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

.crow/process-updates.yaml

@@ -49,109 +49,109 @@ matrix:
       R_VERSION: 4.5.3
       IMG: alpine:3.22
       OS_ID: alpine322
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
     - OS: alpine-322
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: alpine:3.23
       OS_ID: alpine322
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
     - OS: alpine-323
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: alpine:3.23
       OS_ID: alpine323
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
     - OS: alpine-323
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: alpine:3.23
       OS_ID: alpine323
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
     - OS: alpine-324
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: alpine:3.24
       OS_ID: alpine324
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
     - OS: alpine-324
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: alpine:3.24
       OS_ID: alpine324
-      PROCESS_NEW: "FALSE"
+      PROCESS_NEW: 'FALSE'
     - OS: redhat-8
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: redhat:8
       OS_ID: rhel8
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: redhat-8
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: redhat:8
       OS_ID: rhel8
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: redhat-9
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: redhat:9
       OS_ID: rhel9
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: redhat-9
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: redhat:9
       OS_ID: rhel9
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: redhat-10
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: redhat:10
       OS_ID: rhel10
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: redhat-10
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: redhat:10
       OS_ID: rhel10
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: ubuntu-2204
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: ubuntu:jammy
       OS_ID: jammy
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: ubuntu-2204
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: ubuntu:jammy
       OS_ID: jammy
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: ubuntu-2404
       ARCH: amd64
       R_VERSION: 4.4.3
       IMG: ubuntu:noble
       OS_ID: noble
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: ubuntu-2404
       ARCH: arm64
       R_VERSION: 4.4.3
       IMG: ubuntu:noble
       OS_ID: noble
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: ubuntu-2604
       ARCH: amd64
       R_VERSION: 4.5.3
       IMG: ubuntu:resolute
       OS_ID: resolute
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
     - OS: ubuntu-2604
       ARCH: arm64
       R_VERSION: 4.5.3
       IMG: ubuntu:resolute
       OS_ID: resolute
-      PROCESS_NEW: "TRUE"
+      PROCESS_NEW: 'TRUE'
 
 steps:
   - name: 'Processing Updates'
@@ -182,8 +182,10 @@ steps:
       NTFY_AUTH: TRUE
       NTFY_PASSWORD:
         from_secret: ntfy_token
-      # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
-      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      # set the location of uvr's caches, which persist the R package
+      # dependencies needed to install the packages themselves
+      UVR_CACHE_DIR: /mnt/cache/uvr/cache
+      UVR_PACKAGES_DIR: /mnt/cache/uvr/packages
       R_LIBS_USER: /mnt/cache/R-pkgs
       R_VERSION: ${R_VERSION}
       CCACHE_DIR: /mnt/cache/ccache
@@ -194,10 +196,10 @@ steps:
       INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3)
     commands:
       - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
-      - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/R-pkgs/pkgcache /mnt/cache/pkgcache/R/pkgcache
+      - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft
+      - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
       - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")'
-      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
       # rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run
       - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi
       # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise