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:
parent
fe2289af56
commit
f3c18b6805
7 changed files with 327 additions and 245 deletions
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@ -27,7 +27,9 @@ package_cache_files <- c(
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"/mnt/cache/packages/s3_cache.rds"
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)
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if (!all(file.exists(package_cache_files))) {
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message("Package snapshot missing from cache; recomputing via packages-to-build.R")
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message(
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"Package snapshot missing from cache; recomputing via packages-to-build.R"
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)
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dir.create("/mnt/cache/packages", showWarnings = FALSE, recursive = TRUE)
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save_rds_atomic <- function(obj, path) {
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tmp <- paste0(path, ".tmp.", Sys.getpid())
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@ -36,7 +38,10 @@ if (!all(file.exists(package_cache_files))) {
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}
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source(file.path("local", "packages-to-build.R"))
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save_rds_atomic(pkgs, "/mnt/cache/packages/pkgs_to_build.rds")
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save_rds_atomic(pkgs[r_minor_sensitive == TRUE], "/mnt/cache/packages/r_minor_sensitive_pkgs.rds")
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save_rds_atomic(
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pkgs[r_minor_sensitive == TRUE],
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"/mnt/cache/packages/r_minor_sensitive_pkgs.rds"
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)
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message("Package snapshot recomputed.")
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}
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@ -112,20 +117,22 @@ built <- DBI::dbGetQuery(
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)
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DBI::dbDisconnect(con)
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before <- nrow(chunk)
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chunk <- chunk[!paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag), ]
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sprintf("Skipped %d already-attempted package versions; %d remaining for this job", before - nrow(chunk), nrow(chunk))
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chunk <- chunk[
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!paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag),
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]
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sprintf(
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"Skipped %d already-attempted package versions; %d remaining for this job",
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before - nrow(chunk),
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nrow(chunk)
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)
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# Read pre-computed S3 listing from install-deps step
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# This avoids loading s3fs/reticulate/Python in the build container,
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# saving significant memory for pak subprocess forks
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# saving significant memory for the dependency-installer subprocesses
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s3_cache <- readRDS("/mnt/cache/packages/s3_cache.rds")
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sprintf("S3 cache: %s files", length(s3_cache))
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n <- nrow(chunk)
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# Every `trim_every` packages, bound the pkgcache _metadata dir so a full-platform
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# run does not accumulate thousands of ~70 MB snapshots and fill the host disk.
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# No-op on amd64 (R_PKG_CACHE_DIR is empty / cache not persisted).
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trim_every <- 25L
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mapply(
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function(pkg, ver, sens, i) {
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cat(sprintf("[%d/%d] %s_%s (r_minor_sensitive=%s)\n", i, n, pkg, ver, sens))
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@ -151,12 +158,6 @@ mapply(
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upload = TRUE,
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store_build_metadata = TRUE
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)
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if (i %% trim_every == 0L) {
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removed <- trim_pkgcache_metadata()
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if (removed > 0L) {
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cat(sprintf(" [pkgcache trim] removed %d stale _metadata entries\n", removed))
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}
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}
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},
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chunk$Package,
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chunk$Version,
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@ -11,10 +11,11 @@
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#
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# How it works: list the remote tags with `git ls-remote` (no token needed for
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# the public repo), keep the `vX.Y.Z` release tags, pick the highest version,
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# and install it with pak. pak is idempotent on the git ref, so re-running keeps
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# the package when it is already current and only updates when a newer tag ships.
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# Filtering/sorting is done in R (not via git's `--sort`/refspec) so behaviour is
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# identical across git versions and `system2()` argument handling.
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# and install it with uvr via `local/uvr-install.sh`. uvr is idempotent on the
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# git ref, so re-running keeps the package when it is already current and only
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# updates when a newer tag ships. Filtering/sorting is done in R (not via git's
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# `--sort`/refspec) so behaviour is identical across git versions and
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# `system2()` argument handling.
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repo_url <- Sys.getenv(
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"BINCRAFT_GIT_URL",
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@ -44,7 +45,43 @@ latest <- tags[order(package_version(sub("^v", "", tags)), decreasing = TRUE)][
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]
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message(sprintf("Installing latest bincraft release: %s", latest))
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pak::pak(sprintf("git::%s@%s", repo_url, latest))
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# uvr addresses Forgejo repos as `forgejo::host/owner/repo@ref` rather than as a
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# git URL, so drop the scheme and the trailing `.git` from `repo_url`.
