Author	SHA1	Message	Date
pat-s	ee15c50f53	refactor: migrate package installation from pak to uvr (#147) ... `bincraft` dropped pak in favour of uvr (5.0.x, "Dependencies and their system requirements are now installed with `uvr` instead of pak during `build_binary_package()`"), so the pipelines, helper scripts and images in this repo move with it. ## Approach uvr is project-scoped in a way pak is not: `uvr add` refuses to run outside a project and always installs into `.uvr/library/`, and only `uvr sync` honours `--library`. So there is no one-line `pak::pak(...)` equivalent. `local/uvr-install.sh` encapsulates the dance — bootstrap a pinned uvr, mint a throwaway project under `TMPDIR`, `uvr add --no-install`, then `uvr sync --library <target>`. Keeping the project outside the checkout also keeps `uvr init`'s `.Rprofile` from hijacking `.libPaths()` for every other R call in the pipeline. This matches what bincraft itself does (`uvr sync --install-system-deps --library <lib>`), and bincraft requires `uvr` on `PATH`, which the bootstrap provides: every pipeline that calls `bincraft::` runs `install-bincraft.R` (and therefore the bootstrap) first. ## Changes | File | Change | | --- | --- | | `local/uvr-install.sh` | **New.** The single replacement for `pak::pak(...)`. Bootstraps uvr `v0.4.4`, resolves the R interpreter from `UVR_R_BIN`/`R_VERSION`/`PATH`, pins the manifest to that R's exact version, and syncs into `UVR_TARGET_LIB`/`R_LIBS_USER`. | | `local/install-bincraft.R` | Installs `forgejo::codefloe.com/rpkgs/bincraft@<tag>` instead of a `git::` URL; keeps the `git ls-remote` tag resolution. Exports `UVR_R_BIN`/`UVR_TARGET_LIB` from `R.home()`/`.libPaths()[1]` so the per-R-minor passes target their own R and library. | | `.crow/auto-apply-patches.yaml`, `.crow/weekly-patch-proposals.yaml`, `.crow/weekly-audit-missing.yaml`, `.crow/weekly-rebuild-missing.yaml`, `.crow/build-all-versions-install-deps.yaml` | `pak::pak(...)` → `UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh ...`. The explicit `UVR_R_BIN` matters in `build-all-versions-install-deps.yaml`, which has no `R_VERSION` in its step environment. | | `.crow/build-all-versions.yaml`, `.crow/process-updates.yaml`, `.crow/weekly-rebuild-missing.yaml` | `R_PKG_CACHE_DIR` → `UVR_CACHE_DIR` + `UVR_PACKAGES_DIR` on the same `/mnt/cache` volume, preserving the amd64-off/arm64-on split. Drops the `rm -rf .../pkgcache/_metadata/...` cleanup. | | `local/r-minor-helpers.R`, `local/build-all.R`, `local/tests/test-trim-pkgcache.R` | Removes `trim_pkgcache_metadata()`, its every-25-packages call and its tests. uvr's cache does not mint a fresh ~70 MB snapshot per `PACKAGES` change. | | `.crow/build-all-versions-install-deps.yaml` | Drops `pak::sysreqs_db_update()`; uvr resolves sysreqs from its vendored `r-system-requirements` rules via `--install-system-deps`. | | `docker/Containerfile-shiny-app` | Bootstraps uvr and drives both dependency installs through one uvr project with `UVR_LIBRARY` pointed at the image's R library. | | `docker/build-one.Dockerfile` | Ships `uvr-install.sh` at `/work/local/` so `install-bincraft.R` finds it. | | `docker/reprex/alpine.sh` | Replaces `pak::local_install_deps()` with DESCRIPTION parsing + `uvr add`. | | `local/test-package-loading.R` | Installs via the helper instead of `pak::pkg_install()`. | | `README.md` | Documents uvr for sysreq inference, archived-version installs and cache clearing. | | `renovate.json` | Tracks the `UVR_PIN` in `uvr-install.sh` via `github-releases`. | ## Behaviour notes - **`weekly-audit-missing` still takes bincraft from the default branch**, not the latest release tag, matching what the `git::` pak call did. Called out in a comment rather than silently changed. - **The uvr pin is repo-wide.** bincraft resolves `uvr` from `PATH` and pins no version of its own, so `UVR_PIN` in `uvr-install.sh` governs the whole pipeline. - **Persistent caches now also benefit bincraft**, which reads `UVR_CACHE_DIR`/`UVR_PACKAGES_DIR` from the inherited pipeline environment. - **`uvr sync` will not prune the shared library.