From 4bca17e4acae7abea58e478ac56f1725b90cb5dc Mon Sep 17 00:00:00 2001 From: pat-s Date: Wed, 15 Jul 2026 08:28:15 +0000 Subject: [PATCH 01/53] feat(local): auto-apply registry patches with a build-env trial-build gate (#124) Closes the classifier loop (issue #115, step 3): turns the auto-proposable candidates into an actual PR, gated by a real trial build **in our own build-env images**. Chosen model (from the design discussion): **autonomous PR**, **PR-first with a CI trial-build gate**, **bounded top-N batch** per run. ## Creating the patch PR - `propose-patches.R` gains: - `--limit N` -- act on the top-N candidates by failure volume; the rest defer to the next run (logged). - `--open-pr` -- write the entries onto the reused `auto/registry-patch-proposals` branch, push (with `REPO_RW_TOKEN`), and open/update **one** PR via the Forgejo API (so re-runs update the same PR instead of piling up). - `.crow/auto-apply-patches.yaml` -- a single job that runs `--open-pr --limit` on a cron/manual trigger. Needs `FORGEJO_TOKEN` + a write-scoped `REPO_RW_TOKEN`. Novel source diffs and unknown signatures are still never proposed; nothing merges. ## The merge gate (our build-env images) - `.crow/trial-build-registry.yaml` -- matrixed over the real `OS/IMG` build-env matrix (alpine:3.24, redhat:8/9/10, ubuntu:jammy/noble/**resolute** for ubuntu-2604). Each platform runs `local/trial-build-registry.R`, which diffs the branch registry against `main` and trial-builds **only the entries the branch adds** that apply to that platform, inside `reg.devxy.io/rpkgs/build-env-*`. Green only if every new entry builds; a platform with no new entries is a fast no-op. Nothing is uploaded/archived/recorded. - The base-registry read **fails loud** if it can't read `registry.json` at `main`, rather than silently treating the base as empty and trial-building the whole registry. ## Notes / follow-up - The repo uses **no `pull_request` triggers**, so the gate runs manually or on a cron against the branch (`--var patch_branch=...`). Wiring it to fire automatically on the PR needs `event: pull_request` enabled on the Forgejo webhook -- a one-line addition once that's on. - Two new crons to register in the crow UI: `auto-apply-patches` and `trial-build-registry`. New secret needed: `REPO_RW_TOKEN` (write scope) for the push. ## Verification - New pure helpers `entry_applies_to_os()` / `new_registry_packages()` covered by tests (platform codename/family/wildcard matching; added-vs-unchanged entry detection; per-platform filtering). - `--limit` smoke (stubbed DB): top-2 by volume proposed, 3 deferred, candidate registry validates. - Full suite: 105 tests pass; all pre-commit hooks pass (air, prettier, markdownlint, yamllint, validate-patches). Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/124 --- .crow/auto-apply-patches.yaml | 65 ++++++++ .crow/trial-build-registry.yaml | 140 +++++++++++++++++ local/patches/README.md | 13 ++ local/proposal-tracking-lib.R | 33 ++++ local/propose-patches.R | 188 ++++++++++++++++++++++- local/tests/test-proposal-tracking-lib.R | 51 ++++++ local/trial-build-registry.R | 145 +++++++++++++++++ 7 files changed, 633 insertions(+), 2 deletions(-) create mode 100644 .crow/auto-apply-patches.yaml create mode 100644 .crow/trial-build-registry.yaml create mode 100644 local/trial-build-registry.R diff --git a/.crow/auto-apply-patches.yaml b/.crow/auto-apply-patches.yaml new file mode 100644 index 0000000..15cc1ee --- /dev/null +++ b/.crow/auto-apply-patches.yaml @@ -0,0 +1,65 @@ +# Auto-apply registry patches (issue #115, step 3 automation). +# Classifies `single_builds` failures and, for the top-N auto-proposable +# candidates by failure volume, writes the registry entries onto the reused +# `auto/registry-patch-proposals` branch and opens/updates a single PR. +# Nothing merges: the `trial-build-registry` pipeline is the merge gate, and a +# human reviews the PR. Novel source diffs / unknown signatures are never +# proposed. Global across platforms, so a single job -- no matrix. +# +# Needs a write token (REPO_RW_TOKEN) to push and FORGEJO_TOKEN to open the PR. +# Register the `auto-apply-patches` cron in the crow UI, or run manually: +# woodpecker-cli pipeline create --var task=auto-apply-patches --branch=main 7 +variables: + patch_limit: + description: 'Max candidates to propose per run (top by failure volume).' + default: '10' + +when: + - event: manual + evaluate: 'task == "auto-apply-patches"' + - event: cron + cron: auto-apply-patches + +skip_clone: true + +labels: + group: rpkgs-amd64 + +steps: + - name: 'Auto-apply registry patches' + image: reg.devxy.io/rpkgs/build-env-alpine:3.24 + pull: true + environment: + PGPASS: + from_secret: PGPASS + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + REPO_RW_TOKEN: + from_secret: REPO_RW_TOKEN + FORGEJO_TOKEN: + from_secret: FORGEJO_TOKEN + GIT_USER: devxy-bot + GIT_EMAIL: bot@devxy.io + PATCH_LIMIT: ${patch_limit} + R_VERSION: 4.5.3 + R_LIBS_USER: /mnt/cache/R-pkgs + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - mkdir -p /mnt/cache/R-pkgs + - rm -rf /mnt/cache/R-pkgs/00LOCK-* + - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))' + - /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-pr --limit $PATCH_LIMIT + backend_options: + kubernetes: + resources: + requests: + memory: 1Gi + cpu: 2000m + limits: + memory: 2Gi + cpu: 2000m + tolerations: + - key: 'CI' + operator: 'Equal' + value: 'true' + effect: 'NoSchedule' diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml new file mode 100644 index 0000000..1ac71e8 --- /dev/null +++ b/.crow/trial-build-registry.yaml @@ -0,0 +1,140 @@ +# Merge gate for the auto-patch PR (issue #115, step 3). +# For each platform, trial-builds every registry entry the auto-patch branch +# ADDS (vs main) in that platform's own `reg.devxy.io/rpkgs/build-env-*` image, +# with the registry applied. A row with no new entries for its platform is a +# fast no-op. The pipeline is green only if every new entry builds, so it gates +# the PR before merge. Nothing is uploaded/archived/recorded. +# +# The repo uses no `pull_request` triggers, so this runs manually against the +# branch (or on a cron); point it at the auto-patch branch via `patch_branch`: +# woodpecker-cli pipeline create --var task=trial-build-registry \ +# --var patch_branch=auto/registry-patch-proposals --branch=main 7 +variables: + patch_branch: + description: 'Branch whose new registry entries to trial-build.' + default: auto/registry-patch-proposals + +when: + - event: manual + evaluate: 'task == "trial-build-registry"' + - event: cron + cron: trial-build-registry + +skip_clone: true + +labels: + group: rpkgs-${ARCH} + +matrix: + include: + - OS: alpine-322 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-322 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-323 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-323 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-324 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-324 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: redhat-8 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:8 + - OS: redhat-8 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:8 + - OS: redhat-9 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:9 + - OS: redhat-9 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:9 + - OS: redhat-10 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: redhat:10 + - OS: redhat-10 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: redhat:10 + - OS: ubuntu-2204 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + - OS: ubuntu-2204 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + - OS: ubuntu-2404 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + - OS: ubuntu-2404 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: ubuntu:resolute + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: ubuntu:resolute + +steps: + - name: 'Trial-build new registry entries' + image: reg.devxy.io/rpkgs/build-env-${IMG} + pull: true + environment: + B2_S3_ACCESS_KEY: + from_secret: B2_S3_ACCESS_KEY + B2_S3_SECRET_KEY: + from_secret: B2_S3_SECRET_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + GITHUB_PAT: + from_secret: GITHUB_PAT + PLATFORM: ${OS} + ARCH: ${ARCH} + R_VERSION: ${R_VERSION} + R_LIBS_USER: /mnt/cache/R-pkgs + commands: + - git clone -q --branch ${patch_branch} https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - git fetch -q origin main + - mkdir -p /mnt/cache/R-pkgs + - rm -rf /mnt/cache/R-pkgs/00LOCK-* + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - /opt/R/$R_VERSION/bin/Rscript local/trial-build-registry.R origin/main + backend_options: + kubernetes: + resources: + requests: + memory: 2Gi + cpu: 2000m + limits: + memory: 4Gi + cpu: 2000m + tolerations: + - key: 'CI' + operator: 'Equal' + value: 'true' + effect: 'NoSchedule' diff --git a/local/patches/README.md b/local/patches/README.md index 992395f..455a96c 100644 --- a/local/patches/README.md +++ b/local/patches/README.md @@ -81,6 +81,19 @@ Run the trial build inside the failing platform's build-env image; it uploads/ar Rscript local/trial-build-patch.R ``` +#### Autonomous PR + trial-build gate + +`--open-pr` closes the loop: it writes the top-N candidates (by failure volume) onto the reused `auto/registry-patch-proposals` branch and opens/updates a single PR. +`.crow/auto-apply-patches.yaml` runs this on a cron (needs `FORGEJO_TOKEN` and a write-scoped `REPO_RW_TOKEN`). + +```bash +# Bounded batch; opens/updates one PR. +PGPASS=... FORGEJO_TOKEN=... REPO_RW_TOKEN=... Rscript local/propose-patches.R --open-pr --limit 10 +``` + +The merge gate is `.crow/trial-build-registry.yaml`: matrixed over the build-env images, each platform trial-builds only the entries the branch **adds** (`local/trial-build-registry.R`, which diffs the registry against `main`) and is green only if every new entry builds. +The repo uses no `pull_request` triggers, so this gate runs manually or on a cron against the auto-patch branch (`--var patch_branch=...`); wiring it to fire on the PR needs `event: pull_request` enabled on the forge. + `--write` and `--open-issue` also append to `local/patches/proposals-log.json`, a ledger of what was proposed. ### Feedback loop (step 4) diff --git a/local/proposal-tracking-lib.R b/local/proposal-tracking-lib.R index 5efc87c..80c4ab2 100644 --- a/local/proposal-tracking-lib.R +++ b/local/proposal-tracking-lib.R @@ -175,4 +175,37 @@ blocked_summary <- function(report, max_pkgs = 15L) { }) } +# Does a registry entry's `platforms` apply to a build on `os` (e.g. +# "ubuntu-2604")? Mirrors bincraft's token match: an entry applies if any of its +# platform tokens is "*", the OS codename, or the distro family ("ubuntu"). +entry_applies_to_os <- function(entry_platforms, os) { + toks <- as.character(unlist(entry_platforms)) + family <- sub("-.*$", "", os) # ubuntu-2604 -> ubuntu + any(toks %in% c("*", os, family)) +} + +# Registry entries present in `current` but not in `base` (matched on +# package|platforms|versions), optionally restricted to those that apply to a +# given `os`. Used by the trial-build gate to build only the entries a PR adds. +new_registry_packages <- function(current, base, os = NULL) { + key <- function(e) { + sprintf( + "%s|%s|%s", + e$package %||% "?", + paste(sort(as.character(unlist(e$platforms))), collapse = ","), + e$versions %||% "?" + ) + } + base_keys <- vapply(base %||% list(), key, character(1L)) + added <- Filter(function(e) !(key(e) %in% base_keys), current %||% list()) + if (!is.null(os)) { + added <- Filter(function(e) entry_applies_to_os(e$platforms, os), added) + } + unique(vapply( + added, + function(e) as.character(e$package %||% ""), + character(1L) + )) +} + `%||%` <- function(a, b) if (is.null(a)) b else a diff --git a/local/propose-patches.R b/local/propose-patches.R index 7ff195b..fb45ea9 100644 --- a/local/propose-patches.R +++ b/local/propose-patches.R @@ -15,10 +15,17 @@ # # Usage: # PGPASS=... Rscript local/propose-patches.R [--platform P] [--arch A] [--min N] +# [--limit N] # (default) print candidates + validation, take no action # --write append candidates to local/patches/registry.json and # the proposals ledger (commit + open a PR yourself) # --open-issue post/update a Forgejo tracking issue (needs FORGEJO_TOKEN) +# --open-pr write the entries, push the `auto/registry-patch-proposals` +# branch, and open/update a PR autonomously (needs +# FORGEJO_TOKEN, and REPO_RW_TOKEN to push in CI). The +# `trial-build-registry` pipeline is the merge gate. +# --limit N only act on the top-N candidates by failure volume +# (bounded batch; the rest are picked up on the next run) # --json PATH also write the machine-readable candidate list to PATH options(error = function() { @@ -58,6 +65,8 @@ if (is.na(min_count)) { } do_write <- "--write" %in% args do_issue <- "--open-issue" %in% args +do_pr <- "--open-pr" %in% args +limit <- suppressWarnings(as.integer(opt_val("--limit", NA_character_))) if (nchar(Sys.getenv("PGPASS")) == 0L) { stop("PGPASS env var is not set; a DB password is required.") @@ -65,6 +74,8 @@ if (nchar(Sys.getenv("PGPASS")) == 0L) { registry_file <- file.path(script_dir, "patches", "registry.json") ledger_file <- file.path(script_dir, "patches", "proposals-log.json") +# Branch the autonomous PR reuses, so re-runs update one PR instead of piling up. +pr_branch <- "auto/registry-patch-proposals" # --------------------------------------------------------------------------- # Query failing builds (same shape as failing-builds-report.R) @@ -118,7 +129,8 @@ registered_pkgs <- unique(vapply( report <- build_triage_report(failures, registered_pkgs) report <- Filter(function(r) r$build_count >= min_count, report) -# Flatten auto-proposable groups into candidate records. +# Flatten auto-proposable groups into candidate records, carrying the group's +# build volume so we can prioritise the highest-impact fixes. candidates <- list() for (r in report) { if (is.null(r$proposed_entries)) { @@ -130,6 +142,7 @@ for (r in report) { signature = r$signature, confidence = r$confidence, tier = r$tier, + build_count = r$build_count, entry = r$proposed_entries[[pkg]] ) } @@ -173,6 +186,22 @@ if (length(candidates) == 0L) { q(status = 0) } +# Prioritise by failure volume, then apply --limit so one run tackles a bounded +# batch (the rest are picked up on the next run). +candidates <- candidates[order( + -vapply(candidates, function(c) c$build_count %||% 0L, integer(1L)) +)] +deferred <- 0L +if (!is.na(limit) && limit >= 0L && length(candidates) > limit) { + deferred <- length(candidates) - limit + candidates <- utils::head(candidates, limit) + cat(sprintf( + "\nLimiting to top %d candidate(s) by failure volume; %d deferred to a later run.