal resource requests since no building happens.

Resources: ~2Gi memory, 2 CPUs.

Component 4: Rebuild Workflows

Files: 14 files, named weekly-rebuild-missing-{platform}-{arch}.yaml

Example: .crow/weekly-rebuild-missing-ubuntu-2204-amd64.yaml

Trigger:

when:
  - event: cron
    cron: weekly-rebuild-missing-ubuntu-2204-amd64
  - event: manual
    evaluate: 'task == "weekly-rebuild-missing-ubuntu-2204-amd64"'

Step:

  1. Clone repo, install bincraft.
  2. Read local/excluded-packages.json as a safety net.
  3. Read /mnt/cache/packages/weekly_rebuild_{platform}_{arch}.rds. If missing or empty, exit 0.
  4. Filter out excluded packages (double-check).
  5. Iterate and call bincraft::build_binary_package() for each package with tag_limit = 1L. Same S3/DB parameters as existing build workflows.
  6. Uses xvfb-run / xwfb-run for graphical packages (same pattern as existing builds).

Resources: Same as process-updates workflows — 5Gi request, 18Gi limit, 3 CPUs.

Cache volume: Maps ${ARCH}-binaries-r-dep-cache-${PLATFORM}:/mnt/cache (same volumes as existing builds, so the RDS files written by audit are visible).

Secrets Required

All existing secrets are reused:

  • B2_S3_ACCESS_KEY, B2_S3_SECRET_KEY — S3 access
  • PGPASS — PostgreSQL
  • REPO_RO_TOKEN — Git clone
  • GITHUB_PAT — For bincraft GitHub mirror access

New secret needed:

  • FORGEJO_TOKEN — API token for creating/updating issues on git.devxy.io

Cron Schedule

The audit and rebuild workflows each get their own cron names. The cron schedule itself is configured in the Crow/Woodpecker server, not in the YAML. Intended cadence: once per week (e.g. Sunday morning).

File Inventory

File Type Description
local/excluded-packages.json Config Excluded packages with reasons
local/weekly-missing-binaries-audit.R R script Audit logic, parameterized by env vars
.crow/weekly-audit-missing-ubuntu-2204-amd64.yaml Workflow Audit for ubuntu-2204/amd64
.crow/weekly-audit-missing-ubuntu-2204-arm64.yaml Workflow Audit for ubuntu-2204/arm64
.crow/weekly-audit-missing-ubuntu-2404-amd64.yaml Workflow Audit for ubuntu-2404/amd64
.crow/weekly-audit-missing-ubuntu-2404-arm64.yaml Workflow Audit for ubuntu-2404/arm64
.crow/weekly-audit-missing-alpine-321-amd64.yaml Workflow Audit for alpine-321/amd64
.crow/weekly-audit-missing-alpine-321-arm64.yaml Workflow Audit for alpine-321/arm64
.crow/weekly-audit-missing-alpine-322-amd64.yaml Workflow Audit for alpine-322/amd64
.crow/weekly-audit-missing-alpine-322-arm64.yaml Workflow Audit for alpine-322/arm64
.crow/weekly-audit-missing-alpine-323-amd64.yaml Workflow Audit for alpine-323/amd64
.crow/weekly-audit-missing-alpine-323-arm64.yaml Workflow Audit for alpine-323/arm64
.crow/weekly-audit-missing-redhat-8-amd64.yaml Workflow Audit for redhat-8/amd64
.crow/weekly-audit-missing-redhat-8-arm64.yaml Workflow Audit for redhat-8/arm64
.crow/weekly-audit-missing-redhat-9-amd64.yaml Workflow Audit for redhat-9/amd64
.crow/weekly-audit-missing-redhat-9-arm64.yaml Workflow Audit for redhat-9/arm64
.crow/weekly-rebuild-missing-ubuntu-2204-amd64.yaml Workflow Rebuild for ubuntu-2204/amd64
.crow/weekly-rebuild-missing-ubuntu-2204-arm64.yaml Workflow Rebuild for ubuntu-2204/arm64
.crow/weekly-rebuild-missing-ubuntu-2404-amd64.yaml Workflow Rebuild for ubuntu-2404/amd64
.crow/weekly-rebuild-missing-ubuntu-2404-arm64.yaml Workflow Rebuild for ubuntu-2404/arm64
.crow/weekly-rebuild-missing-alpine-321-amd64.yaml Workflow Rebuild for alpine-321/amd64
.crow/weekly-rebuild-missing-alpine-321-arm64.yaml Workflow Rebuild for alpine-321/arm64
.crow/weekly-rebuild-missing-alpine-322-amd64.yaml Workflow Rebuild for alpine-322/amd64
.crow/weekly-rebuild-missing-alpine-322-arm64.yaml Workflow Rebuild for alpine-322/arm64
.crow/weekly-rebuild-missing-alpine-323-amd64.yaml Workflow Rebuild for alpine-323/amd64
.crow/weekly-rebuild-missing-alpine-323-arm64.yaml Workflow Rebuild for alpine-323/arm64
.crow/weekly-rebuild-missing-redhat-8-amd64.yaml Workflow Rebuild for redhat-8/amd64
.crow/weekly-rebuild-missing-redhat-8-arm64.yaml Workflow Rebuild for redhat-8/arm64
.crow/weekly-rebuild-missing-redhat-9-amd64.yaml Workflow Rebuild for redhat-9/amd64
.crow/weekly-rebuild-missing-redhat-9-arm64.yaml Workflow Rebuild for redhat-9/arm64

Total: 29 new files (1 JSON config + 1 R script + 14 audit workflows + 14 rebuild workflows + the design doc itself)