** Pruning is disabled whenever `--library` is passed (`do_prune = prune && library_override.is_none()`), so `/mnt/cache/R-pkgs` keeps bincraft and its dependencies. The wipe-on-ABI-mismatch path is *not* similarly guarded, which is why the helper pins the manifest to the active R's exact version. - **`plans/` and `specs/` are untouched** — they are dated records of decisions made in June 2026 and describe bincraft's then-pak-based internals; rewriting them would misstate history. ## Verification `shellcheck`, all pre-commit hooks (on this commit's file range) and the `local/tests/` suite (100 assertions) pass. Not yet exercised in CI: the build-env images do not ship `uvr`, so the per-step `curl install.sh` bootstrap is untested against a real image. Worth a manual `build-all-versions-install-deps` run before merging. Reviewed-on: #147	2026-07-31 12:19:26 +00:00
pat-s	a4b274f281	fix(ci): bound pkgcache _metadata growth to stop macmini disk-fill (#110) ... ## 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	2026-07-13 09:31:29 +00:00
pat-s	ffc2319558	fix(build-all): exclude previously-errored versions in prefilter (#113) ... ## Motivation Build jobs were cycling through hundreds of packages that were only ever printed as `Skipping … due to previous build error recorded in metadata DB`, wasting wall-clock on per-package preparation before dropping each one. ## Cause The prefilter query in `local/build-all.R` selected only successfully-built versions (`error_occurred = FALSE`) into `built`, so line 112 removed only those from the chunk. Every previously-errored version stayed in the work list and was walked one-by-one, each hitting the internal skip in `build_binary_package()`. This also explains the misleading `Skipped 0 already-built package versions` line for alphabetical chunks whose leading packages only have error records. ## Changes - `local/build-all.R`: drop the `AND error_occurred = FALSE` clause so `built` holds every version already attempted (built or errored) for this platform/arch; the existing filter then removes all of them up front. - Rename the log line to `already-attempted` so the reported count reflects successes and errors. - Update the surrounding comment to explain why errored versions are excluded. ## Behaviour change Previously-errored versions are now dropped before the build loop instead of being iterated and individually skipped. No package that would otherwise build is affected, `build_binary_package()` already skipped these internally. Retrying errored versions is out of scope and would need a separate opt-in flag on both the prefilter and the in-loop skip. Reviewed-on: #113	2026-07-13 09:28:45 +00:00
pat-s	55a18fd87d	feat: patch registry + wiring for per-package patching (#103) ... ## Summary Adds the curated **patch registry** and wiring that drives bincraft's new package-patching mechanism (see bincraft PR `feat/package-patching`). Lets specific packages be patched (env/configure/Makevars overrides or source diffs) before pak installs them — including as transitive dependencies — so compiler-/OS-specific failures like RcppParallel's bundled TBB stop cascading. ## What's included - `local/patches/registry.json` — initial entry: RcppParallel with `RCPP_PARALLEL_USE_TBB=0` for alpine / ubuntu-2604, plus `local/patches/README.md` schema docs. - `local/validate-patches.R` — validates schema, referenced patch files, and ambiguous overlaps; clean failure + exit 1 (no stacktrace). - `.pre-commit-config.yaml` — a `validate-patches` hook (re-runs when the registry or the validator changes). - `local/build-one.R` / `local/build-all.R` — pass `patches = "local/patches"` to `bincraft::build_binary_package()`. - `specs/2026-06-30-package-patching-design.md` and `plans/2026-06-30-package-patching-implementation.md`. ## ⚠️ Merge ordering (blocker) This PR adds a `patches = ...` argument to `build_binary_package()` calls. The `.crow/*.yaml` workflows currently pin bincraft **v4.2.3**, which does not accept that argument — CI will error with `unused argument (patches=...)` until: 1. bincraft **v4.3.0** is released (PR `feat/package-patching`), and 2. the pin is bumped in `.crow/build-all-versions-install-deps.yaml`, `.crow/build-all-versions.yaml`, and `.crow/process-updates.yaml`. The `.crow` pin bump will be added to this PR once bincraft v4.3.0 is tagged. Do not merge before then. Reviewed-on: #103	2026-06-30 08:50:19 +00:00
