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`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
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FROM devxygmbh/r-alpine:4.4-3.20 AS build
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# ARG GITHUB_PAT
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RUN apk add --no-cache curl ca-certificates \
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&& curl -fsSL https://raw.githubusercontent.com/nbafrank/uvr/main/install.sh \
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| UVR_INSTALL_DIR=/usr/local/bin sh
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# One uvr project drives both dependency installs below. UVR_LIBRARY points the
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# syncs at the image's R library instead of the project-local .uvr/library/, so
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# `Rscript app.R` finds the packages without a uvr-aware .Rprofile.
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ENV UVR_LIBRARY=/usr/lib/R/library
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RUN mkdir -p /uvr && cd /uvr && uvr init --here
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COPY --link ./DESCRIPTION .
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COPY --link ./R ./R
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# COPY --link ./man .
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COPY --link ./NAMESPACE .
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COPY --link ./shiny/app.R /app/app.R
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RUN ls -la
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# install R package deps. uvr has no equivalent of bare `pak::pak()`, which
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# reads the DESCRIPTION in the working directory, so extract the dependency
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# names and hand them to `uvr add`.
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RUN R -q --no-echo -e "d <- read.dcf('DESCRIPTION'); f <- intersect(colnames(d), c('Depends', 'Imports', 'LinkingTo')); p <- trimws(sub('[(].*', '', unlist(strsplit(paste(d[, f], collapse = ','), ',')))); writeLines(setdiff(p[nzchar(p)], c('R', rownames(installed.packages()))), '/tmp/deps.txt')" \
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&& cd /uvr && xargs -r uvr add --no-install < /tmp/deps.txt \
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&& uvr sync --install-system-deps
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RUN R CMD INSTALL --no-docs --without-keep.source .
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# install shiny app deps
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RUN R -q -e "install.packages('renv'); pkgs <- renv::dependencies('/app/app.R')[['Package']]; pkgs = setdiff(pkgs, 'bincraft'); writeLines(pkgs, '/tmp/app-deps.txt')" \
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&& cd /uvr && xargs -r uvr add --no-install < /tmp/app-deps.txt \
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&& uvr sync --install-system-deps
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ENV PGPASS=""
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RUN echo "options(shiny.port=3838, shiny.host='0.0.0.0')" >> /root/.Rprofile
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WORKDIR /app
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EXPOSE 3838
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CMD Rscript app.R
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