R2 Migration

Published

August 3, 2026

NotePart of the migration record

A dated snapshot kept as history, not a live view of the current system: corrected if wrong, but not updated to track the estate. The overview links the reference pages that describe the replacement itself.

Full detail lives in the repo’s own README.md and MIGRATION.md — this page is the condensed version for orientation. Don’t duplicate updates here; treat those files as the source of truth and this as a pointer.

Why

Bioconductor’s origin runs off an EBS volume, and crawlers exhaust its IOPS. The traffic that hurts is not page views — it’s bots pulling hundred-megabyte lecture videos out of /help/course-materials/, where a single directory holds 711 MB of .mp4 against 2 MB of HTML, roughly 400:1 from two years of materials alone.

Large immutable files behind a CDN with free egress is what object storage is for. Raising EBS IOPS is the stopgap; this is the replacement.

Architecture

flowchart LR
  W["bioc-web docroot<br/>rrsync over SSH<br/>1.35M files, 447 GB"] -->|"rsync delta, hourly"| Mi["local mirror"]
  O["OSN archive<br/>anonymous S3, 4.66 TB"] -->|"one-time copy, verified"| R
  Mi -->|"rclone --files-from<br/>+ purge changed URLs"| R[("R2 · bioc-site<br/>1.65M objects, 5.1 TB<br/>private")]
  R --> K["Worker<br/>symlink resolution, redirects<br/>ranges, conditional GETs, cache"]
  K --> B["browsers"]
  K --> RR["R: BiocManager::install()"]
  K --> MI["mirror operators<br/>/api/v1/manifest"]

Two filters make the sync affordable: rsync (size+mtime, cheap but coarse) narrows 1.35M files to thousands of candidates, then rclone --checksum (MD5 vs R2 ETag, precise but only affordable over a short list) finds what actually changed. Purging off the second stage — not the first — is what stops a nightly rebuild from purging the whole zone.

Object storage has no symlinks. The docroot has 145, and the Worker resolves them per request against a published _symlinks.json rather than uploading them — so a release roll is data, not a deploy.

Status (measured, not projected)

R2 1,652,759 objects · 5.1 TB · 0 upload errors
Docroot 1,351,530 files · 447 GB
OSN archive 301,217 objects · 4.66 TB · verified, 0 differences
BiocManager::install() 8/8 against the mirror
Cost ~$80/month, of which the OSN archive is ~$70

Progress since 2026-08-03 (updated 2026-08-13)

The table above is the initial load; the operational picture has moved past it:

  • The sync is scheduled and self-checking. An hourly delta sync and a weekly full checksum reconcile run as systemd timers with failure alerting. The most recent weekly pass verified zero drift across 3.7M checked files.
  • Request logging is live and monitored — one structured record per request, all fields, no sampling, delivered continuously to durable object storage, queryable side by side with the historical CloudFront logs through a normalizing view, and gap-alerted daily (the delivery pipeline cannot backfill, so gaps are the failure mode that matters). Details in Download Stats.
  • The release-roll guard is deployed: scheduled detection of an upstream version roll, with destructive sync actions held for explicit human approval — the class of unattended mass-deletion accident a roll could otherwise cause is fenced off.
  • checkResults is mirrored in full for every release; archival releases (≤ 3.22) carry no ongoing sync cost by design.
  • The historical .htaccess behavior is ported, including the package short-URL rewrites and the container-binaries redirect whose failure mode is silent.
  • Public installs are invited: Installing packages from the new site is the two-line BiocManager setup, verified end-to-end against every repository type.

Verdict: the serving replacement is functionally complete; what remains is the cutover decision. The longer-term layout — which repositories hold what, and the route-by-route redesign behind the Worker — is decided and tracked as a phased migration plan (ADR 0008 in the repo, with per-phase issues).

Not in scope

  • AnnotationHub (10.1 TiB) and ExperimentHub (593 GiB) — different service, fetched by their own R packages through a metadata database.
  • Anything dynamic — search, BiocViews queries, live build reports. (Note: package landing pages turned out not to be dynamic — see Current State — which simplifies this boundary somewhat.)

Relationship to the decommission plan

This track solves the served docroot’s IOPS/cost problem. It does not by itself remove staging or master — those boxes still build the docroot and (today) serve it. Retiring them is the separate, harder problem covered in the decommission plan.