fix(index): add a slot repair for a broken Built stamp and retire alpine 3.21
`arm64/alpine321` (22,930 entries) and `arm64/alpine322` (24,696 entries) advertise `Built: R <ver>; NA; ...`. uvr matches the stamp's platform triple plus R minor to pick binary over source, so no client matches those slots and both silently serve as source-only, which is the regression the stamp was added to prevent. The tarballs themselves carry the correct triple; only the index is wrong. Re-running the normal index update does not fix it: `upload_package_index()` reuses the slot's remote `PACKAGES.db` and cranlike's `update_db()` only reparses files whose md5 changed. Dropping `PACKAGES.db` to force a full reparse does work, but for an S3 repo cranlike reads each package's metadata from the CRAN source mirror on GitHub, so a 25k-entry slot means 25k requests to raw.githubusercontent.com and a real risk of being rate-limited part-way. Only the `Built` column is wrong, so correct it in place: patch the column in `PACKAGES.db`, put it back, and let `upload_package_index()` re-emit `PACKAGES*` from it. `update_db()` always rewrites the index files even when nothing was reparsed, so no tarball is re-read and nothing is fetched from GitHub. Alpine 3.21 is EOL: the website advertises only 3.23/3.24 and `process-updates.yaml` dropped it, so remove its two leftover matrix entries from the archive pipeline rather than repairing that slot.
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local/repair-built-stamp.R
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175
local/repair-built-stamp.R
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#!/usr/bin/env Rscript
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### Rewrite a broken `Built` stamp across one arch/codename slot.
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###
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### A slot's index can end up advertising a stamp whose platform triple is
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### unusable, e.g. `Built: R 4.5.0; NA; ...`. uvr picks binary vs source by
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### matching that triple plus the R minor, so no client matches it and the whole
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### slot silently reverts to source-only, which makes uvr compile everything and
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### fail wherever a system `-dev` library is missing.
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###
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### Rewriting it is not a matter of re-running the normal index update.
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### `upload_package_index()` reuses the slot's remote `PACKAGES.db`, and
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### cranlike's `update_db()` only reparses files whose md5 changed, so entries
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### already in the database keep the stamp they were written with. Dropping
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### `PACKAGES.db` to force a full reparse does work, but for an S3 repo cranlike
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### reads each package's metadata from the CRAN *source* mirror on GitHub, so a
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### 25k-entry slot means 25k requests to raw.githubusercontent.com and a real
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### risk of being rate-limited part-way through.
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###
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### Only the `Built` column is wrong, so correct it in place instead: patch the
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### column in `PACKAGES.db`, put the database back, and let
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### `upload_package_index()` re-emit `PACKAGES*` from it. `update_db()` always
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### rewrites the index files even when nothing was reparsed, so no tarball is
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### re-read and nothing is fetched from GitHub.
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###
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### The replacement comes from `bincraft::built_stamp()` under the R running
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### this script, so run it under the R version the slot should advertise (the
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### `R_VERSION` its entry in `.crow/process-updates.yaml` uses). That is what a
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### healthy `upload_package_index()` run would have written.
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###
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### Usage, inside the platform's build image:
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### Rscript local/repair-built-stamp.R <arch> [--apply]
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###
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### Without `--apply` it reports what it would change and touches nothing.
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suppressPackageStartupMessages({
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library(bincraft)
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})
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args <- commandArgs(trailingOnly = TRUE)
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arch <- args[1L]
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apply_changes <- "--apply" %in% args
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if (is.na(arch) || !nzchar(arch)) {
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stop(
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"Usage: Rscript local/repair-built-stamp.R <arch> [--apply]",
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call. = FALSE
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)
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}
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bucket <- "devxy-rpkgs-binaries"
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endpoint <- "https://s3.eu-central-003.backblazeb2.com"
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region <- "eu-central-003"
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codename <- bincraft::set_codename(NULL)
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if (is.null(codename) || is.na(codename) || !nzchar(codename)) {
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stop(
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"Could not detect a codename from /etc/os-release; run this in a build image.",
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call. = FALSE
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)
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}
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# built_stamp() refuses an unusable platform, so a broken build image fails here
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# rather than writing a second bad stamp over the first one.
