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
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1 changed files with 327 additions and 245 deletions
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@ -1,68 +0,0 @@
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source(file.path("..", "r-minor-helpers.R"))
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# Build a fake _metadata dir under a temp R_PKG_CACHE_DIR. Each entry's mtime is
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# set to `age_secs` in the past so we can exercise the age gate deterministically.
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make_meta <- function(patched = 0L, pkgs = 0L, keep_repos = TRUE, age_secs = 3600) {
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root <- tempfile("pkgcache-")
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meta <- file.path(root, "R", "pkgcache", "_metadata")
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dir.create(meta, recursive = TRUE)
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old <- Sys.time() - age_secs
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mk_dir <- function(p) { dir.create(p); Sys.setFileTime(p, old); p }
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mk_file <- function(p) { writeLines("x", p); Sys.setFileTime(p, old); p }
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for (i in seq_len(patched)) mk_dir(file.path(meta, sprintf("patched-%03d", i)))
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for (i in seq_len(pkgs)) mk_file(file.path(meta, sprintf("pkgs-%03d.rds", i)))
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if (keep_repos) {
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mk_dir(file.path(meta, "CRAN-075c426938"))
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mk_dir(file.path(meta, "BioCsoft-1ac964ed6c"))
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mk_file(file.path(meta, "bioc-sysreqs.dcf.gz"))
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mk_dir(file.path(root, "R", "pkgcache", "pkg")) # downloads, must survive
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}
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root
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}
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n_churn <- function(root) {
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meta <- file.path(root, "R", "pkgcache", "_metadata")
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length(Sys.glob(file.path(meta, "patched-*"))) +
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length(Sys.glob(file.path(meta, "pkgs-*.rds")))
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}
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test_that("empty cache_dir is a no-op", {
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expect_identical(trim_pkgcache_metadata("", keep = 5L, min_age_secs = 0), 0L)
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})
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test_that("missing _metadata dir is a no-op", {
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expect_identical(
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trim_pkgcache_metadata(tempfile("absent-"), keep = 5L, min_age_secs = 0),
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0L
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)
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})
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test_that("fewer than keep entries removes nothing", {
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root <- make_meta(patched = 2L, pkgs = 2L)
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expect_identical(trim_pkgcache_metadata(root, keep = 20L, min_age_secs = 0), 0L)
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expect_identical(n_churn(root), 4L)
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})
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test_that("trims down to keep newest, leaving churn == keep", {
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root <- make_meta(patched = 30L, pkgs = 30L) # 60 churn entries, all old
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removed <- trim_pkgcache_metadata(root, keep = 20L, min_age_secs = 0)
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expect_identical(removed, 40L)
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expect_identical(n_churn(root), 20L)
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})
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test_that("entries younger than min_age_secs are protected", {
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root <- make_meta(patched = 30L, pkgs = 0L, keep_repos = FALSE, age_secs = 60)
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# keep=5 would drop 25, but all are 60s old < 600s gate -> nothing removed
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expect_identical(trim_pkgcache_metadata(root, keep = 5L, min_age_secs = 600), 0L)
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expect_identical(n_churn(root), 30L)
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})
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test_that("stable repo dirs and pkg downloads are never touched", {
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root <- make_meta(patched = 30L, pkgs = 30L)
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trim_pkgcache_metadata(root, keep = 0L, min_age_secs = 0)
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meta <- file.path(root, "R", "pkgcache", "_metadata")
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expect_true(dir.exists(file.path(meta, "CRAN-075c426938")))
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expect_true(dir.exists(file.path(meta, "BioCsoft-1ac964ed6c")))
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expect_true(file.exists(file.path(meta, "bioc-sysreqs.dcf.gz")))
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expect_true(dir.exists(file.path(root, "R", "pkgcache", "pkg")))
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})
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