\n", + limit, + deferred + )) +} + cat(sprintf( "\n%d candidate registry %s:\n", length(candidates), @@ -386,8 +415,163 @@ if (do_write) { cat(sprintf("Opened tracking issue #%d.\n", created$number)) } save_ledger(merge_ledger(load_ledger(), new_ledger_records)) +} else if (do_pr) { + forgejo_token <- Sys.getenv("FORGEJO_TOKEN") + if (nchar(forgejo_token) == 0L) { + stop("--open-pr requires FORGEJO_TOKEN (to open the PR).") + } + suppressPackageStartupMessages(library(httr2, quietly = TRUE)) + forgejo_base <- "https://git.devxy.io/api/v1" + repo <- "devxy/build-cran-binaries" + + # Write the entries + ledger, then commit them onto the reused auto branch. + jsonlite::write_json( + merged, + registry_file, + auto_unbox = TRUE, + pretty = TRUE, + null = "null" + ) + save_ledger(merge_ledger(load_ledger(), new_ledger_records)) + + git <- function(...) { + st <- system2("git", c(...), stdout = TRUE, stderr = TRUE) + if (!identical(attr(st, "status"), NULL)) { + stop(sprintf( + "git %s failed:\n%s", + paste(..., collapse = " "), + paste(st, collapse = "\n") + )) + } + invisible(st) + } + git("config", "user.name", Sys.getenv("GIT_USER", "devxy-bot")) + git( + "config", + "user.email", + Sys.getenv("GIT_EMAIL", "bot@devxy.io") + ) + git("checkout", "-B", pr_branch) + git( + "add", + file.path(script_dir, "patches", "registry.json"), + ledger_file + ) + git( + "commit", + "-m", + sprintf( + "feat(patches): auto-propose %d registry %s from classified failures", + length(candidate_entries), + if (length(candidate_entries) == 1L) "entry" else "entries" + ) + ) + # Push with a write token when provided (CI); otherwise rely on origin creds. + rw_token <- Sys.getenv("REPO_RW_TOKEN") + push_target <- if (nchar(rw_token) > 0L) { + sprintf( + "https://%s:%s@git.devxy.io/%s.git", + Sys.getenv("GIT_USER", "devxy-bot"), + rw_token, + repo + ) + } else { + "origin" + } + git("push", "-f", push_target, sprintf("HEAD:refs/heads/%s", pr_branch)) + + pr_title <- sprintf( + "feat(patches): auto-proposed registry patches (%s)", + now + ) + body_lines <- c( + sprintf( + "_Auto-generated %s by `local/propose-patches.R --open-pr` from classified `single_builds` failures._", + now + ), + "", + sprintf( + "Adds %d known-lever registry %s (top by failure volume%s).", + length(candidate_entries), + if (length(candidate_entries) == 1L) "entry" else "entries", + if (deferred > 0L) { + sprintf("; %d deferred to a later run", deferred) + } else { + "" + } + ), + "", + "**Merge gate:** the `trial-build-registry` pipeline builds each new entry in its target build-env image; merge only once it is green.", + "Novel source diffs and unknown signatures are never auto-proposed.", + "", + "| package | signature | platforms |", + "| --- | --- | --- |" + ) + for (c in candidates) { + body_lines <- c( + body_lines, + sprintf( + "| %s | %s | %s |", + c$package, + c$signature, + toString(as.character(c$entry$platforms)) + ) + ) + } + new_body <- paste(body_lines, collapse = "\n") + + # One PR per reused branch: update if open, else create. + pulls_url <- sprintf( + "%s/repos/%s/pulls?state=open&limit=50", + forgejo_base, + repo + ) + open_pulls <- httr2::request(pulls_url) |> + httr2::req_headers(Authorization = paste("token", forgejo_token)) |> + httr2::req_perform() |> + httr2::resp_body_json(simplifyVector = FALSE) + match_idx <- which(vapply( + open_pulls, + function(p) identical(p$head$ref, pr_branch), + logical(1L) + )) + if (length(match_idx) > 0L) { + num <- open_pulls[[match_idx[1]]]$number + httr2::request(sprintf("%s/repos/%s/pulls/%d", forgejo_base, repo, num)) |> + httr2::req_headers( + Authorization = paste("token", forgejo_token), + `Content-Type` = "application/json" + ) |> + httr2::req_body_json(list(title = pr_title, body = new_body)) |> + httr2::req_method("PATCH") |> + httr2::req_perform() + cat(sprintf("\nUpdated auto-patch PR #%d (branch %s).\n", num, pr_branch)) + } else { + created <- httr2::request(sprintf( + "%s/repos/%s/pulls", + forgejo_base, + repo + )) |> + httr2::req_headers( + Authorization = paste("token", forgejo_token), + `Content-Type` = "application/json" + ) |> + httr2::req_body_json(list( + title = pr_title, + head = pr_branch, + base = "main", + body = new_body + )) |> + httr2::req_perform() |> + httr2::resp_body_json() + cat(sprintf( + "\nOpened auto-patch PR #%d (branch %s).\n", + created$number, + pr_branch + )) + } } else { cat( - "\nDry run: no changes made. Re-run with --write or --open-issue to act.\n" + "\nDry run: no changes made. Re-run with --write, --open-issue, or --open-pr to act.\n" ) } diff --git a/local/tests/test-proposal-tracking-lib.R b/local/tests/test-proposal-tracking-lib.R index 02a29f1..05cd0e9 100644 --- a/local/tests/test-proposal-tracking-lib.R +++ b/local/tests/test-proposal-tracking-lib.R @@ -162,6 +162,57 @@ test_that("blocked_summary lists each dependency and its dependent count", { expect_true(b[[1L]]$packages_truncated) }) +test_that("entry_applies_to_os matches codename, family, and wildcard", { + expect_true(entry_applies_to_os(list("ubuntu-2604"), "ubuntu-2604")) + expect_true(entry_applies_to_os(list("ubuntu"), "ubuntu-2604")) # family + expect_true(entry_applies_to_os(list("*"), "ubuntu-2604")) + expect_true(entry_applies_to_os(list("alpine", "ubuntu-2604"), "ubuntu-2604")) + expect_false(entry_applies_to_os(list("alpine-324"), "ubuntu-2604")) + expect_false(entry_applies_to_os(list("ubuntu-2404"), "ubuntu-2604")) # other codename +}) + +test_that("new_registry_packages returns only added entries for the platform", { + base <- list( + list( + package = "RcppParallel", + platforms = list("alpine", "ubuntu-2604"), + versions = "*" + ) + ) + current <- list( + base[[1L]], # unchanged -> not "new" + list(package = "BFpack", platforms = list("ubuntu-2604"), versions = "*"), + list( + package = "someAlpinePkg", + platforms = list("alpine-324"), + versions = "*" + ) + ) + # For ubuntu-2604: only the newly-added BFpack (RcppParallel is unchanged, + # someAlpinePkg does not apply to this OS). + expect_identical( + new_registry_packages(current, base, os = "ubuntu-2604"), + "BFpack" + ) + # For alpine-324: the alpine package is new and applies. + expect_identical( + new_registry_packages(current, base, os = "alpine-324"), + "someAlpinePkg" + ) + # Without an OS filter, both additions are returned. + expect_setequal( + new_registry_packages(current, base), + c("BFpack", "someAlpinePkg") + ) + # A changed platform set on the same package counts as a new entry. + widened <- list(list( + package = "RcppParallel", + platforms = list("*"), + versions = "*" + )) + expect_identical(new_registry_packages(widened, base), "RcppParallel") +}) + test_that("retirement_candidates flags entries whose package no longer fails", { entries <- list( list(package = "RcppParallel"), diff --git a/local/trial-build-registry.R b/local/trial-build-registry.R new file mode 100644 index 0000000..f649b62 --- /dev/null +++ b/local/trial-build-registry.R @@ -0,0 +1,145 @@ +#!/usr/bin/env Rscript + +# Merge gate for the auto-patch PR (issue #115, step 3): for every registry +# entry the PR ADDS that applies to this platform, trial-build the package with +# the registry applied, in this platform's own build-env image. Nothing is +# uploaded, archived, or written to the metadata DB. +# +# Exit 0 only if every new entry's package builds; exit 1 if any fails, so it +# gates the PR. A platform with no new entries is a fast no-op. +# +# Usage (inside a build-env image): +# PLATFORM=ubuntu-2604 Rscript local/trial-build-registry.R [base_ref] +# base_ref git ref to diff the registry against (default: origin/main) + +options(error = function() { + cat("ERROR:", geterrmessage(), "\n", file = stdout()) + q(status = 1) +}) + +suppressPackageStartupMessages({ + library(jsonlite, quietly = TRUE) + library(bincraft, quietly = TRUE) +}) + +script_path <- local({ + a <- commandArgs(trailingOnly = FALSE) + f <- sub("^--file=", "", a[grepl("^--file=", a)]) + if (length(f) == 1L && nzchar(f)) normalizePath(f) else NA_character_ +}) +script_dir <- if (is.na(script_path)) "local" else dirname(script_path) +source(file.path(script_dir, "proposal-tracking-lib.R")) + +args <- commandArgs(trailingOnly = TRUE) +base_ref <- if (length(args) >= 1L) { + args[[1L]] +} else { + Sys.getenv("BASE_REF", "origin/main") +} +os <- Sys.getenv("PLATFORM", "") +if (!nzchar(os)) { + stop("PLATFORM env var is not set (e.g. ubuntu-2604).") +} + +patches_dir <- file.path(script_dir, "patches") +registry_file <- file.path(patches_dir, "registry.json") +current <- if (file.exists(registry_file)) { + jsonlite::fromJSON(registry_file, simplifyVector = FALSE) +} else { + list() +} +# Read the registry at base_ref. Fail loud if the ref or file can't be read: +# silently treating the base as empty would trial-build the WHOLE registry +# instead of just the entries the branch adds. +registry_rel <- "local/patches/registry.json" +ref_ok <- suppressWarnings(system2( + "git", + c("rev-parse", "--verify", "--quiet", sprintf("%s^{commit}", base_ref)), + stdout = TRUE, + stderr = FALSE +)) +if (!is.null(attr(ref_ok, "status"))) { + stop(sprintf("base ref %s does not resolve to a commit.", base_ref)) +} +in_base <- suppressWarnings(system2( + "git", + c("ls-tree", base_ref, "--", registry_rel), + stdout = TRUE, + stderr = FALSE +)) +file_in_base <- length(in_base) > 0L && any(nzchar(in_base)) +base_json <- suppressWarnings(system2( + "git", + c("show", sprintf("%s:%s", base_ref, registry_rel)), + stdout = TRUE, + stderr = FALSE +)) +show_ok <- is.null(attr(base_json, "status")) +if (file_in_base && !show_ok) { + stop(sprintf( + "could not read %s at %s; refusing to build the whole registry.", + registry_rel, + base_ref + )) +} +base <- if (show_ok && length(base_json) > 0L) { + jsonlite::fromJSON(paste(base_json, collapse = "\n"), simplifyVector = FALSE) +} else { + list() # file genuinely absent at base -> every entry is new +} + +pkgs <- new_registry_packages(current, base, os = os) +if (length(pkgs) == 0L) { + cat(sprintf( + "No new registry entries apply to %s; nothing to trial-build.\n", + os + )) + q(status = 0) +} + +cat(sprintf( + "Trial-building %d new registry %s on %s (vs %s):\n %s\n", + length(pkgs), + if (length(pkgs) == 1L) "entry" else "entries", + os, + base_ref, + toString(pkgs) +)) + +results <- vapply( + pkgs, + function(pkg) { + cat(sprintf("\n=== trial build: %s ===\n", pkg)) + tryCatch( + { + bincraft::build_binary_package( + pkg, + tag_limit = 1L, + patches = patches_dir, + archive = FALSE, + upload = FALSE, + store_build_metadata = FALSE + ) + TRUE + }, + error = function(e) { + cat(sprintf("FAILED %s: %s\n", pkg, conditionMessage(e))) + FALSE + } + ) + }, + logical(1L) +) + +failed <- pkgs[!results] +cat(sprintf( + "\n%d/%d passed on %s.%s\n", + sum(results), + length(results), + os, + if (length(failed) > 0L) sprintf(" Failed: %s", toString(failed)) else "" +)) +if (length(failed) > 0L) { + q(status = 1) +} +q(status = 0) From 1bca6004fd7a219560e468aa7e7de66bc2aa532b Mon Sep 17 00:00:00 2001 From: pat-s Date: Wed, 15 Jul 2026 14:50:19 +0000 Subject: [PATCH 02/53] chore(local): reuse FORGEJO_TOKEN for the auto-patch push (#125) Follow-up to #124 (merged): the auto-patch pipeline required a separate write-scoped `REPO_RW_TOKEN` to push the branch. Reuse the existing `FORGEJO_TOKEN` instead. - `propose-patches.R --open-pr` now pushes `auto/registry-patch-proposals` over HTTPS with `FORGEJO_TOKEN` (the same token used for the PR API); the read-only `origin` clone URL can't push, so it builds an authenticated URL explicitly. - Drop `REPO_RW_TOKEN` from `.crow/auto-apply-patches.yaml` and the docs. No new secret needed: the pipeline's secrets are now `PGPASS`, `REPO_RO_TOKEN`, and `FORGEJO_TOKEN` (all existing). `FORGEJO_TOKEN` must have repository write scope for the push to succeed. 105 tests pass; all pre-commit hooks pass. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/125 --- .crow/auto-apply-patches.yaml | 7 +++---- local/patches/README.md | 5 +++-- local/propose-patches.R | 25 +++++++++++-------------- 3 files changed, 17 insertions(+), 20 deletions(-) diff --git a/.crow/auto-apply-patches.yaml b/.crow/auto-apply-patches.yaml index 15cc1ee..2ac6886 100644 --- a/.crow/auto-apply-patches.yaml +++ b/.crow/auto-apply-patches.yaml @@ -6,8 +6,9 @@ # human reviews the PR. Novel source diffs / unknown signatures are never # proposed. Global across platforms, so a single job -- no matrix. # -# Needs a write token (REPO_RW_TOKEN) to push and FORGEJO_TOKEN to open the PR. -# Register the `auto-apply-patches` cron in the crow UI, or run manually: +# FORGEJO_TOKEN is used for both the branch push and opening the PR (no separate +# write-scoped secret needed). Register the `auto-apply-patches` cron in the crow +# UI, or run manually: # woodpecker-cli pipeline create --var task=auto-apply-patches --branch=main 7 variables: patch_limit: @@ -34,8 +35,6 @@ steps: from_secret: PGPASS REPO_RO_TOKEN: from_secret: REPO_RO_TOKEN - REPO_RW_TOKEN: - from_secret: REPO_RW_TOKEN FORGEJO_TOKEN: from_secret: FORGEJO_TOKEN GIT_USER: devxy-bot diff --git a/local/patches/README.md b/local/patches/README.md index 455a96c..ce60c9a 100644 --- a/local/patches/README.md +++ b/local/patches/README.md @@ -84,11 +84,12 @@ Rscript local/trial-build-patch.R #### Autonomous PR + trial-build gate `--open-pr` closes the loop: it writes the top-N candidates (by failure volume) onto the reused `auto/registry-patch-proposals` branch and opens/updates a single PR. -`.crow/auto-apply-patches.yaml` runs this on a cron (needs `FORGEJO_TOKEN` and a write-scoped `REPO_RW_TOKEN`). +`.crow/auto-apply-patches.yaml` runs this on a cron. +`FORGEJO_TOKEN` is used for both the branch push and the PR (no separate write-scoped secret). ```bash # Bounded batch; opens/updates one PR. -PGPASS=... FORGEJO_TOKEN=... REPO_RW_TOKEN=... Rscript local/propose-patches.R --open-pr --limit 10 +PGPASS=... FORGEJO_TOKEN=... Rscript local/propose-patches.R --open-pr --limit 10 ``` The merge gate is `.crow/trial-build-registry.yaml`: matrixed over the build-env images, each platform trial-builds only the entries the branch **adds** (`local/trial-build-registry.R`, which diffs the registry against `main`) and is green only if every new entry builds. diff --git a/local/propose-patches.R b/local/propose-patches.R index fb45ea9..11085f0 100644 --- a/local/propose-patches.R +++ b/local/propose-patches.R @@ -21,8 +21,8 @@ # the proposals ledger (commit + open a PR yourself) # --open-issue post/update a Forgejo tracking issue (needs FORGEJO_TOKEN) # --open-pr write the entries, push the `auto/registry-patch-proposals` -# branch, and open/update a PR autonomously (needs -# FORGEJO_TOKEN, and REPO_RW_TOKEN to push in CI). The +# branch, and open/update a PR autonomously. Uses +# FORGEJO_TOKEN for both the push and the PR API. The # `trial-build-registry` pipeline is the merge gate. # --limit N only act on the top-N candidates by failure volume # (bounded batch; the rest are picked up on the next run) @@ -466,18 +466,15 @@ if (do_write) { if (length(candidate_entries) == 1L) "entry" else "entries" ) ) - # Push with a write token when provided (CI); otherwise rely on origin creds. - rw_token <- Sys.getenv("REPO_RW_TOKEN") - push_target <- if (nchar(rw_token) > 0L) { - sprintf( - "https://%s:%s@git.devxy.io/%s.git", - Sys.getenv("GIT_USER", "devxy-bot"), - rw_token, - repo - ) - } else { - "origin" - } + # Push over HTTPS with FORGEJO_TOKEN (same token used for the PR API), so no + # separate write-scoped secret is needed. The read-only `origin` clone URL + # can't push, so build an authenticated URL explicitly. + push_target <- sprintf( + "https://%s:%s@git.devxy.io/%s.git", + Sys.getenv("GIT_REMOTE_USER", "pat-s"), + forgejo_token, + repo + ) git("push", "-f", push_target, sprintf("HEAD:refs/heads/%s", pr_branch)) pr_title <- sprintf( From ed1485c542d4768e75537cf3728423b1c5ee564b Mon Sep 17 00:00:00 2001 From: pat-s Date: Wed, 15 Jul 2026 16:51:15 +0200 Subject: [PATCH 03/53] ci: remove evaluate conditions --- .crow/auto-apply-patches.yaml | 1 - .crow/trial-build-registry.yaml | 1 - 2 files changed, 2 deletions(-) diff --git a/.crow/auto-apply-patches.yaml b/.crow/auto-apply-patches.yaml index 2ac6886..b9c8697 100644 --- a/.crow/auto-apply-patches.yaml +++ b/.crow/auto-apply-patches.yaml @@ -17,7 +17,6 @@ variables: when: - event: manual - evaluate: 'task == "auto-apply-patches"' - event: cron cron: auto-apply-patches diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml index 1ac71e8..9871238 100644 --- a/.crow/trial-build-registry.yaml +++ b/.crow/trial-build-registry.yaml @@ -16,7 +16,6 @@ variables: when: - event: manual - evaluate: 'task == "trial-build-registry"' - event: cron cron: trial-build-registry From ff9f5f5177529553d89a289e8682681289b46be9 Mon Sep 17 00:00:00 2001 From: pat-s Date: Wed, 15 Jul 2026 15:43:02 +0000 Subject: [PATCH 04/53] fix(local): shell-quote git args in the auto-patch push and trial-build gate (#126) ## Problem The first real `auto-apply-patches` run classified, limited to the top-10, and validated the candidate registry cleanly, then died at the push step: ``` Validating candidate registry: Patch registry OK (13 entries). sh: syntax error: unexpected "(" Error in git("commit", "-m", ...): git commit -m feat(patches): auto-propose 10 registry entries ... failed ``` Root cause: R's `system2()` with captured output (`stdout=TRUE`) runs the command through `/bin/sh`, and the arguments were passed **unquoted**. The commit message `feat(patches): ...` contains `()`, which the shell tried to interpret. The same class of bug affects the `^{commit}` and `ref:path` git refs in the trial-build gate. ## Fix `shQuote()` every git argument: - `propose-patches.R` -- the `git()` helper used by `--open-pr` (commit, push, checkout). - `trial-build-registry.R` -- the base-ref reads (`rev-parse ... ^{commit}`, `ls-tree`, `show ref:path`). ## Verification - Reproduced against a real git repo: the unquoted call fails with status 2 (the same `unexpected "("`); the `shQuote`d call commits successfully, and `rev-parse HEAD^{commit}` resolves. - 105 tests pass; all pre-commit hooks pass. Everything else in that run was correct: 842,659 failing builds classified, RcppParallel's 895 dependents correctly reported as blocked (not proposed), top-10 tbb-stddef candidates selected, 69 deferred, registry validated. Only the shell quoting was broken. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/126 --- local/propose-patches.R | 4 +++- local/trial-build-registry.R | 13 ++++++++++--- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/local/propose-patches.R b/local/propose-patches.R index 11085f0..7008251 100644 --- a/local/propose-patches.R +++ b/local/propose-patches.R @@ -435,7 +435,9 @@ if (do_write) { save_ledger(merge_ledger(load_ledger(), new_ledger_records)) git <- function(...) { - st <- system2("git", c(...), stdout = TRUE, stderr = TRUE) + # system2() with captured output runs via /bin/sh, so shell-quote every arg + # (commit messages contain "()", refs contain "^{}", etc.). + st <- system2("git", shQuote(c(...)), stdout = TRUE, stderr = TRUE) if (!identical(attr(st, "status"), NULL)) { stop(sprintf( "git %s failed:\n%s", diff --git a/local/trial-build-registry.R b/local/trial-build-registry.R index f649b62..0749bf7 100644 --- a/local/trial-build-registry.R +++ b/local/trial-build-registry.R @@ -52,9 +52,16 @@ current <- if (file.exists(registry_file)) { # silently treating the base as empty would trial-build the WHOLE registry # instead of just the entries the branch adds. registry_rel <- "local/patches/registry.json" +# system2() with captured output runs via /bin/sh, so shell-quote the git args +# (refs contain "^{}" and ":" that the shell would otherwise mangle). ref_ok <- suppressWarnings(system2( "git", - c("rev-parse", "--verify", "--quiet", sprintf("%s^{commit}", base_ref)), + shQuote(c( + "rev-parse", + "--verify", + "--quiet", + sprintf("%s^{commit}", base_ref) + )), stdout = TRUE, stderr = FALSE )) @@ -63,14 +70,14 @@ if (!is.null(attr(ref_ok, "status"))) { } in_base <- suppressWarnings(system2( "git", - c("ls-tree", base_ref, "--", registry_rel), + shQuote(c("ls-tree", base_ref, "--", registry_rel)), stdout = TRUE, stderr = FALSE )) file_in_base <- length(in_base) > 0L && any(nzchar(in_base)) base_json <- suppressWarnings(system2( "git", - c("show", sprintf("%s:%s", base_ref, registry_rel)), + shQuote(c("show", sprintf("%s:%s", base_ref, registry_rel))), stdout = TRUE, stderr = FALSE )) From 875b0861226d55b1762a1f5a181940b5e9be43d4 Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 16 Jul 2026 08:23:44 +0000 Subject: [PATCH 05/53] ci(crow): enable verbose patched builds in the trial-build gate (#129) Companion to bincraft codefloe #65. Sets `BINCRAFT_VERBOSE_PATCH_BUILD=TRUE` in the trial-build gate so a failed isolated patched build prints the real compiler error instead of `System command 'R' failed`. Harmless on bincraft versions without the flag (unknown env var is ignored). Takes effect once bincraft #65 is released and the build-env images pick it up. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/129 --- .crow/trial-build-registry.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml index 9871238..602837f 100644 --- a/.crow/trial-build-registry.yaml +++ b/.crow/trial-build-registry.yaml @@ -116,6 +116,10 @@ steps: ARCH: ${ARCH} R_VERSION: ${R_VERSION} R_LIBS_USER: /mnt/cache/R-pkgs + # Surface the real compiler error when an isolated patched build fails, + # instead of bincraft's opaque "System command 'R' failed" (needs bincraft + # with BINCRAFT_VERBOSE_PATCH_BUILD support; harmless on older versions). + BINCRAFT_VERBOSE_PATCH_BUILD: 'TRUE' commands: - git clone -q --branch ${patch_branch} https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git fetch -q origin main From f9d399fac0e60f748eaa2c65d23f2c34c437d3a1 Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 16 Jul 2026 08:23:54 +0000 Subject: [PATCH 06/53] feat(local): detect dependency-cascade failures generally, not just RcppParallel (#128) ## Why (from the #127 trial-build gate) The gate did its job: 0/3 passed, merge blocked. The log showed *why* -- BFpack, BayesERtools, GMLTM all fail while building their shared dependency **`rstan`**, not in their own code: ``` Failed to build source package rstan. .../StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: tbb/tbb_stddef.h: No such file or directory ``` So the per-package `-DTBB_INTERFACE_NEW` makevars entries the classifier proposed are useless for these packages -- they're blocked on `rstan` (which already has a registry entry). This is the **same dependency cascade** the RcppParallel `applies_to` guard catches, but `tbb-stddef-removed` is a generic signature with no such pin, so ~73 Stan packages kept getting proposed. ## What Generalise cascade detection beyond the RcppParallel special case: - `failing_dependency(error_text, package)` -- when the log names a **different** package as the one that failed to compile (`Failed to build source package X`, `compilation failed for package 'X'`, `dependency 'X' ... not available`), that package is the real cause. - `build_triage_report()` now blocks any package whose **every** failing build is such a cascade: reported as `blocked_on` that dependency, never proposed a bogus per-package entry. A package that fails in its **own** compilation is still proposed. - The `applies_to` (RcppParallel) and data-driven (rstan) cases are unified into one `blocked_packages` / `blocked_on` model; the report, proposer, and `blocked_summary` count the actually-blocked packages, and the blocked note shows even when a group also has genuine proposals. ## Effect Next auto-apply run will stop proposing the rstan-blocked Stan packages (and any future dependency cascade) and surface them as "blocked on rstan" instead. Fixing `rstan` once clears the whole cluster. ## Verification - New tests: `failing_dependency` (cascade vs own-compile vs none), and an end-to-end split where BFpack/GMLTM (blocked on rstan) are not proposed while an own-compile package still is. - Full suite: 112 tests pass; all pre-commit hooks pass. Refs #120, #127. (Separate follow-ups: fixing rstan's build itself, and quieting the gate's metadata-DB retry storm -- both root-caused to bincraft.) Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/128 --- local/failing-builds-classify.R | 77 +++++++++++++++++++--- local/failing-builds-report.R | 12 ++-- local/proposal-tracking-lib.R | 19 ++++-- local/propose-patches.R | 7 +- local/tests/test-failing-builds-classify.R | 43 ++++++++++++ 5 files changed, 135 insertions(+), 23 deletions(-) diff --git a/local/failing-builds-classify.R b/local/failing-builds-classify.R index 4ce30cf..716fab2 100644 --- a/local/failing-builds-classify.R +++ b/local/failing-builds-classify.R @@ -155,6 +155,44 @@ fingerprint_error <- function(error_text, package = NULL, max_chars = 200L) { fp } +# --------------------------------------------------------------------------- +# Dependency-cascade detection +# --------------------------------------------------------------------------- +# If a build's error_text shows the failure was actually in a DIFFERENT package +# (a dependency that would not compile), return that dependency's name; +# otherwise NA. Used to avoid proposing a per-package fix for a package that +# only fails because a shared dependency does not build (e.g. the ~73 Stan +# packages that fail while building `rstan`). Generalises the RcppParallel +# `applies_to` guard to any dependency named in the log. +failing_dependency <- function(error_text, package) { + if (length(error_text) == 0L || is.na(error_text) || !nzchar(error_text)) { + return(NA_character_) + } + x <- as.character(error_text) + # optional opening quote before the package name: apostrophe, double-quote, + # backtick, or curly quotes -- written as \u escapes so the pattern stays + # valid UTF-8 regardless of source encoding. + q <- "[\u0027\u0022\u0060\u2018\u2019]?" + name <- "([A-Za-z][A-Za-z0-9._]+)" + # Markers R/pak emit naming the package that actually failed to compile. + pats <- c( + paste0("compilation failed for package ", q, name), + paste0("Failed to build source package ", q, name), + paste0("Error in building package ", q, name), + paste0("dependenc(?:y|ies) ", q, name, q, "?