pat-s	83c761b736	feat(ci): OS/OS_VERSION manual dropdowns + restore lost crow fix (#97) ... ## Summary Two changes: 1. **`OS`/`OS_VERSION` manual-run dropdowns** — give these form variables explicit `options:` lists (like `target_arch` and `R_VERSION`), so the manual-run form shows dropdowns instead of free-text, in both `build-all-versions.yaml` and `build-all-versions-install-deps.yaml`. Crow form variables are independent (no cascading), so the operator still has to pick a coherent `OS` + `OS_VERSION` combination (e.g. `redhat` + `9`, not `alpine` + `jammy`). 2. **Repairs `main`** — the crow fix from PR #96 (`bc2f6f1`) was lost when that PR was squashed (only the first commit was captured). As a result `main` currently carries the `OS: ${OS}` env vars that break Crow parsing (`unable to parse variable name`) and the unfixed `build-all.R`. This PR re-applies that fix: drop the env additions and derive `platform`/`arch` inside `build-all.R` from the container (bincraft codename → platform mapping + `Sys.info()` arch). ## Notes - `OS_VERSION` options are quoted strings so tags like `8`/`9`/`10` aren't parsed as integers. - Validated: both YAMLs parse, `build-all.R` parses. Reviewed-on: #97	2026-06-18 11:39:11 +00:00
pat-s	fa955c10bf	fix: recompute package snapshot when missing from cache (#95) ... ## Summary `build-all.R` reads three snapshot files from `/mnt/cache/packages/` that the `build-all-versions-install-deps` step precomputes: `pkgs_to_build.rds`, `r_minor_sensitive_pkgs.rds`, and `s3_cache.rds`. That cache volume is **per-agent**, so a build job scheduled on a different (fresh) agent than the one that ran install-deps finds the snapshot absent and dies at `readRDS` (`cannot open compressed file '/mnt/cache/packages/pkgs_to_build.rds'`). This adds a conditional guard at the top of `build-all.R`: when any of the three files is missing, it sources `local/packages-to-build.R` (which has all needed creds via `PGPASS` / `B2_S3_*` env, already present in the build step) and writes the derived `.rds` files — exactly mirroring the install-deps command. - The first build job on a fresh agent repopulates the shared cache, so subsequent jobs on that agent reuse it. - Concurrent jobs that also miss simply redo the work (accepted tradeoff vs. slow shared storage like NFS). - Saves use a temp-file + atomic `file.rename`, so a concurrent reader never sees a half-written `.rds`. Reviewed-on: #95	2026-06-17 17:49:04 +00:00
pat-s	1cd86b65e1	feat(build): skip already-built package versions on workflow restart (#91) ... ## Summary When a `build-all-*` workflow is restarted, the build job re-reads the static `pkgs_to_build.rds` that the install-deps step produced once, so it cycles over every package an interrupted run already built. This adds a DB-based skip filter so a restart only processes what is genuinely left. - At job start, `build-all.R` queries the `single_builds` metadata table for `(name, tag)` already built successfully (`error_occurred = FALSE`) on this `platform`/`arch`, and drops those pairs from the chunk before the build loop. It logs how many it skipped. - One indexed query, one round trip, run before the pak forks — no extra S3 listing and no new Python/s3fs memory pressure (`RPostgres`/`DBI` are already used in the container). - Errored versions are intentionally **not** skipped, so transient failures still get retried on restart. ## Dependency Correctness depends on a `error_occurred = FALSE` row meaning the binary is actually published. That guarantee is added in rpkgs/bincraft#56 (success row written only after a confirmed S3 upload). This PR should land together with / after a bincraft release including that fix. Reviewed-on: #91	2026-06-16 07:27:20 +00:00