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spec <- sprintf(
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"forgejo::%s@%s",
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sub("\\.git$", "", sub("^[a-z]+://", "", repo_url)),
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latest
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)
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# `local/uvr-install.sh` when run from the repo root, `/work/local/` in the
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# build-one image, which copies the two scripts into a flatter layout.
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helper <- Sys.getenv("UVR_INSTALL_SH", unset = "")
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if (!nzchar(helper)) {
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candidates <- c("local/uvr-install.sh", "/work/local/uvr-install.sh")
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found <- candidates[file.exists(candidates)]
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if (length(found) == 0L) {
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stop("Could not locate uvr-install.sh; set UVR_INSTALL_SH", call. = FALSE)
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}
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helper <- found[1L]
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}
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# Point uvr at the R running this script and at the library it would install
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# into, so the per-R-minor passes in the build pipelines (which call a different
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# Rscript with R_LIBS_USER pointed elsewhere) target their own R and library.
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Sys.setenv(
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UVR_R_BIN = file.path(R.home("bin"), "R"),
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UVR_TARGET_LIB = .libPaths()[1L]
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)
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status <- system2(helper, shQuote(spec))
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if (!identical(status, 0L)) {
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stop(
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sprintf("uvr failed to install %s (exit %s)", spec, status),
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call. = FALSE
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)
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}
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message(sprintf(
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"bincraft %s installed (%s)",
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as.character(utils::packageVersion("bincraft")),
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@ -15,15 +15,15 @@ suppressPackageStartupMessages(library(data.table))
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# Sys.setenv("OS_VERSION" = "3.22")
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# Sys.setenv("ARCH" = "arm64")
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arch = Sys.getenv("ARCH")
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arch <- Sys.getenv("ARCH")
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# target: alpine-322, ubuntu-2404, redhat-9, etc.
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platform = paste(
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platform <- paste(
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Sys.getenv("OS"),
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gsub("[.]", "", Sys.getenv("OS_VERSION")),
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sep = "-"
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)
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# Use bincraft's codename detection for S3 paths (e.g. "rhel10" not "redhat10")
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codename = bincraft::set_codename(NULL)
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codename <- bincraft::set_codename(NULL)
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con <- DBI::dbConnect(
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RPostgres::Postgres(),
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@ -35,8 +35,8 @@ con <- DBI::dbConnect(
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sslmode = "require"
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)
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cran_archive = tools::CRAN_archive_db()
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cran_release = tools::CRAN_package_db()
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cran_archive <- tools::CRAN_archive_db()
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cran_release <- tools::CRAN_package_db()
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# Subset cran_archive to only those packages
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cran_archive_in_release <- cran_archive[
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names(cran_archive) %in% cran_release$Package
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@ -84,13 +84,14 @@ s3fs::s3_file_system(
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region_name = "eu-central-003",
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refresh = TRUE
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)
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s3_pkgs = s3fs::s3_dir_ls(
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s3_pkgs <- s3fs::s3_dir_ls(
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sprintf("devxy-rpkgs-binaries/%s/%s/latest/src/contrib", arch, codename),
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recurse = TRUE
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)
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# Save the raw S3 file listing for the build step to use as s3_package_cache
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# This avoids loading s3fs/reticulate in the build container, saving memory for pak forks
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# This avoids loading s3fs/reticulate in the build container, saving memory for
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# the dependency-installer subprocesses
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saveRDS(basename(s3_pkgs), "/mnt/cache/packages/s3_cache.rds")
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file_names <- basename(s3_pkgs)
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@ -31,42 +31,3 @@ parse_build_args <- function(args) {
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ncpus = as.integer(pos[3L])
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)
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}
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# Bound the {pkgcache} metadata dir, which otherwise grows without limit: the
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# "patched" repo mints a new content hash on every PACKAGES change, so each build
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# writes a fresh ~70 MB _metadata/pkgs-<hash>.rds (+ patched-<hash>/) that is
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# never reused. Keep the `keep` newest entries by mtime; only remove entries
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# older than `min_age_secs`, so a concurrent split-job's in-flight files are
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# never deleted (each build uses a unique hash, so aged entries are
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# unreferenced). Stable repo dirs (CRAN-*, BioC*, INLA-*) and pkg/ downloads are
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# not matched and thus preserved. Returns the number of entries removed.