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stamp <- bincraft::built_stamp()
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message(sprintf("Slot: %s/%s", arch, codename))
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message(sprintf("New stamp: %s", stamp))
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s3fs::s3_file_system(
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aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"),
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aws_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"),
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endpoint = endpoint,
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region_name = region,
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refresh = TRUE
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)
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base_dir <- file.path(bucket, arch, codename, "latest", "src", "contrib")
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# A stamp is broken when its platform component is absent or literally "NA".
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broken_stamp_where <- paste(
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"Built IS NULL",
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"OR Built LIKE '%; NA;%'",
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"OR Built LIKE '%; ;%'"
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)
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# The generic slot plus every per-minor sub-slot, which carry the same stamp and
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# are poisoned by the same run.
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r_minors <- sub(
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"^.*/R/([0-9]+\\.[0-9]+)\\.[0-9]+$",
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"\\1",
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list.dirs("/opt/R", recursive = FALSE)
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)
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r_minors <- unique(grep("^[0-9]+\\.[0-9]+$", r_minors, value = TRUE))
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slots <- c(base_dir, file.path(base_dir, r_minors))
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repair_slot <- function(slot) {
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db_remote <- file.path(slot, "PACKAGES.db")
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if (!s3fs::s3_file_exists(db_remote)) {
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message(sprintf(" %s: no PACKAGES.db, skipping", slot))
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return(invisible(NULL))
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}
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db_local <- tempfile(fileext = ".db")
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s3fs::s3_file_download(db_remote, db_local, overwrite = TRUE)
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con <- DBI::dbConnect(RSQLite::SQLite(), db_local)
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on.exit(DBI::dbDisconnect(con), add = TRUE)
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total <- DBI::dbGetQuery(con, "SELECT COUNT(*) AS n FROM packages")$n
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broken <- DBI::dbGetQuery(
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con,
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sprintf("SELECT COUNT(*) AS n FROM packages WHERE %s", broken_stamp_where)
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)$n
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message(sprintf(" %s: %s entries, %s broken", slot, total, broken))
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if (broken == 0L) {
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return(invisible(NULL))
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}
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if (!apply_changes) {
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message(" (dry run, pass --apply to rewrite)")
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return(invisible(NULL))
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}
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DBI::dbExecute(
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con,
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sprintf("UPDATE packages SET Built = ? WHERE %s", broken_stamp_where),
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params = list(stamp)
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)
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DBI::dbDisconnect(con)
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on.exit()
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s3fs::s3_file_upload(db_local, db_remote, overwrite = TRUE)
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message(sprintf(" rewrote %s entries and uploaded PACKAGES.db", broken))
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invisible(NULL)
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}
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invisible(lapply(slots, repair_slot))
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if (!apply_changes) {
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message("Dry run complete; nothing was changed.")
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quit(save = "no")
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}
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# Re-emit PACKAGES/PACKAGES.gz/PACKAGES.rds from the corrected database. Nothing
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# is reparsed, because no tarball's md5 changed.
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message("Re-emitting index files from the corrected database...")
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bincraft::upload_package_index(
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codename = codename,
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s3_endpoint = endpoint,
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s3_region = region,
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s3_bucket = bucket,
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s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"),
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s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY")
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)
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for (minor in r_minors) {
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try(
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bincraft::upload_package_index(
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codename = codename,
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r_minor = minor,
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s3_endpoint = endpoint,
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s3_region = region,
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s3_bucket = bucket,
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s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"),
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s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY")
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),
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silent = FALSE
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)
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}
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message("Done. Verify with:")
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message(sprintf(
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" curl -sS https://cran.devxy.io/%s/%s/latest/src/contrib/PACKAGES | grep '^Built:' | sort | uniq -c",
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arch,
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codename
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))
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