[^\\n]*not available") + ) + deps <- character(0L) + for (p in pats) { + hits <- regmatches(x, gregexpr(p, x, perl = TRUE))[[1L]] + if (length(hits) > 0L) { + deps <- c(deps, sub(p, "\\1", hits, perl = TRUE)) + } + } + deps <- sub("[._]+$", "", deps) # drop a trailing sentence period (e.g. "rstan.") + deps <- setdiff(unique(deps), package) # a package failing on its OWN code is not a cascade + if (length(deps) == 0L) NA_character_ else deps[[1L]] +} + # --------------------------------------------------------------------------- # Classification # --------------------------------------------------------------------------- @@ -291,18 +329,38 @@ build_triage_report <- function( unregistered <- setdiff(pkgs, registered_pkgs) auto_proposable <- isTRUE(sig$auto) && sig$matched - # A signature whose fix is package-specific (`applies_to`) may only be - # proposed for that package. Everything else matching it is a downstream - # failure blocked on that package (e.g. RcppParallel dependents carrying - # RcppParallel's own error text) -- never propose those a bogus entry. + # Decide, per package, whether it is genuinely fixable or merely blocked on + # a dependency (so a per-package entry would be useless). Two blocking modes: + # 1. `applies_to`: a package-specific patch (e.g. RcppParallel's) is only + # valid for its own package; other matches are downstream of it. + # 2. data-driven cascade: the package's error_text shows a *different* + # package failed to compile (e.g. the ~73 Stan packages blocked on rstan). + # `blocked_map` maps a blocked package -> the dependency it waits on. + g$blocked_dep <- vapply( + seq_len(nrow(g)), + function(i) failing_dependency(g$error_text[[i]], g$name[[i]]), + character(1L) + ) proposable <- unregistered - blocked_on <- NULL + blocked_map <- list() if (!is.null(sig$applies_to)) { - proposable <- intersect(unregistered, sig$applies_to) - downstream <- setdiff(pkgs, sig$applies_to) - if (length(downstream) > 0L) { - blocked_on <- sig$applies_to + for (p in setdiff(pkgs, sig$applies_to)) { + blocked_map[[p]] <- sig$applies_to } + proposable <- intersect(proposable, sig$applies_to) + } + for (p in proposable) { + deps <- g$blocked_dep[g$name == p] + if (!any(is.na(deps))) { + # every failing build of p is a cascade -> blocked, not fixable here + blocked_map[[p]] <- unique(deps) + } + } + proposable <- setdiff(proposable, names(blocked_map)) + blocked_packages <- names(blocked_map) + blocked_on <- unique(unlist(blocked_map, use.names = FALSE)) + if (length(blocked_on) == 0L) { + blocked_on <- NULL } proposed <- list() @@ -326,6 +384,7 @@ build_triage_report <- function( suggested_fix = sig$fix, applies_to = sig$applies_to, blocked_on = blocked_on, + blocked_packages = blocked_packages, fingerprint = names(fp_tab)[[1L]], fingerprint_variants = length(fp_tab), build_count = nrow(g), diff --git a/local/failing-builds-report.R b/local/failing-builds-report.R index 51f5bc7..ce7b683 100644 --- a/local/failing-builds-report.R +++ b/local/failing-builds-report.R @@ -194,15 +194,17 @@ for (r in report) { ) cat(paste0(" ", gsub("\n", "\n ", j)), "\n", sep = "") } - } else if (!is.null(r$blocked_on)) { + } else if (r$auto_proposable && length(r$blocked_packages) == 0L) { + cat(" (all affected packages already have a registry entry)\n") + } + # Blocked packages are shown even when the group also has proposals. + if (length(r$blocked_packages) > 0L) { cat(sprintf( - " (blocked on %s -- these %d package(s) fail because that dependency does not build; fix %s, do not patch each dependent)\n", + " (blocked on %s -- %d package(s) fail because that dependency does not build; fix %s, do not patch each dependent)\n", toString(r$blocked_on), - length(r$packages), + length(r$blocked_packages), toString(r$blocked_on) )) - } else if (r$auto_proposable) { - cat(" (all affected packages already have a registry entry)\n") } } diff --git a/local/proposal-tracking-lib.R b/local/proposal-tracking-lib.R index 80c4ab2..9568d78 100644 --- a/local/proposal-tracking-lib.R +++ b/local/proposal-tracking-lib.R @@ -160,17 +160,22 @@ unclassified_summary <- function(report, max_groups = 30L, max_pkgs = 15L) { ) } -# Groups blocked on a dependency (a package-specific fix pinned via `applies_to` -# whose dependents merely carry its error): report the dependency + how many -# dependents wait on it, so fixing it once is recognised as clearing the batch. +# Groups with packages blocked on a dependency (a package-specific fix pinned +# via `applies_to`, or a data-driven cascade where the package fails building a +# dependency): report the dependency + how many dependents wait on it, so fixing +# it once is recognised as clearing the batch. blocked_summary <- function(report, max_pkgs = 15L) { - bl <- Filter(function(g) !is.null(g$blocked_on), report) + bl <- Filter( + function(g) length(g$blocked_packages %||% character(0L)) > 0L, + report + ) lapply(bl, function(g) { + pkgs <- g$blocked_packages list( blocked_on = g$blocked_on, - n_packages = length(g$packages), - packages = utils::head(g$packages, max_pkgs), - packages_truncated = length(g$packages) > max_pkgs + n_packages = length(pkgs), + packages = utils::head(pkgs, max_pkgs), + packages_truncated = length(pkgs) > max_pkgs ) }) } diff --git a/local/propose-patches.R b/local/propose-patches.R index 7008251..cfce338 100644 --- a/local/propose-patches.R +++ b/local/propose-patches.R @@ -150,14 +150,17 @@ for (r in report) { # Groups blocked on a dependency (e.g. RcppParallel dependents) are reported, # not proposed: fixing the named dependency clears them all at once. -blocked <- Filter(function(r) !is.null(r$blocked_on), report) +blocked <- Filter( + function(r) length(r$blocked_packages) > 0L, + report +) if (length(blocked) > 0L) { cat("\nBlocked on a dependency (fix the dependency, not each dependent):\n") for (r in blocked) { cat(sprintf( " %s: %d package(s) fail because %s does not build\n", toString(r$blocked_on), - length(r$packages), + length(r$blocked_packages), toString(r$blocked_on) )) } diff --git a/local/tests/test-failing-builds-classify.R b/local/tests/test-failing-builds-classify.R index a365e14..d4df9f5 100644 --- a/local/tests/test-failing-builds-classify.R +++ b/local/tests/test-failing-builds-classify.R @@ -105,6 +105,49 @@ test_that("RcppParallel dependents are blocked, not proposed a per-package patch expect_identical(grp$blocked_on, "RcppParallel") }) +test_that("failing_dependency names the dependency that actually failed", { + # A leaf package (BFpack) that fails building its rstan dependency. + txt <- paste( + "Error in installing dependencies for package BFpack with tag 1.6.1", + "Failed to build source package rstan.", + "ERROR: compilation failed for package ‘rstan’", + sep = "\n" + ) + expect_identical(failing_dependency(txt, "BFpack"), "rstan") + # A package failing in its OWN compilation is not a cascade. + own <- "ERROR: compilation failed for package ‘BFpack’" + expect_true(is.na(failing_dependency(own, "BFpack"))) + expect_true(is.na(failing_dependency(NA_character_, "x"))) + expect_true(is.na(failing_dependency("some unrelated error", "x"))) +}) + +test_that("Stan packages blocked on rstan are not proposed a per-package entry", { + # BFpack/GMLTM fail building rstan; the tbb error is in rstan's compile. + cascade <- paste( + "Failed to build source package rstan.", + "fatal error: tbb/tbb_stddef.h: No such file or directory", + sep = "\n" + ) + failures <- data.frame( + name = c("BFpack", "GMLTM", "someOwnPkg"), + platform = "ubuntu-2604", + arch = "amd64", + error_text = c( + cascade, + cascade, + # someOwnPkg fails in its OWN compile on the same header -> fixable. + "someOwnPkg.cpp: fatal error: tbb/tbb_stddef.h: No such file or directory" + ), + stringsAsFactors = FALSE + ) + report <- build_triage_report(failures, registered_pkgs = character(0L)) + grp <- Filter(function(g) g$signature == "tbb-stddef-removed", report)[[1L]] + # Only the own-compile package is proposed; the rstan cascades are blocked. + expect_identical(names(grp$proposed_entries), "someOwnPkg") + expect_setequal(grp$blocked_packages, c("BFpack", "GMLTM")) + expect_identical(grp$blocked_on, "rstan") +}) + test_that("RcppParallel itself is still proposed when it is the failing package", { failures <- data.frame( name = "RcppParallel", From 118a92889f323f01363c7eed9573e203666ee8a0 Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 16 Jul 2026 08:24:03 +0000 Subject: [PATCH 07/53] fix(local): make the trial-build gate detect non-throwing build failures (#130) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Critical: the gate was false-green The latest run printed **`3/3 passed on alpine-324`** while all three builds actually **failed** (their `rstan` dependency won't compile). A false-green gate would let broken registry entries merge — worse than no gate. Root cause: `bincraft::build_binary_package()` catches build failures internally and **returns `"error"`** for the failed tag rather than throwing. The gate's `tryCatch` only treated a *thrown* exception as failure, so every non-throwing failure looked like a pass. Fix: inspect the return value. A tag passes only if the flattened result is non-empty and contains no `"error"` sentinel; a thrown error still counts as failure. Verified the verdict against `error`/`skipped`/`TRUE`/`list(success=TRUE)`/`NULL`/mixed inputs. With this, the current rstan-blocked entries will correctly show **0/3 (red)** — which is the right answer until rstan builds. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/130 --- local/trial-build-registry.R | 39 +++++++++++++++++++++++------------- 1 file changed, 25 insertions(+), 14 deletions(-) diff --git a/local/trial-build-registry.R b/local/trial-build-registry.R index 0749bf7..9708408 100644 --- a/local/trial-build-registry.R +++ b/local/trial-build-registry.R @@ -117,23 +117,34 @@ results <- vapply( pkgs, function(pkg) { cat(sprintf("\n=== trial build: %s ===\n", pkg)) - tryCatch( - { - bincraft::build_binary_package( - pkg, - tag_limit = 1L, - patches = patches_dir, - archive = FALSE, - upload = FALSE, - store_build_metadata = FALSE - ) - TRUE - }, + # bincraft::build_binary_package() catches build failures internally and + # RETURNS "error" for the failed tag rather than throwing, so a green gate + # must inspect the return value -- checking only for a thrown exception + # reports a broken build as passing. + res <- tryCatch( + bincraft::build_binary_package( + pkg, + tag_limit = 1L, + patches = patches_dir, + archive = FALSE, + upload = FALSE, + store_build_metadata = FALSE + ), error = function(e) { - cat(sprintf("FAILED %s: %s\n", pkg, conditionMessage(e))) - FALSE + cat(sprintf("FAILED %s (threw): %s\n", pkg, conditionMessage(e))) + "error" } ) + flat <- as.character(unlist(res)) + ok <- length(flat) > 0L && !("error" %in% flat) + if (!ok) { + cat(sprintf( + "FAILED %s: build did not succeed (result: %s)\n", + pkg, + if (length(flat) > 0L) toString(flat) else "" + )) + } + ok }, logical(1L) ) From 6c03f278ecac4d3df58d1d8674259eee45dfe6fd Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 16 Jul 2026 21:24:03 +0000 Subject: [PATCH 08/53] feat(local): aggregate blocked-on-dependency reporting by dependency (#131) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Why With cascade detection (#128) live, the latest `auto-apply-patches` run did exactly the right thing — **proposed nothing** (`No auto-proposable candidates`) because every failure is a dependency cascade, and it surfaced the ~30 root-cause dependencies to fix. But the "Blocked on a dependency" list printed **one line per fingerprint group**, so the same dependency repeated (rstan ×4, lpsymphony ×4, salso ×2, BH ×2, GO.db ×2, RcppCWB ×2, …), burying the priority. ## What Aggregate blocked packages across all groups **by the dependency they wait on**: - Expose `blocked_map` (package → dependency) from `build_triage_report()`. - Add `blocked_by_dependency()` — dedupes dependents (a package in two groups counts once) and ranks dependencies by how many distinct dependents they block. - Proposer and tracker (log + issue) now print one line per dependency, sorted by impact. Replaces the per-group `blocked_summary`. ## Result (same data, aggregated) ``` Blocked on a dependency (3 dependencies block 6 dependents; fix the dependency, not each dependent): RcppParallel 3 dependent(s) rstan 2 dependent(s) sf 1 dependent(s) ``` So the real run becomes a crisp, ranked worklist: RcppParallel (894), sf (128), rstan (~96), Rfast (33), clarabel/DescTools (26), Rglpk (22), xgboost (18), … ## Verified New test covers cross-group aggregation, dedup (a dependent in two groups counted once), the example cap, and ranking. 112 tests pass; hooks pass. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/131 --- local/failing-builds-classify.R | 1 + local/proposal-tracking-lib.R | 38 ++++++++++++++++-------- local/proposal-tracking.R | 8 ++--- local/propose-patches.R | 27 ++++++++--------- local/tests/test-proposal-tracking-lib.R | 33 ++++++++++++++------ 5 files changed, 68 insertions(+), 39 deletions(-) diff --git a/local/failing-builds-classify.R b/local/failing-builds-classify.R index 716fab2..73922b3 100644 --- a/local/failing-builds-classify.R +++ b/local/failing-builds-classify.R @@ -385,6 +385,7 @@ build_triage_report <- function( applies_to = sig$applies_to, blocked_on = blocked_on, blocked_packages = blocked_packages, + blocked_map = if (length(blocked_map) > 0L) blocked_map else NULL, fingerprint = names(fp_tab)[[1L]], fingerprint_variants = length(fp_tab), build_count = nrow(g), diff --git a/local/proposal-tracking-lib.R b/local/proposal-tracking-lib.R index 9568d78..28f65db 100644 --- a/local/proposal-tracking-lib.R +++ b/local/proposal-tracking-lib.R @@ -160,24 +160,38 @@ unclassified_summary <- function(report, max_groups = 30L, max_pkgs = 15L) { ) } -# Groups with packages blocked on a dependency (a package-specific fix pinned -# via `applies_to`, or a data-driven cascade where the package fails building a -# dependency): report the dependency + how many dependents wait on it, so fixing -# it once is recognised as clearing the batch. -blocked_summary <- function(report, max_pkgs = 15L) { - bl <- Filter( - function(g) length(g$blocked_packages %||% character(0L)) > 0L, - report - ) - lapply(bl, function(g) { - pkgs <- g$blocked_packages +# Aggregate blocked packages across ALL groups by the dependency they wait on, +# so one dependency (RcppParallel, rstan, sf, ...) is a single line -- deduped +# and ranked by how many distinct dependents it blocks -- instead of repeating +# once per fingerprint group. Reads each group's `blocked_map` (package -> the +# dependency it is blocked on). Returns records sorted by dependent count desc, +# each with up to `max_pkgs` example dependents. +blocked_by_dependency <- function(report, max_pkgs = 15L) { + acc <- list() # dependency -> character vector of dependent packages + for (g in report) { + bm <- g$blocked_map + if (is.null(bm) || length(bm) == 0L) { + next + } + for (pkg in names(bm)) { + for (dep in as.character(unlist(bm[[pkg]]))) { + acc[[dep]] <- unique(c(acc[[dep]], pkg)) + } + } + } + if (length(acc) == 0L) { + return(list()) + } + out <- lapply(names(acc), function(dep) { + pkgs <- acc[[dep]] list( - blocked_on = g$blocked_on, + dependency = dep, n_packages = length(pkgs), packages = utils::head(pkgs, max_pkgs), packages_truncated = length(pkgs) > max_pkgs ) }) + out[order(-vapply(out, function(x) x$n_packages, integer(1L)))] } # Does a registry entry's `platforms` apply to a build on `os` (e.g. diff --git a/local/proposal-tracking.R b/local/proposal-tracking.R index 4d82a11..f8e1284 100644 --- a/local/proposal-tracking.R +++ b/local/proposal-tracking.R @@ -127,13 +127,13 @@ if (length(retire) > 0L) { # --------------------------------------------------------------------------- # Blind spots: failures the classifier could not auto-propose. # --------------------------------------------------------------------------- -blocked <- blocked_summary(report) +blocked <- blocked_by_dependency(report) unmatched <- unclassified_summary(report) cat("\nBlocked on a dependency (fix the dependency, not each dependent):\n") if (length(blocked) > 0L) { for (b in blocked) { - cat(sprintf(" %s: %d dependent(s) waiting\n", b$blocked_on, b$n_packages)) + cat(sprintf(" %-20s %5d dependent(s)\n", b$dependency, b$n_packages)) } } else { cat(" (none)\n") @@ -207,8 +207,8 @@ if (do_issue) { body_lines <- c( body_lines, sprintf( - "- **%s**: %d dependent(s) waiting (e.g. %s%s)", - b$blocked_on, + "- **%s**: %d dependent(s) (e.g. %s%s)", + b$dependency, b$n_packages, toString(b$packages), if (isTRUE(b$packages_truncated)) ", ..." else "" diff --git a/local/propose-patches.R b/local/propose-patches.R index cfce338..360df9f 100644 --- a/local/propose-patches.R +++ b/local/propose-patches.R @@ -148,21 +148,20 @@ for (r in report) { } } -# Groups blocked on a dependency (e.g. RcppParallel dependents) are reported, -# not proposed: fixing the named dependency clears them all at once. -blocked <- Filter( - function(r) length(r$blocked_packages) > 0L, - report -) +# Packages blocked on a dependency are reported (aggregated by dependency, +# ranked by impact), not proposed: fixing the named dependency clears the batch. +blocked <- blocked_by_dependency(report) if (length(blocked) > 0L) { - cat("\nBlocked on a dependency (fix the dependency, not each dependent):\n") - for (r in blocked) { - cat(sprintf( - " %s: %d package(s) fail because %s does not build\n", - toString(r$blocked_on), - length(r$blocked_packages), - toString(r$blocked_on) - )) + n_blocked_pkgs <- length(unique(unlist( + lapply(report, function(r) r$blocked_packages) + ))) + cat(sprintf( + "\nBlocked on a dependency (%d dependencies block %d dependents; fix the dependency, not each dependent):\n", + length(blocked), + n_blocked_pkgs + )) + for (b in blocked) { + cat(sprintf(" %-20s %5d dependent(s)\n", b$dependency, b$n_packages)) } } diff --git a/local/tests/test-proposal-tracking-lib.R b/local/tests/test-proposal-tracking-lib.R index 05cd0e9..869d2b3 100644 --- a/local/tests/test-proposal-tracking-lib.R +++ b/local/tests/test-proposal-tracking-lib.R @@ -146,20 +146,35 @@ test_that("unclassified_summary ranks unknown groups and caps output", { expect_identical(capped$dropped_groups, 1L) }) -test_that("blocked_summary lists each dependency and its dependent count", { +test_that("blocked_by_dependency aggregates across groups, deduped and ranked", { + # RcppParallel dependents split across platforms/fingerprints -> separate + # groups, but one aggregated line; a dependent seen twice is counted once. failures <- data.frame( - name = c("ACEsimFit", "AovBay", "AdaptGauss"), - platform = "ubuntu-2604", + name = c("ACEsimFit", "AovBay", "AdaptGauss", "ACEsimFit", "loner"), + platform = c( + "ubuntu-2604", + "ubuntu-2604", + "alpine-324", + "alpine-324", + "ubuntu-2604" + ), arch = "amd64", - error_text = "Error: USE_TBB=Linux is not supported on this toolchain", + error_text = c( + rep("Error: USE_TBB=Linux is not supported on this toolchain", 4L), + "Failed to build source package rstan.\nfatal error: tbb/tbb_stddef.h" + ), stringsAsFactors = FALSE ) report <- build_triage_report(failures, registered_pkgs = character(0L)) - b <- blocked_summary(report, max_pkgs = 2L) - expect_length(b, 1L) - expect_identical(b[[1L]]$blocked_on, "RcppParallel") - expect_identical(b[[1L]]$n_packages, 3L) - expect_true(b[[1L]]$packages_truncated) + agg <- blocked_by_dependency(report, max_pkgs = 2L) + deps <- vapply(agg, function(b) b$dependency, character(1L)) + expect_true("RcppParallel" %in% deps && "rstan" %in% deps) + rcpp <- Filter(function(b) b$dependency == "RcppParallel", agg)[[1L]] + # ACEsimFit appears in two groups -> counted once (3 distinct dependents). + expect_identical(rcpp$n_packages, 3L) + expect_true(rcpp$packages_truncated) # capped at max_pkgs = 2 + # Ranked by dependent count: RcppParallel (3) before rstan (1). + expect_identical(deps[[1L]], "RcppParallel") }) test_that("entry_applies_to_os matches codename, family, and wildcard", { From 13fcad6dc4711c05813132b505c215a986f1b1df Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 17 Jul 2026 10:27:58 +0000 Subject: [PATCH 09/53] fix(crow): make the trial-build gate no-op when the auto-patch branch is absent (#132) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem The trial pipeline errored: ``` git clone -q --branch auto/registry-patch-proposals ... fatal: Remote branch auto/registry-patch-proposals not found in upstream origin ``` I deleted the stale `auto/registry-patch-proposals` branch during cleanup, and — now that cascade detection (#128) makes the proposer correctly find **no candidates** — the proposer exits before ever recreating it. So the branch is legitimately absent, and the gate's hard `git clone --branch` fails. ## Fix "Branch absent" = "no pending auto-patch proposals" = **nothing to verify**, which should be a clean no-op, not a failure. Clone `main`, then fetch + checkout the patch branch only if it exists; otherwise log and `exit 0`. A present branch is verified exactly as before (checkout its tip, diff registry vs `main`). This also means the gate now runs `main`'s `trial-build-registry.R` (with the #130 fix) rather than a possibly-stale copy on the branch. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/132 --- .crow/trial-build-registry.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml index 602837f..3ec0417 100644 --- a/.crow/trial-build-registry.yaml +++ b/.crow/trial-build-registry.yaml @@ -121,8 +121,13 @@ steps: # with BINCRAFT_VERBOSE_PATCH_BUILD support; harmless on older versions). BINCRAFT_VERBOSE_PATCH_BUILD: 'TRUE' commands: - - git clone -q --branch ${patch_branch} https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + # Clone main, then check out the auto-patch branch if it exists. When the + # proposer had no candidates it never (re)creates that branch, so a missing + # branch means "nothing to verify" -- no-op cleanly instead of failing the + # clone. + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git fetch -q origin main + - 'if git fetch -q origin ${patch_branch}; then git checkout -q FETCH_HEAD; else echo "No ${patch_branch} branch; no pending auto-patch proposals to verify."; exit 0; fi' - mkdir -p /mnt/cache/R-pkgs - rm -rf /mnt/cache/R-pkgs/00LOCK-* - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R From a30c6f953273ec6001ed7f1834f4f4f8e7427448 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 17 Jul 2026 11:52:07 +0000 Subject: [PATCH 10/53] fix(crow): probe the auto-patch branch with git ls-remote to avoid a scary fatal (#133) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Follow-up to #132. The no-op path already worked (the `else` branch runs and `exit 0`s), but using `git fetch` as the *existence check* printed `fatal: couldn't find remote ref auto/registry-patch-proposals` to stderr — which looks like a failure even though the step succeeds. Probe with `git ls-remote --exit-code --heads origin ${patch_branch}` instead: verified against the live repo it exits 0 for an existing branch and 2 for a missing one, **silently** (no `fatal`). Only fetch + checkout when the branch actually exists. Net: same behavior, clean log — a run with no pending auto-patch branch prints just `No ... branch; no pending auto-patch proposals to verify.` and exits 0. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/133 --- .crow/trial-build-registry.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml index 3ec0417..cb8df8b 100644 --- a/.crow/trial-build-registry.yaml +++ b/.crow/trial-build-registry.yaml @@ -127,7 +127,7 @@ steps: # clone. - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - git fetch -q origin main - - 'if git fetch -q origin ${patch_branch}; then git checkout -q FETCH_HEAD; else echo "No ${patch_branch} branch; no pending auto-patch proposals to verify."; exit 0; fi' + - 'if git ls-remote --exit-code --heads origin ${patch_branch} >/dev/null 2>&1; then git fetch -q origin ${patch_branch} && git checkout -q FETCH_HEAD; else echo "No ${patch_branch} branch; no pending auto-patch proposals to verify."; exit 0; fi' - mkdir -p /mnt/cache/R-pkgs - rm -rf /mnt/cache/R-pkgs/00LOCK-* - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R From b4b7d53a832fc8d041849169fc94077679c88c1c Mon Sep 17 00:00:00 2001 From: pat-s Date: Sat, 18 Jul 2026 08:37:04 +0000 Subject: [PATCH 11/53] fix(local): make trial-build-patch.R detect non-throwing build failures (#134) `local/trial-build-patch.R` -- the single-package acceptance gate the proposer prints for humans to run (`PGPASS=... Rscript local/trial-build-patch.R `) -- reported **`Trial build OK`** for rstan even though rstan.so failed to load (`symbol not found: tbb::detail::r1::observe`). Same false-green as the registry gate before #130: `build_binary_package()` catches failures internally and returns `"error"` rather than throwing, so a `tryCatch` that only treats a thrown exception as failure passes a broken build. Now inspects the return value (mirrors trial-build-registry.R). Found while verifying the rstan/oneTBB unblock. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/134 --- local/trial-build-patch.R | 31 +++++++++++++++++-------------- 1 file changed, 17 insertions(+), 14 deletions(-) diff --git a/local/trial-build-patch.R b/local/trial-build-patch.R index 4e8030a..2229074 100644 --- a/local/trial-build-patch.R +++ b/local/trial-build-patch.R @@ -40,23 +40,26 @@ cat(sprintf( patches_dir )) -ok <- tryCatch( - { - bincraft::build_binary_package( - package, - tag_limit = 1L, - patches = patches_dir, - archive = FALSE, - upload = FALSE, - store_build_metadata = FALSE - ) - TRUE - }, +# build_binary_package() catches build failures internally and RETURNS "error" +# for the failed tag rather than throwing (bincraft >= v4.4.7), so inspect the +# return value -- checking only for a thrown exception reports a broken build as +# passing (false green). +res <- tryCatch( + bincraft::build_binary_package( + package, + tag_limit = 1L, + patches = patches_dir, + archive = FALSE, + upload = FALSE, + store_build_metadata = FALSE + ), error = function(e) { - cat(sprintf("Trial build FAILED: %s\n", conditionMessage(e))) - FALSE + cat(sprintf("Trial build FAILED (threw): %s\n", conditionMessage(e))) + "error" } ) +flat <- as.character(unlist(res)) +ok <- length(flat) > 0L && !("error" %in% flat) if (ok) { cat(sprintf("Trial build OK: %s builds with the proposed patch.