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trim_pkgcache_metadata <- function(cache_dir = Sys.getenv("R_PKG_CACHE_DIR"),
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keep = 20L,
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min_age_secs = 600) {
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meta <- file.path(cache_dir, "R", "pkgcache", "_metadata")
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if (!nzchar(cache_dir) || !dir.exists(meta)) {
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return(0L)
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}
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entries <- c(
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Sys.glob(file.path(meta, "patched-*")),
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Sys.glob(file.path(meta, "pkgs-*.rds"))
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)
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if (length(entries) == 0L) {
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return(0L)
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}
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info <- file.info(entries)
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order_new_first <- order(info$mtime, decreasing = TRUE)
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ranked <- entries[order_new_first]
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ranked_mtime <- info$mtime[order_new_first]
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if (length(ranked) <= keep) {
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return(0L)
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}
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candidates <- ranked[(keep + 1L):length(ranked)]
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candidate_age <- as.numeric(Sys.time()) - as.numeric(ranked_mtime[(keep + 1L):length(ranked)])
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removable <- candidates[candidate_age >= min_age_secs]
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if (length(removable) == 0L) {
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return(0L)
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}
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unlink(removable, recursive = TRUE, force = TRUE)
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length(removable)
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}
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@ -1,22 +1,28 @@
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install.packages(
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"pak",
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repos = sprintf(
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"https://r-lib.github.io/p/pak/stable/%s/%s/%s",
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.Platform$pkgType,
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R.Version()$os,
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R.Version()$arch
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# Installs every CRAN package one by one and checks that it loads. Dependencies
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# go through uvr via local/uvr-install.sh, which bootstraps the uvr binary on
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# first use and installs into .libPaths()[1].
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uvr_install <- function(pkg) {
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Sys.setenv(
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UVR_R_BIN = file.path(R.home("bin"), "R"),
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UVR_TARGET_LIB = .libPaths()[1L]
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)
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)
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status <- system2("local/uvr-install.sh", shQuote(pkg))
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if (!identical(status, 0L)) {
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stop(
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sprintf("uvr failed to install %s (exit %s)", pkg, status),
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call. = FALSE
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)
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}
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}
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Sys.setenv(PKG_SYSREQS = TRUE)
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all_pkgs <- rownames(available.packages())
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to_skip = c("ABRSQOL", "ACA", "ACE.CoCo")
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all_pkgs = setdiff(all_pkgs, to_skip)
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to_skip <- c("ABRSQOL", "ACA", "ACE.CoCo")
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all_pkgs <- setdiff(all_pkgs, to_skip)
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for (i in all_pkgs) {
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message(sprintf("\nInstalling %s", i))
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pak::pkg_install(i)
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uvr_install(i)
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library(i, character.only = TRUE)
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}
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@ -323,7 +329,7 @@ if (length(to_process) == 0) {
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} else {
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for (i in to_process) {
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message(sprintf("\nInstalling %s", i))
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pak::pkg_install(i)
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uvr_install(i)
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library(i, character.only = TRUE)
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}
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# Update to_skip to include all up to the last processed
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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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90
local/uvr-install.sh
Executable file
90
local/uvr-install.sh
Executable file
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@ -0,0 +1,90 @@
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#!/bin/sh
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# Install R packages into the CI library with uvr (https://github.com/nbafrank/uvr).
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#
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# Usage:
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# local/uvr-install.sh httr2 jsonlite
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# local/uvr-install.sh forgejo::codefloe.com/rpkgs/bincraft@v4.4.3
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#
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# Replaces `pak::pak(...)`. uvr is project-scoped: `uvr add` refuses to run
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# outside a project and always writes to `.uvr/library/`, and only
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# `uvr sync --library` can target an existing library. The project is therefore
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# minted in a scratch directory under TMPDIR and thrown away afterwards; that
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# also keeps `uvr init`'s `.Rprofile` out of the repo checkout, where it would
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# hijack `.libPaths()` for every other R call in the pipeline.
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#
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# Pruning is a no-op here: uvr disables it whenever `--library` is passed,
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# precisely because such a target may be shared (`/mnt/cache/R-pkgs` holds
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# bincraft and its dependencies alongside whatever this script installs).
