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Quick Reference Guide

Starting a New Build

  1. Go to Actions → Start New Build Cycle
  2. Click Run workflow
  3. Enter container image (e.g., ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_20)
  4. Click Run workflow

A new branch will be created: build/YYYY-MM-DD-HHMMSS-container-tag

Enabling Automatic Builds on Build Branch

After the branch is created:

  1. Switch to the build branch
  2. Edit .github/workflows/run.yaml
  3. Uncomment these lines (around line 6-7): 
    schedule:
  - cron: '*/5 * * * *'
  4. Commit and push

Builds will now run automatically every 5 minutes.

Monitoring Build Progress

Check these files on the build branch:

  • logs/successful-packages.txt - Completed packages
  • logs/failed-packages.txt - Failed packages
  • logs/dispatched-packages.txt - All dispatched packages
  • remaining-packages.json - Packages still waiting
  • logs/PackageName/build-*.log - Individual package logs

Finishing a Build

When all packages are done:

  1. Switch to the build branch in GitHub
  2. Go to Actions → Finish Build Cycle
  3. Click Run workflow

This creates the PACKAGES index and syncs to the repository.

File Reference

File Purpose
CONTAINER_BASE_IMAGE.bioc Docker image used for builds
biocdeps.json Package dependency graph
ready_packages.txt Packages ready to build now
bioc_version Bioconductor version
r_version R version
null_push_counter No-activity cycle counter
PACKAGES Final package index (after finish)
cycle_complete_time Build completion timestamp

Kubernetes Resources

Each build creates:

  • Namespace: ns-YYYY-MM-DD-HHMMSS-container-tag
  • PVC: bioc-pvc-YYYY-MM-DD-HHMMSS-container-tag
  • Jobs: One per package with label app=bioc-builder

Common Commands

Check build branch status

git checkout build/2025-10-30-123456-container-tag
cat logs/successful-packages.txt | wc -l  # Count successful builds
cat logs/failed-packages.txt | wc -l      # Count failures

View a package log

cat logs/PackageName/build-success.log
# or
cat logs/PackageName/build-fail.log

Check Kubernetes jobs

kubectl get jobs -n ns-YYYY-MM-DD-HHMMSS-container-tag -l app=bioc-builder

Clean up old build branches

git branch -d build/2025-05-28-142558-container-tag
git push origin --delete build/2025-05-28-142558-container-tag

Troubleshooting

Build seems stuck

  • Check null_push_counter - if high, builds may be waiting on dependencies
  • Check Kubernetes jobs: kubectl get jobs -n ns-...
  • Look for failed packages: cat logs/failed-packages.txt

Need to restart a build

Option 1: Create a new branch with the start_cycle workflow Option 2: Manually reset files on current branch and re-run workflow

Package keeps failing

  1. Check the log: logs/PackageName/build-fail.log
  2. Look for dependency issues
  3. Check if package is archived on CRAN

Important Notes

  • Main branch: Does not run builds automatically (schedule is commented out)
  • Build branches: Edit workflow to uncomment schedule for automatic builds
  • Keep branches: Don't delete build branches until you're sure you don't need them
  • Log sizes: Large logs are gitignored to keep repo size manageable