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
This commit is contained in:
Patrick Schratz 2026-07-31 12:16:32 +00:00
commit f3c18b6805
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@ -1,22 +1,28 @@
install.packages(
"pak",
repos = sprintf(
"https://r-lib.github.io/p/pak/stable/%s/%s/%s",
.Platform$pkgType,
R.Version()$os,
R.Version()$arch
# Installs every CRAN package one by one and checks that it loads. Dependencies
# go through uvr via local/uvr-install.sh, which bootstraps the uvr binary on
# first use and installs into .libPaths()[1].
uvr_install <- function(pkg) {
Sys.setenv(
UVR_R_BIN = file.path(R.home("bin"), "R"),
UVR_TARGET_LIB = .libPaths()[1L]
)
)
status <- system2("local/uvr-install.sh", shQuote(pkg))
if (!identical(status, 0L)) {
stop(
sprintf("uvr failed to install %s (exit %s)", pkg, status),
call. = FALSE
)
}
}
Sys.setenv(PKG_SYSREQS = TRUE)
all_pkgs <- rownames(available.packages())
to_skip = c("ABRSQOL", "ACA", "ACE.CoCo")
all_pkgs = setdiff(all_pkgs, to_skip)
to_skip <- c("ABRSQOL", "ACA", "ACE.CoCo")
all_pkgs <- setdiff(all_pkgs, to_skip)
for (i in all_pkgs) {
message(sprintf("\nInstalling %s", i))
pak::pkg_install(i)
uvr_install(i)
library(i, character.only = TRUE)
}
@ -323,7 +329,7 @@ if (length(to_process) == 0) {
} else {
for (i in to_process) {
message(sprintf("\nInstalling %s", i))
pak::pkg_install(i)
uvr_install(i)
library(i, character.only = TRUE)
}
# Update to_skip to include all up to the last processed