refactor: migrate package installation from pak to uvr

bincraft dropped pak in favour of uvr, so the pipelines, helper scripts
and images in this repo move with it.

- add local/uvr-install.sh as the single replacement for pak::pak(); it
  bootstraps a pinned uvr, mints a throwaway project under TMPDIR and
  runs `uvr add --no-install` + `uvr sync --library`, because `uvr add`
  refuses to run outside a project and only `sync` honours --library
- install bincraft via its Forgejo spec (forgejo::codefloe.com/rpkgs/
  bincraft@<tag>) instead of a git:: URL, keeping the git ls-remote tag
  resolution
- pass UVR_R_BIN/UVR_TARGET_LIB from install-bincraft.R so the
  per-R-minor passes target their own R and library
- replace R_PKG_CACHE_DIR with UVR_CACHE_DIR/UVR_PACKAGES_DIR on the
  persistent volume, preserving the amd64-off/arm64-on split
- drop trim_pkgcache_metadata() and its test; uvr's cache does not grow
  the way pkgcache's _metadata dir did
- let uvr install system requirements from its vendored
  r-system-requirements rules, replacing pak::sysreqs_db_update()
- migrate the shiny app image, the alpine reprex and the CRAN loading
  test; ship uvr-install.sh in the build-one image
- track the uvr pin with renovate

docker/Containerfile-shiny-app

@@ -1,7 +1,15 @@
 FROM devxygmbh/r-alpine:4.4-3.20 AS build
 
 # ARG GITHUB_PAT
-RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
+RUN apk add --no-cache curl ca-certificates \
+  && curl -fsSL https://raw.githubusercontent.com/nbafrank/uvr/main/install.sh \
+    | UVR_INSTALL_DIR=/usr/local/bin sh
+
+# One uvr project drives both dependency installs below. UVR_LIBRARY points the
+# syncs at the image's R library instead of the project-local .uvr/library/, so
+# `Rscript app.R` finds the packages without a uvr-aware .Rprofile.
+ENV UVR_LIBRARY=/usr/lib/R/library
+RUN mkdir -p /uvr && cd /uvr && uvr init --here
 
 COPY --link ./DESCRIPTION .
 COPY --link ./R ./R
@@ -11,13 +19,19 @@ COPY --link ./shiny/app.R /app/app.R
 
 RUN ls -la
 
-# install R package deps
-RUN R -q -e 'pak::pak()'
+# install R package deps. uvr has no equivalent of bare `pak::pak()`, which
+# reads the DESCRIPTION in the working directory, so extract the dependency
+# names and hand them to `uvr add`.
+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')" \
+  && cd /uvr && xargs -r uvr add --no-install < /tmp/deps.txt \
+  && uvr sync --install-system-deps
 
 RUN R CMD INSTALL --no-docs --without-keep.source  .
 
 # install shiny app deps
-RUN R -q -e "install.packages('renv'); pkgs <- renv::dependencies('/app/app.R')[['Package']]; pkgs = setdiff(pkgs, 'bincraft'); pak::pak(pkgs)"
+RUN R -q -e "install.packages('renv'); pkgs <- renv::dependencies('/app/app.R')[['Package']]; pkgs = setdiff(pkgs, 'bincraft'); writeLines(pkgs, '/tmp/app-deps.txt')" \
+  && cd /uvr && xargs -r uvr add --no-install < /tmp/app-deps.txt \
+  && uvr sync --install-system-deps
 
 ENV PGPASS=""
 

docker/build-one.Dockerfile

@@ -17,7 +17,10 @@ ARG CACHEBUST
 WORKDIR /work
 COPY build-one.R /work/build-one.R
 # Resolve and install the latest bincraft release dynamically (no hardcoded pin).
+# uvr-install.sh lands under /work/local/ because install-bincraft.R looks for it
+# there when the working directory is not a repo checkout.
 COPY install-bincraft.R /work/install-bincraft.R
+COPY uvr-install.sh /work/local/uvr-install.sh
 # Ship the patch registry so build-one.R's `patches = "local/patches"` resolves
 # (build context is `local/`, CWD is /work).
 COPY patches /work/local/patches

docker/reprex/alpine.sh

@@ -1,10 +1,14 @@
 docker run --rm -it --platform linux/arm64 alpine sh
 
-apk add --no-cache R R-dev g++
+apk add --no-cache R R-dev g++ curl ca-certificates
 
-R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
+curl -fsSL https://raw.githubusercontent.com/nbafrank/uvr/main/install.sh | UVR_INSTALL_DIR=/usr/local/bin sh
 
-R -q -e 'pak::pak(c("gert", "purrr"))'
+# `uvr add` always writes to .uvr/library/; only `uvr sync` honours UVR_LIBRARY,
+# so add without installing and let the sync place the packages.
+export UVR_LIBRARY=/usr/lib/R/library
+mkdir -p /uvr && cd /uvr && uvr init --here
+uvr add --no-install gert purrr && uvr sync --install-system-deps
 
 R
 
@@ -22,14 +26,20 @@ unlink(sprintf("%s/%s", tempdir(), "tmp1"), force = TRUE, recursive = TRUE)
 tag <- all_tags$name
 package_name <- rep(package_name, length(tag))
 
+# uvr has no `pak::local_install_deps()`; read the DESCRIPTION of the checkout
+# and `uvr add` the dependency names instead.
 purrr::walk2(package_name[1], tag, \(x, y) {
   print(y)
   system("git config --global advice.detachedHead false")
+  src <- sprintf("/tmp/%s_%s", x[1], y)
   system2("git", args = c(
     "clone", "-q", sprintf("--branch=%s", tail(y, 1)),
-    sprintf("https://github.com/cran/%s", x[1]), sprintf("/tmp/%s_%s", x[1], y)
+    sprintf("https://github.com/cran/%s", x[1]), src
   ))
-  pak::local_install_deps(sprintf("/tmp/%s_%s", x[1], y))
+  d <- read.dcf(file.path(src, "DESCRIPTION"))
+  f <- intersect(colnames(d), c("Depends", "Imports", "LinkingTo"))
+  deps <- trimws(sub("[(].*", "", unlist(strsplit(paste(d[, f], collapse = ","), ","))))
+  deps <- setdiff(deps[nzchar(deps)], "R")
+  system2("uvr", c("add", "--no-install", deps))
+  system2("uvr", c("sync", "--install-system-deps"))
 })
-
-