Author	SHA1	Message	Date
pat-s	aa4c95457f	fix(rebuild): harden split workflow setup (#164) ... ## Motivation Weekly rebuild shards can all hit a transient CRAN DNS/index outage at once, and the dependent CDN purge always fails because it tries to clone over the checkout preserved from the re-index step. ## Changes - Retry `uvr add` resolution up to four times with bounded backoff. - Reuse the existing Crow workspace checkout in the CDN purge step. - Remove the purge step's unused Git package and repository token. ## Validation - `crow lint .crow/` - `shellcheck local/uvr-install.sh scripts/purge_cdn_zone.sh` - `git diff --check` Reviewed-on: #164	2026-08-13 13:38:28 +00:00
automation-bot	caf3276fb9	chore(deps): update dependency nbafrank/uvr to v0.4.6	2026-08-11 00:31:56 +00:00
pat-s	6372f0f928	fix(ci): refresh the apt index before uvr installs system dependencies (#161) ... Unblocks the ubuntu 26.04 builds without waiting for an image rebuild. ## What broke ``` i Installing R package dependencies ! Error in installing dependencies for package huge with tag 2.0.1: uvr sync --install-system-deps --library /mnt/cache/R-pkgs-4.4 failed (exit 1) ! WARN Missing system dependencies for 1 package(s) igraph needs: libglpk-dev > Running: apt-get install -y libglpk-dev E: Unable to locate package libglpk-dev ``` Neither the package name nor the sysreq mapping is wrong. `libglpk-dev` is `5.0-2build1` in `universe`, which `ubuntu:resolute` enables by default. What is missing is the apt index: uvr v0.4.5 runs `apt-get install` with no `apt-get update` before it, and every ubuntu build image ends its apt layers with `rm -rf /var/lib/apt/lists/*`, so the shipped image has no index at all. Not specific to 26.04 — jammy and noble fail identically for any sysreq the image's preinstall line doesn't already cover. 26.04 surfaced it first, through `igraph` and everything depending on it (`huge` was the first to fail). ## Fix `apt-get update` before the sync in `local/uvr-install.sh`. That one site covers every pipeline: `build-all-versions`, `build-all-versions-install-deps`, `weekly-rebuild-missing`, `weekly-audit-missing`, `trial-build-registry`, `auto-apply-patches` and `weekly-patch-proposals` all reach it, either directly or through `install-bincraft.R`. The index it populates persists for the rest of the step, so the bincraft-driven `uvr sync` calls that follow are covered too. Guarded on `apt-get` and non-fatal: `apk add` fetches its index implicitly and dnf refreshes expired metadata on its own, so alpine and redhat are unaffected and skip it. ## Why here as well as in the image The real fix is upstream `e491b2e`, which refreshes the index before the auto-install. It landed one day after v0.4.5 was tagged, so no release carries it ([nbafrank/uvr#250](https://github.com/nbafrank/uvr/issues/250)); [build-env-images#23](https://codefloe.com/rpkgs/build-env-images/pulls/23) pins the ubuntu image to a commit that has it. That only reaches CI after an image rebuild is triggered. This change takes effect on the next pipeline run. It also stays useful afterwards: a baked index goes stale within weeks, and a stale index turns the same install into a 404 on the `.deb`. ## Verified In `ubuntu:resolute`, with the image state reproduced exactly (R installed, then `rm -rf /var/lib/apt/lists/*` to empty the index again): | Check | Result | |---|---| | `apt-get install -y libglpk-dev`, empty index | `E: Unable to locate package libglpk-dev` — the reported failure, reproduced | | Same container after `apt-get update` | `Candidate: 5.0-2build1`, `Components: main universe restricted multiverse` | | `igraph` + `UVR_INSTALL_SYSREQS=1 uvr sync`, empty index, uvr with the refresh | `Setting up libglpk-dev:amd64 (5.0-2build1)`, `System dependencies installed.`, `Installed 11 package(s)` | | `sh -n` and `shellcheck local/uvr-install.sh` | pass | ## Reverting Delete the guarded block. It is marked TEMPORARY with the upstream reference, and can go once the images ship a uvr above v0.4.5. Reviewed-on: #161	2026-08-10 06:30:25 +00:00
automation-bot	e02be7518f	chore(deps): update dependency nbafrank/uvr to v0.4.5	2026-08-04 02:32:01 +00:00
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