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pat-s
a4b274f281
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## Problem
The arm64 `build-all` pipeline fills the macmini (gaia) host disk despite an 8h prune.
Root cause is not images or job volumes: it is the persistent dep-cache volume, specifically `pkgcache/R/pkgcache/_metadata`, which grew to ~165 GB.
`{pkgcache}` mints a new content hash for the "patched" binaries repo on every PACKAGES change, so each per-package build writes a fresh ~70 MB `pkgs-<hash>.rds` (+ `patched-<hash>/`) that is never evicted (2407 snapshots observed).
When the disk hits 100% OrbStack stops and the on-host prune can no longer connect to the daemon, so it never self-heals.
## Change (Workstream A of the disk-fill fix)
- Add `trim_pkgcache_metadata()` to `local/r-minor-helpers.R`: keeps the newest `keep` (default 20) `patched-*`/`pkgs-*.rds` entries under `_metadata`, deleting only entries older than `min_age_secs` (default 600s) so it never races the up-to-4 concurrent split-jobs sharing the volume.
Preserves `pkg/` downloads and the stable CRAN/BioC/INLA repo dirs.
No-op when `R_PKG_CACHE_DIR` is empty (amd64) or `_metadata` is absent (first run).
- Call it every 25 packages inside the build loop in `local/build-all.R`.
- Add a defensive start-of-run cleanup of `_metadata/patched-*` + `pkgs-*.rds` to the two workflows that mount the persistent volume (`build-all-versions.yaml`, `build-all-versions-install-deps.yaml`).
Only these paths are touched; `process-updates.yaml`/`weekly-rebuild-missing.yaml` (no persistent volume) are unchanged.
Follow-ups (separate workstreams): on-host self-healing prune watcher + OrbStack disk cap (ansible), and Prometheus/Grafana alerting (k8s-talos).
Upstream: bincraft patched-repo hash churn is the true source fix.
New unit tests (6) for the helper; full suite 24/24 green.
Reviewed-on: #110
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| .. | ||
| patches | ||
| tests | ||
| archive-missed-pkgs.R | ||
| build-all.R | ||
| build-one.R | ||
| check-cdn-cache.sh | ||
| check-NA.R | ||
| debug-packages-writing.R | ||
| detect-duplicates.R | ||
| excluded-packages.json | ||
| fetch-rebuild-packages-from-issue.R | ||
| find-R-api-packages.sh | ||
| install-bincraft.R | ||
| label-removed-cran-packages.R | ||
| last-processed-by-platform.R | ||
| migrate-s3-hetzner-to-backblaze.sh | ||
| missing-cran-packages-db.R | ||
| missing-cran-packages.R | ||
| missing-packages-in-index.R | ||
| packages-to-build.R | ||
| packages-without-any-binary.R | ||
| query-pkgs-without-old-versions.R | ||
| r-minor-helpers.R | ||
| test-package-loading.R | ||
| validate-patches.R | ||
| weekly-missing-binaries-audit.R | ||