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#
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# System dependencies come from uvr's vendored r-system-requirements rules, so
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# `pak::sysreqs_db_update()` and `PKG_SYSREQS_PLATFORM` are no longer needed.
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#
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# Environment:
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# UVR_R_BIN R interpreter to install for; set by install-bincraft.R so
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# the per-R-minor passes target their own R, not the primary
|
||||
# R_VERSION fallback interpreter selector (/opt/R/<version>/bin/R)
|
||||
# UVR_TARGET_LIB target library; defaults to R_LIBS_USER, then to the
|
||||
# active R's .libPaths()[1] (which is where pak wrote)
|
||||
# UVR_INSTALL_DIR where the uvr binary lands (default /usr/local/bin)
|
||||
|
||||
set -eu
|
||||
|
||||
# renovate: datasource=github-releases depName=nbafrank/uvr
|
||||
UVR_PIN="v0.4.4"
|
||||
|
||||
if [ "$#" -eq 0 ]; then
|
||||
echo "usage: $0 <pkg-spec>..." >&2
|
||||
exit 2
|
||||
fi
|
||||
|
||||
# The build images keep R under /opt/R/<version> and off PATH. uvr resolves the
|
||||
# interpreter via PATH and never downloads one unless `uvr r install` is run, so
|
||||
# put the requested R first.
|
||||
r_bin="${UVR_R_BIN:-}"
|
||||
if [ -z "$r_bin" ] && [ -n "${R_VERSION:-}" ] && [ -x "/opt/R/${R_VERSION}/bin/R" ]; then
|
||||
r_bin="/opt/R/${R_VERSION}/bin/R"
|
||||
fi
|
||||
if [ -n "$r_bin" ]; then
|
||||
PATH="$(dirname "$r_bin"):$PATH"
|
||||
export PATH
|
||||
else
|
||||
r_bin="$(command -v R)"
|
||||
fi
|
||||
|
||||
target_lib="${UVR_TARGET_LIB:-${R_LIBS_USER:-}}"
|
||||
if [ -z "$target_lib" ]; then
|
||||
target_lib="$("$r_bin" --no-echo --no-save -e 'cat(.libPaths()[1])')"
|
||||
fi
|
||||
if [ -z "$target_lib" ]; then
|
||||
echo "error: could not determine a target library; set UVR_TARGET_LIB" >&2
|
||||
exit 2
|
||||
fi
|
||||
mkdir -p "$target_lib"
|
||||
|
||||
# Pin the manifest to the active R so the lockfile's R stays in step with the
|
||||
# library's R sentinel. Without that, uvr can decide the library is ABI-stale
|
||||
# and wipe it -- and this target is shared with bincraft. uvr only discovers R
|
||||
# via PATH/R_HOME (it does not scan /opt/R), so the R put on PATH above is the
|
||||
# only candidate this constraint can resolve to.
|
||||
# shellcheck disable=SC2016 # $major/$minor are R expressions, not shell vars
|
||||
r_full="$("$r_bin" --no-echo --no-save -e 'cat(paste(R.version$major, R.version$minor, sep = "."))')"
|
||||
|
||||
install_dir="${UVR_INSTALL_DIR:-/usr/local/bin}"
|
||||
uvr_bin="${install_dir}/uvr"
|
||||
if [ ! -x "$uvr_bin" ]; then
|
||||
echo "Bootstrapping uvr ${UVR_PIN} into ${install_dir}"
|
||||
UVR_INSTALL_DIR="$install_dir" UVR_VERSION="$UVR_PIN" \
|
||||
sh -c 'curl -fsSL https://raw.githubusercontent.com/nbafrank/uvr/main/install.sh | sh'
|
||||
fi
|
||||
|
||||
project_dir="${TMPDIR:-/tmp}/uvr-ci-$$"
|
||||
rm -rf "$project_dir"
|
||||
mkdir -p "$project_dir"
|
||||
trap 'rm -rf "$project_dir"' EXIT
|
||||
cd "$project_dir"
|
||||
|
||||
"$uvr_bin" init --here --r-version "$r_full"
|
||||
# --no-install: resolve and lock only. The install happens in the sync below,
|
||||
# which is the only command that honours --library.
|
||||
"$uvr_bin" add --no-install "$@"
|
||||
"$uvr_bin" sync --library "$target_lib" --install-system-deps
|
||||
Loading…
Reference in a new issue