\n", package)) From 6df945d1472beb6fd3f0372a31085af38225b119 Mon Sep 17 00:00:00 2001 From: pat-s Date: Mon, 20 Jul 2026 09:56:21 +0000 Subject: [PATCH 12/53] fix(patches): build RcppParallel against system oneTBB instead of disabling TBB (#135) ## What Replace RcppParallel's `disable-tbb` registry patch with `system-tbb`: build RcppParallel against the system oneTBB instead of stripping TBB entirely. ## Why `disable-tbb` skipped the bundled Intel TBB build by forcing the TinyThread backend, which also removed RcppParallel's TBB linkage. That broke every dependent that links TBB through `RcppParallelLibs()` -- `rstan` and the whole Stan cluster -- with `symbol not found: tbb::detail::r1::observe`. This is the root cause behind the large "blocked on RcppParallel" / rstan clusters (issues #115, #120): the packages were not individually broken, they were all waiting on one TBB-linkage regression. ## Change `system-tbb.patch` leaves `USE_TBB` unset (so the bundled build is still skipped on musl and g++ 15) but keeps the TBB backend and links the system oneTBB now shipped in the build-env images: ``` PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -DTBB_INTERFACE_NEW PKG_LIBS += -ltbb -ltbbmalloc ``` Scoped to `alpine` + `ubuntu-2604`, the only platforms where the bundled build fails; redhat and older ubuntus keep the bundled TBB. ## Requires The companion image change that exports `TBB_INC`/`TBB_LIB` so `RcppParallelLibs()` hands the system-TBB flags to dependents: build-env-images PR #12. Both must ship together. ## Verified In `build-env-alpine:3.24` with the new images: - RcppParallel builds against oneTBB 2022, no ABI errors, patch applies cleanly to the target clone. - `RcppParallelLibs()` returns `-L/usr/lib -Wl,-rpath,/usr/lib -ltbb -ltbbmalloc`. - rstan links (`-ltbb -ltbbmalloc`) and loads with no missing symbol -- `* DONE (rstan)`, trial build exit 0. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/135 --- local/patches/RcppParallel/disable-tbb.patch | 16 ---------------- local/patches/RcppParallel/system-tbb.patch | 19 +++++++++++++++++++ local/patches/registry.json | 17 ++++++++++++----- 3 files changed, 31 insertions(+), 21 deletions(-) delete mode 100644 local/patches/RcppParallel/disable-tbb.patch create mode 100644 local/patches/RcppParallel/system-tbb.patch diff --git a/local/patches/RcppParallel/disable-tbb.patch b/local/patches/RcppParallel/disable-tbb.patch deleted file mode 100644 index 0fe8ad9..0000000 --- a/local/patches/RcppParallel/disable-tbb.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/src/Makevars.in b/src/Makevars.in -index be8445f..faee771 100644 ---- a/src/Makevars.in -+++ b/src/Makevars.in -@@ -60,7 +60,10 @@ else - endif - - ifeq ($(UNAME), Linux) -- USE_TBB=Linux -+ # bincraft patch: the bundled Intel TBB build hangs/fails on musl (Alpine) -+ # and newer toolchains (g++ 15). Skip it (leave USE_TBB unset) and force the -+ # TinyThread backend so RcppParallel still builds. -+ PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=0 - endif - - ifeq ($(UNAME), SunOS) diff --git a/local/patches/RcppParallel/system-tbb.patch b/local/patches/RcppParallel/system-tbb.patch new file mode 100644 index 0000000..263a593 --- /dev/null +++ b/local/patches/RcppParallel/system-tbb.patch @@ -0,0 +1,19 @@ +diff --git a/src/Makevars.in b/src/Makevars.in +index be8445f..7cb6c9e 100644 +--- a/src/Makevars.in ++++ b/src/Makevars.in +@@ -60,7 +60,13 @@ else + endif + + ifeq ($(UNAME), Linux) +- USE_TBB=Linux ++ # bincraft patch: link the system oneTBB (installed in the build-env images) ++ # instead of building the bundled Intel TBB, which fails on musl (Alpine) and ++ # newer toolchains (g++ 15). Leaving USE_TBB unset skips the bundled build; ++ # -DRCPP_PARALLEL_USE_TBB=1 keeps the TBB backend so dependents (rstan, ...) ++ # link TBB, and -ltbb/-ltbbmalloc pull the system library from default paths. ++ PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -DTBB_INTERFACE_NEW ++ PKG_LIBS += -ltbb -ltbbmalloc + endif + + ifeq ($(UNAME), SunOS) diff --git a/local/patches/registry.json b/local/patches/registry.json index e53f1c9..c446fda 100644 --- a/local/patches/registry.json +++ b/local/patches/registry.json @@ -2,17 +2,22 @@ { "package": "RcppParallel", "versions": "*", - "platforms": ["alpine", "ubuntu-2604"], + "platforms": [ + "alpine", + "ubuntu-2604" + ], "env": {}, "configure_args": [], "makevars": {}, - "patch": "RcppParallel/disable-tbb.patch", - "reason": "bundled Intel TBB build hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604); patch unsets USE_TBB and forces -DRCPP_PARALLEL_USE_TBB=0 so RcppParallel skips the bundled build and uses the TinyThread backend" + "patch": "RcppParallel/system-tbb.patch", + "reason": "bundled Intel TBB build hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604); link the system oneTBB (now in the build-env images) instead, keeping the TBB backend so dependents (rstan, ...) link TBB" }, { "package": "fs", "versions": "*", - "platforms": ["*"], + "platforms": [ + "*" + ], "env": {}, "configure_args": [], "makevars": {}, @@ -22,7 +27,9 @@ { "package": "rstan", "versions": "*", - "platforms": ["*"], + "platforms": [ + "*" + ], "env": {}, "configure_args": [], "makevars": { From 61e1c0188d79f8dd03b5a523ef5e0a1542a469ef Mon Sep 17 00:00:00 2001 From: pat-s Date: Mon, 20 Jul 2026 15:24:17 +0200 Subject: [PATCH 13/53] chore: adjust weekly audit runs --- .crow/weekly-audit-missing.yaml | 36 ++++++++++++++++++++----------- .crow/weekly-rebuild-missing.yaml | 26 +++++++++++++++++++--- 2 files changed, 46 insertions(+), 16 deletions(-) diff --git a/.crow/weekly-audit-missing.yaml b/.crow/weekly-audit-missing.yaml index 6ff71e3..d66a37b 100644 --- a/.crow/weekly-audit-missing.yaml +++ b/.crow/weekly-audit-missing.yaml @@ -11,12 +11,12 @@ variables: description: "Manual run target: a specific -, or 'all' for every os/arch." options: - all - - alpine-321-amd64 - - alpine-321-arm64 - alpine-322-amd64 - alpine-322-arm64 - alpine-323-amd64 - alpine-323-arm64 + - alpine-324-amd64 + - alpine-324-arm64 - redhat-8-amd64 - redhat-8-arm64 - redhat-9-amd64 @@ -27,6 +27,8 @@ variables: - ubuntu-2204-arm64 - ubuntu-2404-amd64 - ubuntu-2404-arm64 + - ubuntu-2604-amd64 + - ubuntu-2604-arm64 default: all when: @@ -42,27 +44,27 @@ labels: matrix: include: - - OS: alpine-321 - ARCH: amd64 - R_VERSION: 4.5.3 - IMG: alpine:3.24 - - OS: alpine-321 - ARCH: arm64 - R_VERSION: 4.5.3 - IMG: alpine:3.24 - OS: alpine-322 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 - OS: alpine-322 ARCH: arm64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 - OS: alpine-323 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 - OS: alpine-323 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + - OS: alpine-324 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-324 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.24 @@ -106,6 +108,14 @@ matrix: ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:noble + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: ubuntu:resolute + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: ubuntu:resolute steps: - name: 'Audit missing binaries' diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index 934c518..53f178f 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -16,6 +16,8 @@ variables: - alpine-322-arm64 - alpine-323-amd64 - alpine-323-arm64 + - alpine-324-amd64 + - alpine-324-arm64 - redhat-8-amd64 - redhat-8-arm64 - redhat-9-amd64 @@ -26,6 +28,8 @@ variables: - ubuntu-2204-arm64 - ubuntu-2404-amd64 - ubuntu-2404-arm64 + - ubuntu-2604-amd64 + - ubuntu-2604-arm64 default: all when: @@ -44,16 +48,24 @@ matrix: - OS: alpine-322 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 - OS: alpine-322 ARCH: arm64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 - OS: alpine-323 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 - OS: alpine-323 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + - OS: alpine-324 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-324 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.24 @@ -97,6 +109,14 @@ matrix: ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:noble + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute steps: - name: 'Rebuild missing binaries' From 3cc323d99e4de7ad3261f926a9da28d54ed3ff2f Mon Sep 17 00:00:00 2001 From: pat-s Date: Mon, 20 Jul 2026 20:59:47 +0000 Subject: [PATCH 14/53] fix(patches): widen RcppParallel system-tbb scope to all oneTBB-2021 platforms (#137) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## What Widen the RcppParallel `system-tbb` registry patch scope from `[alpine, ubuntu-2604]` to `[alpine, ubuntu, redhat-10]`. ## Why #135 fixed the TBB cluster on alpine + ubuntu-2604 only. A per-image audit showed the problem is broader: RcppParallel's bundled Intel TBB build fails on **every** build image with a modern toolchain (alpine/musl, ubuntu jammy/noble/resolute g++ 11/13/15, redhat-10 GCC 14), and only redhat-8/9 (older toolchains + pre-oneTBB system TBB) tolerate the bundled build. The system-TBB fix applies wherever the image ships **oneTBB 2021+** (has the `tbb::detail::r1` namespace rstan needs): | platform | system TBB | in scope? | |---|---|---| | alpine (all) | oneTBB 2022 | ✅ | | ubuntu 2204/2404/2604 | oneTBB 2021.5 / 2021.11 / 2022 | ✅ (via `ubuntu` family token) | | redhat-10 | oneTBB 2021.11 | ✅ | | redhat-8 | TBB 2018 (classic) | ❌ pre-oneTBB → bundled | | redhat-9 | TBB 2020.3 (classic) | ❌ pre-oneTBB, bundled works → bundled | ## Requires The matching build-env-images env (`TBB_INC`/`TBB_LIB`) extended to all ubuntu + el10: build-env-images #13. Ship together. ## Verified RcppParallel + rstan build and link (no `symbol not found`) on alpine, redhat-10, ubuntu noble and ubuntu resolute; RcppParallel builds on ubuntu jammy. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/137 --- local/patches/registry.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/local/patches/registry.json b/local/patches/registry.json index c446fda..b444986 100644 --- a/local/patches/registry.json +++ b/local/patches/registry.json @@ -4,13 +4,14 @@ "versions": "*", "platforms": [ "alpine", - "ubuntu-2604" + "ubuntu", + "redhat-10" ], "env": {}, "configure_args": [], "makevars": {}, "patch": "RcppParallel/system-tbb.patch", - "reason": "bundled Intel TBB build hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604); link the system oneTBB (now in the build-env images) instead, keeping the TBB backend so dependents (rstan, ...) link TBB" + "reason": "RcppParallel bundles an old Intel TBB whose build fails on musl and modern toolchains (g++ 14/15); link the system oneTBB (2021+) shipped in the build-env images instead, keeping the TBB backend so dependents (rstan, ...) link TBB. Scoped to platforms with oneTBB 2021+ (alpine, all ubuntu, el10); el8/el9 ship pre-oneTBB TBB and are left on the bundled build." }, { "package": "fs", From 71f3f0c6011576c751fda00e64fffd059e26ab6e Mon Sep 17 00:00:00 2001 From: pat-s Date: Tue, 21 Jul 2026 08:51:23 +0000 Subject: [PATCH 15/53] fix(audit): replace arch subsection in place instead of appending duplicates (#138) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem A fresh `weekly-audit-missing` run followed by `weekly-rebuild-missing` reported that almost every package "already exists in the remote bucket", even though the audit had just flagged them as missing. Root cause: the audit's Forgejo-issue update matched the existing `### ` subsection by its **bare** header (`### arm64`) while writing headers with a ` (N missing, M to rebuild)` suffix. The equality test never matched, so every run **appended** a new block instead of replacing the old one. Issue #63 had accumulated 38 arch subsections under `## alpine-323` where 2 are expected (75 total across the alpine platforms; body ~77k lines). `fetch-rebuild-packages-from-issue.R` reads the **first** matching block, which was the oldest snapshot. So the rebuild kept re-checking a months-old list (180 packages, mostly already built), while the genuinely-missing packages, ~1921 for alpine-323/arm64 in the freshest block, were never fed to the rebuild and the backlog grew silently. ## Changes - **`local/weekly-missing-binaries-audit.R`**: match arch subsections by prefix (`^### ( |$)`) and remove **all** blocks for that arch before writing one fresh block. Accumulation now self-heals on every run. - **`local/dedupe-audit-issue.R`** (new): one-off cleanup that collapses each `## platform` section to the freshest block per arch across the three OS-family issues. Supports `DRY_RUN=1`. - **`local/fetch-rebuild-packages-from-issue.R`**: prefer the audit's freshly-written RDS (overwritten each run, immune to issue-body drift), falling back to issue parsing when absent. ## Validation Simulated the dedupe logic against the live #63 body: **75 → 8** arch subsections, body 77k → 28k lines, and the kept alpine-323/arm64 block correctly resolves to `GARCH.X (3.0)` (the stale first block held `2.0`). ## Follow-ups (not in this PR) - `alpine-321` is audited but has no row in the rebuild matrix (7,230 missing, never rebuilt). - An `alpine-324` section exists in the issue but is in neither matrix. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/138 --- local/dedupe-audit-issue.R | 150 ++++++++++++++++++++++ local/fetch-rebuild-packages-from-issue.R | 31 ++++- local/weekly-missing-binaries-audit.R | 54 ++++---- 3 files changed, 211 insertions(+), 24 deletions(-) create mode 100644 local/dedupe-audit-issue.R diff --git a/local/dedupe-audit-issue.R b/local/dedupe-audit-issue.R new file mode 100644 index 0000000..c78015a --- /dev/null +++ b/local/dedupe-audit-issue.R @@ -0,0 +1,150 @@ +# One-off maintenance: collapse the duplicate arch subsections that accumulated +# in the "Missing package binaries for latest version ()" issues. +# +# A bug in weekly-missing-binaries-audit.R matched the existing "### " +# subsection by its bare header while writing headers with a +# " (N missing, M to rebuild)" suffix, so every audit run appended a fresh block +# instead of replacing it. This script rewrites each "## " section to +# keep only the *last* (freshest) block per arch. The audit fix prevents further +# accumulation; this cleans up what is already there. +# +# Env: FORGEJO_TOKEN (required). DRY_RUN=1 to preview counts without patching. + +library(httr2, quietly = TRUE) + +forgejo_base <- "https://git.devxy.io/api/v1" +repo <- "devxy/build-cran-binaries" +token <- Sys.getenv("FORGEJO_TOKEN") +dry_run <- nchar(Sys.getenv("DRY_RUN")) > 0 + +if (nchar(token) == 0) { + stop("FORGEJO_TOKEN env var is not set") +} + +issue_titles <- c( + "Missing package binaries for latest version (Alpine)", + "Missing package binaries for latest version (Ubuntu)", + "Missing package binaries for latest version (Red Hat)" +) + +# Collapse one "## " block: keep only the last block per arch, +# emitted in order of first appearance. `pl[1]` is the "## " header. +dedupe_platform <- function(pl) { + sub_hdr <- which(grepl("^### ", pl)) + if (length(sub_hdr) == 0) { + return(pl) + } + preamble <- pl[seq_len(sub_hdr[1] - 1)] + sub_end <- c(sub_hdr[-1] - 1, length(pl)) + blocks <- lapply(seq_along(sub_hdr), function(k) { + pl[seq(sub_hdr[k], sub_end[k])] + }) + arches <- vapply( + blocks, + function(b) sub("^### (\\S+).