pat-s	d558e27c11	feat: R-minor-sensitive binary builds (full + iterative) (#84) ... ## Summary Builds R-minor-sensitive CRAN packages once per installed R minor version (into per-minor S3 slots `…/contrib/<x.y>/`) and everything else once into the generic slot, driven by bincraft 4.2.0's ABI classifier. Both the full and iterative pipelines are covered. ## What's in here **Detection / precompute** - `local/r-minor-helpers.R` — pure `classify_from_metadata()` (NeedsCompilation / risky `LinkingTo`) + `parse_build_args()`, with unit tests. - `local/packages-to-build.R` — adds a per-package `r_minor_sensitive` flag: cheap CRAN-metadata rules first, source download + `bincraft::needs_per_minor_recompile()` only for the ambiguous compiled subset (fail-safe to sensitive). Classified once per package, applied to all versions. **Full build** - `local/build-all.R` — passes the per-row `is_r_minor_sensitive` flag; new `--sensitive-only` mode builds just the risky subset. - `.crow/build-all-versions-{amd64,arm64}.yaml` — install-deps persists the sensitive subset; build step runs a sensitive-only pass under each non-primary `/opt/R/*` minor; new step uploads the generic index plus a per-minor index for each minor. **Iterative build** - All 14 `.crow/process-updates-*.yaml` — primary pass uses `r_minor_detection = 'classifier'`; a sensitive-only multi-R pass builds risky updates under each other minor; per-minor index upload added. **Tooling / housekeeping** - Pins bincraft `v4.1.1` → `v4.2.0` across all workflows; removes the superseded standalone `build-r-minor-sensitive-packages.yaml`. - Adds prek/pre-commit hooks (prettier, markdownlint, editorconfig-checker, yamllint, air) and applies them repo-wide; excludes the verbatim GPL `LICENSE.md` and auxiliary shell scripts. - Design + implementation docs under `docs/superpowers/`. ## Requires before merge - A `v4.2.0` git tag must be pushed on the bincraft repo (codefloe.com/rpkgs/bincraft) — the workflow install steps pin `@v4.2.0`. The full-build install-deps clones `main`, so it is unaffected. Reviewed-on: #84	2026-06-14 08:04:40 +00:00
pat-s	53da568749	refactor: single source of truth for excluded packages (#79) ... ## Summary `local/build-all.R` had a 75-name hardcoded `exclude <- c(...)` vector that had drifted from `local/excluded-packages.json` — `RcmdrPlugin.ROC` was in the R vector but missing from the JSON. `.crow/weekly-rebuild-missing-*.yaml` already reads the JSON via `jsonlite::fromJSON(...)[["package"]]`. This brings `build-all.R` in line with that pattern. Changes: - **`local/excluded-packages.json`**: add the missing `RcmdrPlugin.ROC` entry (reason `"hang"`, matching siblings). - **`local/build-all.R`**: replace the 16-line hardcoded vector with one `jsonlite::fromJSON(...)` call. - **`.crow/build-all-versions-install-deps-{amd,arm}64.yaml`**: add `jsonlite` to the install-deps `pak::pak()` list so it's available in `/mnt/cache/R-pkgs` for the build step. - **`.crow/build-all-versions-arm64.yaml`**: drop the dead base64-encoded `SKIP_PKGS` docs comment that nobody was passing as a `--var` anyway; replace with a one-line pointer to the JSON. Reviewed-on: #79	2026-06-08 08:30:19 +00:00
pat-s	8a98cf96a6	fix: save S3 listing in precompute step, avoid loading s3fs in build step ... s3fs uses reticulate/Python which significantly increases R process memory. When pak tries to fork R to install package dependencies, the enlarged process can't be duplicated within the container memory limit. Now the install-deps step saves the S3 file listing as s3_cache.rds, and the build step reads it with readRDS() — no s3fs loading needed.	2026-04-17 20:05:26 +02:00
pat-s	bc3dbd6126	fix: map x86_64/aarch64 to amd64/arm64 for S3 cache path	2026-04-17 19:04:18 +02:00
pat-s	9b27b3e650	refactor: extract build-all R one-liner into local/build-all.R ... - Load bincraft eagerly via library() to avoid lazy-load memory spike - Do bulk S3 listing upfront and pass as s3_package_cache to avoid per-package S3 calls that accumulate memory and trigger fork failures - Consolidate amd64/arm64 exclude lists into single script - Much easier to read and maintain than a YAML-embedded one-liner	2026-04-17 19:01:08 +02:00