*", "\\1", b[1]), + character(1) + ) + # Index of the last block for each arch, kept in first-appearance order. + last_idx <- vapply( + unique(arches), + function(a) max(which(arches == a)), + integer(1) + ) + keep <- sort(last_idx) + out <- preamble + for (i in keep) { + out <- c(out, blocks[[i]]) + } + out +} + +process_issue <- function(title) { + search_url <- sprintf( + "%s/repos/%s/issues?type=issues&state=open&q=%s&limit=50", + forgejo_base, + repo, + utils::URLencode(title, reserved = TRUE) + ) + resp <- request(search_url) |> + req_headers(Authorization = paste("token", token)) |> + req_perform() + issues <- resp_body_json(resp, simplifyVector = FALSE) + match_idx <- which(vapply(issues, function(x) x$title, character(1)) == title) + if (length(match_idx) == 0) { + cat(sprintf("[skip] No issue found: %s\n", title)) + return(invisible()) + } + + issue_number <- issues[[match_idx[1]]]$number + body <- issues[[match_idx[1]]]$body + if (is.null(body) || nchar(body) == 0) { + cat(sprintf("[skip] Empty body: #%d %s\n", issue_number, title)) + return(invisible()) + } + + lines <- strsplit(body, "\n", fixed = TRUE)[[1]] + before <- sum(grepl("^### ", lines)) + + # Split off the "## Excluded packages" footer so it is preserved verbatim. + excl_idx <- which(lines == "## Excluded packages") + footer <- character(0) + if (length(excl_idx) > 0) { + pre_dash <- which(lines == "---" & seq_along(lines) < excl_idx[1]) + cut <- if (length(pre_dash) > 0) pre_dash[length(pre_dash)] else excl_idx[1] + footer <- lines[seq(cut, length(lines))] + lines <- lines[seq_len(cut - 1)] + } + + # Platform headers ("## "); everything before the first is preamble. + plat_idx <- which(grepl("^## ", lines)) + if (length(plat_idx) == 0) { + cat(sprintf("[skip] No platform sections: #%d %s\n", issue_number, title)) + return(invisible()) + } + top <- lines[seq_len(plat_idx[1] - 1)] + plat_end <- c(plat_idx[-1] - 1, length(lines)) + + new_lines <- top + for (j in seq_along(plat_idx)) { + pl <- lines[seq(plat_idx[j], plat_end[j])] + new_lines <- c(new_lines, dedupe_platform(pl)) + } + if (length(footer) > 0) { + new_lines <- c(new_lines, footer) + } + + after <- sum(grepl("^### ", new_lines)) + cat(sprintf( + "#%d %s: %d -> %d arch subsections%s\n", + issue_number, + title, + before, + after, + if (dry_run) " (dry run, not patched)" else "" + )) + + if (dry_run) { + return(invisible()) + } + + patch_url <- sprintf( + "%s/repos/%s/issues/%d", + forgejo_base, + repo, + issue_number + ) + request(patch_url) |> + req_headers( + Authorization = paste("token", token), + `Content-Type` = "application/json" + ) |> + req_body_json(list(body = paste(new_lines, collapse = "\n"))) |> + req_method("PATCH") |> + req_perform() + cat(sprintf(" patched #%d\n", issue_number)) +} + +for (t in issue_titles) { + process_issue(t) +} +cat("Done.\n") diff --git a/local/fetch-rebuild-packages-from-issue.R b/local/fetch-rebuild-packages-from-issue.R index 26e544d..9d8043c 100644 --- a/local/fetch-rebuild-packages-from-issue.R +++ b/local/fetch-rebuild-packages-from-issue.R @@ -4,7 +4,6 @@ forgejo_base <- "https://git.devxy.io/api/v1" repo <- "devxy/build-cran-binaries" platform <- Sys.getenv("PLATFORM") arch <- Sys.getenv("ARCH") -token <- Sys.getenv("FORGEJO_TOKEN") output_file <- Sys.getenv("REBUILD_PKG_LIST", "/tmp/rebuild_pkgs.txt") if (nchar(platform) == 0) { @@ -13,6 +12,36 @@ if (nchar(platform) == 0) { if (nchar(arch) == 0) { stop("ARCH env var is not set") } + +# Prefer the audit's freshly-written RDS. The audit overwrites it each run +# (saveRDS), so unlike the Forgejo issue body it is never subject to the +# duplicate-subsection accumulation bug. Fall back to parsing the issue when the +# RDS is absent (e.g. a fresh runner with no shared cache). +rds_file <- file.path( + Sys.getenv("REBUILD_PKG_RDS_DIR", "/mnt/cache/packages"), + sprintf("weekly_rebuild_%s_%s.rds", platform, arch) +) +if (file.exists(rds_file)) { + pkgs <- tryCatch(as.character(readRDS(rds_file)), error = function(e) NULL) + if (!is.null(pkgs) && length(pkgs) > 0) { + cat(sprintf( + "Using audit RDS %s: %d rebuildable packages for %s/%s\n", + rds_file, + length(pkgs), + platform, + arch + )) + writeLines(pkgs, output_file) + cat(sprintf("Wrote package list to %s\n", output_file)) + q("no") + } + cat(sprintf( + "RDS %s present but empty/unreadable -- falling back to issue\n", + rds_file + )) +} + +token <- Sys.getenv("FORGEJO_TOKEN") if (nchar(token) == 0) { stop("FORGEJO_TOKEN env var is not set") } diff --git a/local/weekly-missing-binaries-audit.R b/local/weekly-missing-binaries-audit.R index 6b32037..7b0b65d 100644 --- a/local/weekly-missing-binaries-audit.R +++ b/local/weekly-missing-binaries-audit.R @@ -328,7 +328,6 @@ if (nchar(forgejo_token) == 0) { } plat_header <- sprintf("## %s", platform) - arch_header <- sprintf("### %s", arch) plat_idx <- which(lines == plat_header) @@ -359,31 +358,40 @@ if (nchar(forgejo_token) == 0) { } plat_lines <- lines[seq(pi, plat_end)] - arch_local_idx <- which(plat_lines == arch_header) - if (length(arch_local_idx) == 0) { - # Append arch subsection at end of platform block - lines <- c( - lines[seq_len(plat_end)], - "", - arch_lines, - lines[seq(plat_end + 1, length(lines))] - ) + # Arch subsection headers within the platform block (### arm64 / ### amd64). + # Match by prefix: headers carry a " (N missing, M to rebuild)" suffix, so + # exact-equality matching never found the existing block and silently + # appended a duplicate on every run. Remove *all* blocks for this arch + # (collapsing any previously accumulated duplicates), then write one fresh + # block, so the issue holds a single current subsection per arch. + sub_hdr <- which(grepl("^### ", plat_lines)) + arch_re <- sprintf("^### %s( |$)", arch) + + if (length(sub_hdr) == 0) { + # No arch subsections yet -- append after the platform header/preamble. + new_plat_lines <- c(plat_lines, "", arch_lines) } else { - ai <- pi + arch_local_idx[1] - 1 # absolute line index - - # End of arch subsection - next_arch <- which( - grepl("^### |^## |^---", lines) & seq_along(lines) > ai - ) - arch_end <- if (length(next_arch) > 0) next_arch[1] - 1 else plat_end - - lines <- c( - lines[seq_len(ai - 1)], - arch_lines, - lines[seq(arch_end + 1, length(lines))] - ) + preamble <- plat_lines[seq_len(sub_hdr[1] - 1)] + # Each subsection runs from its ### header to the line before the next + # ### header (#### known-failures stays inside its own block). + sub_end <- c(sub_hdr[-1] - 1, length(plat_lines)) + kept <- character(0) + for (k in seq_along(sub_hdr)) { + block <- plat_lines[seq(sub_hdr[k], sub_end[k])] + if (!grepl(arch_re, block[1])) { + kept <- c(kept, block) + } + } + new_plat_lines <- c(preamble, kept, "", arch_lines) } + + tail_lines <- if (plat_end < length(lines)) { + lines[seq(plat_end + 1, length(lines))] + } else { + character(0) + } + lines <- c(lines[seq_len(pi - 1)], new_plat_lines, tail_lines) } # Rebuild excluded footer From 736564a4ff39c7f46b0c72a6bc742062deca9694 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 24 Jul 2026 11:18:28 +0200 Subject: [PATCH 16/53] fix: prevent renovate bumps for fixed matrix assignments --- .crow/process-updates.yaml | 8 ++++---- .crow/trial-build-registry.yaml | 8 ++++---- renovate.json | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.crow/process-updates.yaml b/.crow/process-updates.yaml index 3da41fd..59b1c26 100644 --- a/.crow/process-updates.yaml +++ b/.crow/process-updates.yaml @@ -47,25 +47,25 @@ matrix: - OS: alpine-322 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 OS_ID: alpine322 PROCESS_NEW: "FALSE" - OS: alpine-322 ARCH: arm64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 OS_ID: alpine322 PROCESS_NEW: "FALSE" - OS: alpine-323 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 OS_ID: alpine323 PROCESS_NEW: "FALSE" - OS: alpine-323 ARCH: arm64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 OS_ID: alpine323 PROCESS_NEW: "FALSE" - OS: alpine-324 diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml index cb8df8b..73856a1 100644 --- a/.crow/trial-build-registry.yaml +++ b/.crow/trial-build-registry.yaml @@ -29,19 +29,19 @@ matrix: - OS: alpine-322 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 - OS: alpine-322 ARCH: arm64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.22 - OS: alpine-323 ARCH: amd64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 - OS: alpine-323 ARCH: arm64 R_VERSION: 4.5.3 - IMG: alpine:3.24 + IMG: alpine:3.23 - OS: alpine-324 ARCH: amd64 R_VERSION: 4.5.3 diff --git a/renovate.json b/renovate.json index 53c7306..8c8e208 100644 --- a/renovate.json +++ b/renovate.json @@ -1,7 +1,7 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", "extends": ["local>devxy/renovate-config"], - "ignorePaths": ["docker/**"], + "ignorePaths": ["docker/**", ".crow/process-updates.yaml", ".crow/build-all-versions.yaml", ".crow/weekly-rebuild-missing.yaml"], "customManagers": [ { "customType": "regex", From 36c963eac9b13eb525a4aa2a14f5dea2494cfe28 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Tue, 28 Jul 2026 00:32:39 +0000 Subject: [PATCH 17/53] chore(deps): update pre-commit hook davidanson/markdownlint-cli2 to v0.23.2 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a0f4422..df8af14 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,7 +16,7 @@ repos: args: - --markdown-linebreak-ext=md - repo: https://github.com/DavidAnson/markdownlint-cli2 - rev: v0.23.0 + rev: v0.23.2 hooks: - id: markdownlint-cli2 - repo: https://github.com/rbubley/mirrors-prettier From adcc74ba4fec1c02d51778c36532cd72058f74ce Mon Sep 17 00:00:00 2001 From: automation-bot Date: Tue, 28 Jul 2026 00:32:55 +0000 Subject: [PATCH 18/53] chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.6 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index df8af14..cee748e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,7 @@ repos: hooks: - id: markdownlint-cli2 - repo: https://github.com/rbubley/mirrors-prettier - rev: v3.9.4 + rev: v3.9.6 hooks: - id: prettier - repo: https://github.com/posit-dev/air-pre-commit From c7293aefa1bde9ed214eec9702f63c25e4244f2f Mon Sep 17 00:00:00 2001 From: automation-bot Date: Tue, 28 Jul 2026 02:33:47 +0000 Subject: [PATCH 19/53] chore(deps): update terraform bunnynet to v0.15.2 --- .terraform.lock.hcl | 70 ++++++++++++++++++++++----------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index 6ef10fa..b18d5af 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -38,43 +38,43 @@ provider "registry.opentofu.org/hashicorp/http" { } provider "registry.terraform.io/bunnyway/bunnynet" { - version = "0.15.1" + version = "0.15.2" constraints = "~> 0.15" hashes = [ - "h1:/2NUpbtjkc+w6n5V3kGP0rSzGjN0K2Wdfe2K+CZdmhU=", - "h1:1TOrpmCR0aT5xX1sjt70zqlYkMJnVe6r0nx2B0DS/mE=", - "h1:4uC8r8ILr+vZJ230uGqIUaWQ7uORCrIzoEuYrAq2JuE=", - "h1:6b+2osJUfwcaYZ6mathLPf/58sr/4XkLXQrcSufnkMk=", - "h1:CPldfjf79QS8mIP+GWoS0FVhrFlyjvN2+39zfyP76Ik=", - "h1:EvXICHyGIKpoYlDeKHOPzfmpvdRdhgsOMcR2nb6+tKY=", - "h1:GZLq+nDxS1CyBH0ELGTSQj9X7ozemJ1jpPA4KwbtR+c=", - "h1:ISNFqL745IQgZ6yMLy8ofV8ixbYqZYa9JKdi2W3pmNk=", - "h1:IrNrEuvFd0nYDGQefwmT8d1CSJb9e8LN5w9vw1ODp7E=", - "h1:Ms79slY9bZ94+n4cwIHvI9+/cvbucwo6S1+z5KAiznw=", - "h1:NWA9XSEBcpSkgwwIvl6tHrxGQY3uYhqNS4Vnb9RLyLQ=", - "h1:UjvxxxggicLtiE3yTe1Gx0oLUTeZpWmgIfXuHzWHn1c=", - "h1:VgJjo14DGkU4Jwo4D3GT4/5sq1tdjiZscKS5l3cb890=", - "h1:dBu3AW5YNLIvbBIMNk3wUHKw4TW+BDbj34a+mCqYhWE=", - "h1:i5oGD06nQ3JRsBIa2u4wCej+ETgp970CFl75dOKkHno=", - "h1:mTqR+vD1AWPx+mu7S0/pzBy71z7WOrjH7arOP77PXh4=", - "h1:nmTM61G8vYjpofeEqspMORpsNvTGCNZySGfjdXardL0=", - "zh:0f9bf5aaa47164a4d6ae4433d5e285a9456a5053401b2bad4ed68622f574ddee", - "zh:3039bee421fb8855a919f449fc731d145254371f5f0c39cc4660f3aeed6a8b10", - "zh:36664b08186e0c194747b18dee24ed97327c6e704133d4cf0df27abef1652f86", - "zh:3c7eae99d8c5ff65dfb99c8b9c1980147282d68971e1ef1ff0f126a6bff59d8f", - "zh:5293cc21abf54f4e5745437ca2d40d206aae323b2e1d41cf45dcc63a8868cbb3", - "zh:5994e5145e616e7e881010717e4c7def2945eb6d933f62db4ec3167732ccac84", - "zh:7994db9ed3fdb6cbf21f2154ea962cf82f04e425988bedc6657de2497d6cb6c3", + "h1:1OktRVcHWTvR/KKK4UWVm49JKibjyKOu0Epew+TawZI=", + "h1:4L1bPF0zW5z7Y6BEuPLXWP1RiOr/V8G5dhaRStV1yQM=", + "h1:4fpJGk4TRnWa0ZsNxBLWLlFgOb5WLyohpJ61Lsk5D0Y=", + "h1:7JTOjvrbATIKRCI+NKXCTMMSmUHYnKgsCsbKV+peAFM=", + "h1:8NDV2elfSxmixLUDqGpCSkKVm1pk7hgToP/L5bmEb4g=", + "h1:CYoaY53mSTjxq8nTMXuu7ET53q4Qe1+M6SfH9UaxE80=", + "h1:JbepdZF6DL97FUxGUI0Fi4sH9txTgzYk5q89Tzltifo=", + "h1:T6u0dqstAgR3L+8oPlNfcmOHVYZjIJ3UNvgdUyucpNA=", + "h1:U0Benusw0c0fJSdFvICBxuBxV1nAVOplY+AfLuda6ds=", + "h1:XZkiPAERPz4PKOMqohfMsA1qlnGhb2++R7rbMYAiDpo=", + "h1:Znc6swnxXdPeMarUgImUtbmw2iP83xVWUb4ShJC+F+U=", + "h1:aTJTUfP8tC71u1qgf4fqKv7RWd5dDTSpRQvD2Co2tWY=", + "h1:fozSGXAjeabAda2lqjXxqZ4haDE/QQAR1T6wV/t/NNw=", + "h1:pVBNrDoiSd5Pmf0lNa0uVFMl2u447kT0iXhDBT67mXk=", + "h1:rLnEQPCr3YbxzUWgmBITbyXzNaraTJGaW0mNEANzOPQ=", + "h1:wNSoVvpO1Y9vFTx3XbWYW5WSb2Go6EoRyci6l/kgBPE=", + "h1:x2gE2pPOUypQL5nCIak13MMqmGIlozwVpaaXfdZakSw=", + "zh:03acea3774550e25e7bf214ea3a8a9163b68d2009eb613c71d7f57c333cd8416", + "zh:13acba069e86d6a5d4d176952950c77fd8bd81629ed6b861349e5f74b0e78cb8", + "zh:275b9567ea05d5a5f0fb4d846032ed01482220a290aeb5d28e0bfa159779e3db", + "zh:444b008de5cbc7275f6d4230219a464e7b97daeea938223d693a3161c1158caf", + "zh:533b4cea6b5aa2351335453f45406eadb6d4485d5c339a0d5d5e0d84df21c22b", + "zh:55f0323631a34d1aa96178d08ec7eb7ec317306886daa00fd3a7dca61b00315b", + "zh:6e077b28e89f4364bbddf4dd783fc657c13df7d1a385f04629ba8deb1eb0a332", + "zh:6e10e279e7c1d44d3fe287c033d10068b5194621f6da03f28fa7b91fa4f2ef19", + "zh:74c1d79356f2c213ef19c7b478162c4f77ab8b840438b83701088554bd4090a1", "zh:890df766e9b839623b1f0437355032a3c006226a6c200cd911e15ee1a9014e9f", - "zh:93aa863e536ba9376ccf9e614e9edc9b214a2ce8c4316d416a8e249b436f52d2", - "zh:ab5cb4baeda57559686a0ccf0e09158aa64624ee6ba0ef32b769f13b11a43068", - "zh:ae9388b62eede8fd9272407bf75f8241a965bd489d45ec9dd3f9fac696d500e1", - "zh:caa5befd16960e2f69c7ec483e228e5ff43ab0979c17f1b874c9ffaa1c7c0e43", - "zh:cddd3e1067defa06a4e4ad5cb3940c7943e29c42417de57236aa7d3e2aeaae13", - "zh:cdfa44d591d0805116159556947904d70f534c6816188c45cf3a7544d2722ac9", - "zh:d607e9f1f3e09f13404f219e1893e3b3c77aece4afb54e999f934c021f41f576", - "zh:d8a397aca95125c6a0c0c78d2ded5843b9204effa9f5cf7419f017b500ad9228", - "zh:f5499eaff0d221725ad209d27d87c5b46d5c554caad7dc42947c760377abe3b0", - "zh:fc5f5cf433abc83e5169fa222992ec521c0c802075970251e3dd2c1d50c4f5c1", + "zh:9ebabdd167d1fd13d357517007027ad34acb7db130fdc75fd3b2652560c0399e", + "zh:a185124d2b93dff80203074c0f4a9dea8f21965c3cbc0592929b4ae58692b045", + "zh:a46483a7cd69699488c82406519769361b65eb59c39ab1bfd42f4d84d1bd30fd", + "zh:b29e2807adf9a0965f33246c59eb04bc2ac089fe44f2e439ece7c53bdee033a1", + "zh:b550a4c5eb7b17ca85b2f76c4b10bf0523b9c22f6104fe9fd5dce7b3c3bbbf37", + "zh:b9a9685c9fa99674ddbb11633bb9648152f8fbf92881deae1dd28ebca95b150e", + "zh:e412569cf41ebb5106d034f148df3968fafcf75de804713a20bee7d3d4e74c36", + "zh:fb639b074ee65c08590b971866e10e61aa85c7937a7b7f941899ac8cbcd9157d", ] } From 463054625afaa404a8f5a93e362957785836efab Mon Sep 17 00:00:00 2001 From: automation-bot Date: Tue, 28 Jul 2026 02:34:05 +0000 Subject: [PATCH 20/53] chore(deps): update pre-commit hook posit-dev/air-pre-commit to v0.11.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cee748e..140ae88 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: hooks: - id: prettier - repo: https://github.com/posit-dev/air-pre-commit - rev: 0.10.0 + rev: 0.11.0 hooks: - id: air-format - repo: https://github.com/editorconfig-checker/editorconfig-checker From 8d0c4b7ccdca01863be1c6976d154a0074c94a36 Mon Sep 17 00:00:00 2001 From: pat-s Date: Tue, 28 Jul 2026 06:57:08 +0000 Subject: [PATCH 21/53] fix(patches): widen RcppParallel system-tbb scope to the whole redhat family (#139) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Extends #137. el8/el9 were excluded because they ship only classic Intel TBB. build-env-images now vendors oneTBB 2021 into `/usr/local` on el8/el9, so every platform has oneTBB 2021+. Widen the scope `redhat-10` → `redhat` (family token covers el8/el9/el10) and fix the reason text (no longer 'left on bundled'). **Requires the el8/el9 images rebuilt with the vendored oneTBB (build-env-images PR).** Verified: patched RcppParallel builds + links the vendored oneTBB on both el8 (g++ 8.5) and el9 (g++ 11.5). Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/139 --- local/patches/registry.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/local/patches/registry.json b/local/patches/registry.json index b444986..99b80e3 100644 --- a/local/patches/registry.json +++ b/local/patches/registry.json @@ -5,13 +5,13 @@ "platforms": [ "alpine", "ubuntu", - "redhat-10" + "redhat" ], "env": {}, "configure_args": [], "makevars": {}, "patch": "RcppParallel/system-tbb.patch", - "reason": "RcppParallel bundles an old Intel TBB whose build fails on musl and modern toolchains (g++ 14/15); link the system oneTBB (2021+) shipped in the build-env images instead, keeping the TBB backend so dependents (rstan, ...) link TBB. Scoped to platforms with oneTBB 2021+ (alpine, all ubuntu, el10); el8/el9 ship pre-oneTBB TBB and are left on the bundled build." + "reason": "RcppParallel bundles an old Intel TBB whose build fails on musl and modern toolchains (g++ 8-15 + modern make); link the system oneTBB (2021+) instead, keeping the TBB backend so dependents (rstan, ...) link TBB. All build-env platforms now provide oneTBB 2021+: native on alpine/ubuntu/el10, built from source into /usr/local on el8/el9 (their stock TBB is classic 2018/2020, too old)." }, { "package": "fs", From 86707e3de4f69e912c2e060386f08dbcd4f25cb9 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Fri, 31 Jul 2026 00:32:20 +0000 Subject: [PATCH 22/53] chore(deps): update terraform bunnynet to ~> 0.16 --- .terraform.lock.hcl | 72 ++++++++++++++++++++++----------------------- provider.tf | 2 +- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index b18d5af..fdf41e1 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -38,43 +38,43 @@ provider "registry.opentofu.org/hashicorp/http" { } provider "registry.terraform.io/bunnyway/bunnynet" { - version = "0.15.2" - constraints = "~> 0.15" + version = "0.16.0" + constraints = "~> 0.16" hashes = [ - "h1:1OktRVcHWTvR/KKK4UWVm49JKibjyKOu0Epew+TawZI=", - "h1:4L1bPF0zW5z7Y6BEuPLXWP1RiOr/V8G5dhaRStV1yQM=", - "h1:4fpJGk4TRnWa0ZsNxBLWLlFgOb5WLyohpJ61Lsk5D0Y=", - "h1:7JTOjvrbATIKRCI+NKXCTMMSmUHYnKgsCsbKV+peAFM=", - "h1:8NDV2elfSxmixLUDqGpCSkKVm1pk7hgToP/L5bmEb4g=", - "h1:CYoaY53mSTjxq8nTMXuu7ET53q4Qe1+M6SfH9UaxE80=", - "h1:JbepdZF6DL97FUxGUI0Fi4sH9txTgzYk5q89Tzltifo=", - "h1:T6u0dqstAgR3L+8oPlNfcmOHVYZjIJ3UNvgdUyucpNA=", - "h1:U0Benusw0c0fJSdFvICBxuBxV1nAVOplY+AfLuda6ds=", - "h1:XZkiPAERPz4PKOMqohfMsA1qlnGhb2++R7rbMYAiDpo=", - "h1:Znc6swnxXdPeMarUgImUtbmw2iP83xVWUb4ShJC+F+U=", - "h1:aTJTUfP8tC71u1qgf4fqKv7RWd5dDTSpRQvD2Co2tWY=", - "h1:fozSGXAjeabAda2lqjXxqZ4haDE/QQAR1T6wV/t/NNw=", - "h1:pVBNrDoiSd5Pmf0lNa0uVFMl2u447kT0iXhDBT67mXk=", - "h1:rLnEQPCr3YbxzUWgmBITbyXzNaraTJGaW0mNEANzOPQ=", - "h1:wNSoVvpO1Y9vFTx3XbWYW5WSb2Go6EoRyci6l/kgBPE=", - "h1:x2gE2pPOUypQL5nCIak13MMqmGIlozwVpaaXfdZakSw=", - "zh:03acea3774550e25e7bf214ea3a8a9163b68d2009eb613c71d7f57c333cd8416", - "zh:13acba069e86d6a5d4d176952950c77fd8bd81629ed6b861349e5f74b0e78cb8", - "zh:275b9567ea05d5a5f0fb4d846032ed01482220a290aeb5d28e0bfa159779e3db", - "zh:444b008de5cbc7275f6d4230219a464e7b97daeea938223d693a3161c1158caf", - "zh:533b4cea6b5aa2351335453f45406eadb6d4485d5c339a0d5d5e0d84df21c22b", - "zh:55f0323631a34d1aa96178d08ec7eb7ec317306886daa00fd3a7dca61b00315b", - "zh:6e077b28e89f4364bbddf4dd783fc657c13df7d1a385f04629ba8deb1eb0a332", - "zh:6e10e279e7c1d44d3fe287c033d10068b5194621f6da03f28fa7b91fa4f2ef19", - "zh:74c1d79356f2c213ef19c7b478162c4f77ab8b840438b83701088554bd4090a1", + "h1:+7y/HM0f4/cm7dpL5RulSZ3k5EDokVaIutfuanc1hhA=", + "h1:/4n/gUEzVa7LArNrNbZa4RyGC3+MRCCYTuqRqF36Z7U=", + "h1:4cSbrSalUxXnG0RVwrQG51NNleZNFU9GJxWCLK1M9WM=", + "h1:AlidPvq+LqsveQVhc9JYa7OKf4mcR+DjCzMomoBcmkw=", + "h1:Beny1tSl5O/jM7sSP7qYv+NEVTTyS/BGtSxvMFsII/o=", + "h1:E50kVGCtxWYoJgOLtdat1JFc9KCIeMByk65XSIpuaB0=", + "h1:ErNz5hzwf70NouW7a1DAknWI/0/BFUEX53hQ4BnUxWg=", + "h1:GTB8ugjpBEsRZpdVmKJw70IF2B1/fd1Gwven6XKghpk=", + "h1:JEEDgEc2gwjwfvnDwWO2ZHaf9T5WHtb7A6ABx6rQqhE=", + "h1:OVd3EgjJDuyMBFQ4XZYrs09NNEtFw4jGAbwyeos2H3M=", + "h1:U/9QeqZ+Q2MQ7eNfD1eWomLFlbYGwpliHcD/UTFe/D0=", + "h1:VPUe+m5Fx31TAR7udJPGGzk3EpCNizf0TmnKplOJyRM=", + "h1:YkJwUFpUemqi6bwRIEJW4xSpI7CAEXirqhyjl6Rmm68=", + "h1:a/15E8lijUcqvhUGxtqKmJT6jYGmQW9z7yBoOjusDm8=", + "h1:hii960NFcNpr0eZ/dcbnYOf2oZuo2IZl+z1IMTwh5YA=", + "h1:mq/KWNt6PPZLdNpO1ekzrn6EfWz6l8sTHG74dgy07nI=", + "h1:vso6Er2XV/MsUTMtXIlz0AhIFx0TZnK73YNSZfA/9ZY=", + "zh:1f581ed8bc8b676f0127af7c018912ca82972e9348370d9f4dbe5b44005bb0ec", + "zh:1fa5b9c01ffbc7fdc507bbcffc177a1f1deb9f56f3d27183c6d92a11ea3208f8", + "zh:42b6524a9658df7093199b65eb210b3246a9f9822c8778a77e2d00a222441c03", + "zh:4c4f17fe2ae86087626dfd1055b0faea6a23fe3a12aabb2a7de3b9b2df6e3e41", + "zh:5346bb67d7154a8bc8c887b4b86bef95b3e92857d4304f55afea6d56ed152932", + "zh:591df2c3d4552f6f613415c900023d43e73e00e90312b7b1a666fe567219120f", + "zh:7156849aa03348c7556b746d3d9956293678de4a9e30c80480358dcdacb2a7fa", + "zh:75dee86262352f061ad072a5b873d3b3eabbb124ab0f20a803cfd44a87a31067", + "zh:7c33954aff1878bec78a50742897fae78dd2fbd19abeaeaca0c560ccc8f78810", + "zh:7d9cf36633dd991b41891d1c91b45b5c803852a902705453d6be4513524a574c", "zh:890df766e9b839623b1f0437355032a3c006226a6c200cd911e15ee1a9014e9f", - "zh:9ebabdd167d1fd13d357517007027ad34acb7db130fdc75fd3b2652560c0399e", - "zh:a185124d2b93dff80203074c0f4a9dea8f21965c3cbc0592929b4ae58692b045", - "zh:a46483a7cd69699488c82406519769361b65eb59c39ab1bfd42f4d84d1bd30fd", - "zh:b29e2807adf9a0965f33246c59eb04bc2ac089fe44f2e439ece7c53bdee033a1", - "zh:b550a4c5eb7b17ca85b2f76c4b10bf0523b9c22f6104fe9fd5dce7b3c3bbbf37", - "zh:b9a9685c9fa99674ddbb11633bb9648152f8fbf92881deae1dd28ebca95b150e", - "zh:e412569cf41ebb5106d034f148df3968fafcf75de804713a20bee7d3d4e74c36", - "zh:fb639b074ee65c08590b971866e10e61aa85c7937a7b7f941899ac8cbcd9157d", + "zh:9552ed1be3059b31544632d6293c2bfcd2474983e116c42702a6c408deb8e44d", + "zh:b3cb1f2bde0fd591d18109119f6235ff41c7ea6441777a356a64c348ee4ccdf7", + "zh:b5c1748403bf43274eba2574219cfa082351c8b1c1537a768acebef5cc5b2c0a", + "zh:c1b032e33aee40945770bbdf6002f777ee7b4ca541c00f4cf5eb23c09d32ef54", + "zh:d469680df9845fb506be27b2c838d39ccd8e98e26540b99936775f954299c35c", + "zh:dd59fa97fea4b10b901a6a749ebff81895f54126a2f08b4cd8f5baf6cfbbd854", + "zh:fb142d8ea02909587a4858374fe33d8609347150f4d32b7e15423320ffbd07b1", ] } diff --git a/provider.tf b/provider.tf index b267fcc..c22ce2d 100644 --- a/provider.tf +++ b/provider.tf @@ -2,7 +2,7 @@ terraform { required_providers { bunnynet = { source = "registry.terraform.io/BunnyWay/bunnynet" - version = "~> 0.15" + version = "~> 0.16" } } } From 98371fb9c585d9e30439c97ad08bec3d61993aff Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 31 Jul 2026 06:41:46 +0000 Subject: [PATCH 23/53] fix(patches): replace the RcppParallel system-TBB patch with a link-order fix (#145) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Why Every build logs: ``` ! Patch for RcppParallel 6.2.0 did not apply cleanly; skipping patched build. ``` RcppParallel 6.x rewrote its build system. `src/Makevars.in` no longer contains the `USE_TBB=Linux` block that `system-tbb.patch` edited (it is now a short `@VAR@` template driven by `tools/config/configure.R`), so the patch can never apply again. The workaround it implemented is obsolete too. 6.x bundles **oneTBB 2022** and builds it with cmake, which works on musl and with g++ 8-15, so the 5.x reason for linking a system TBB is gone. Linking one is now harmful: `install.libs.R` symlinks the system libraries into `RcppParallel/lib`, so the published binary depends on a TBB the consumer does not have — the same failure mode as `fs` and libuv. What is still broken upstream is the **link order**. `configure.R` names the TBB directory with `-Wl,-L`, and gcc expands its own search dirs into `-L` options ahead of anything forwarded verbatim with `-Wl,`: ``` $ gcc -v -o t t.c -Wl,-L/usr/local/lib64 -ltbb -L/usr/lib/gcc/x86_64-redhat-linux/8 -L/lib/../lib64 -L/usr/lib/../lib64 ... -L/usr/local/lib64 ``` So on any build host with a distro TBB installed, `-ltbb` resolves to that library and `RcppParallel.so` records *its* SONAME (`libtbb.so.12`, or `libtbb.so.2` for the classic Intel TBB on el8/el9) instead of the bundled `libtbb.so`. ## Changes - Replace `RcppParallel/system-tbb.patch` with `RcppParallel/bundled-tbb-link-order.patch`, which changes the three `-Wl,-L` occurrences in `tools/config/configure.R` to plain `-L`. - Scope the RcppParallel entry to `>=6.0.0` and widen `platforms` to `*`. - Drop the `rstan` entry: its `-DTBB_INTERFACE_NEW` is already emitted by `RcppParallel::CxxFlags()` once the bundled oneTBB is used, and its `-I/usr/local/include` was an el8/el9 path applied on every platform. - `.pre-commit-config.yaml`: exclude `local/patches/*.patch` from `trailing-whitespace`, `end-of-file-fixer` and `editorconfig-checker`. They rewrite blank context lines (` ` -> ``) in every diff in the registry; `git apply` happens to tolerate it today, but a patch with meaningful trailing whitespace would be silently corrupted. The excludes are per-hook so `validate patch registry` still runs. - README: the RcppParallel example described the 5.x problem. ## Verification Built in the published images: | image | NEEDED | RPATH | loads with system libtbb removed | | --- | --- | --- | --- | | `build-env-alpine:3.24` | `libtbb.so` | `$ORIGIN/../lib` | yes | | `build-env-redhat:8` | `libtbb.so`, `libtbbmalloc.so` | `$ORIGIN/../lib` | yes | | `build-env-ubuntu:noble` | `libtbb.so` | `$ORIGIN/../lib` | yes | Without the patch the same builds record `libtbb.so.12` (alpine, ubuntu) or `libtbb.so.2` (el8, the classic 2018 TBB) and fall back to the system library at load time. rstan 2.32.7 compiles and loads against the patched RcppParallel on ubuntu noble with no makevars override and with the system libtbb moved away. On el8 it also compiles; loading it there is blocked by an unrelated image bug (see below). ## Behaviour change Requires the paired build-env-images PR (drops `TBB_INC`/`TBB_LIB`) and an image rebuild — with those env vars set, configure still takes the system-TBB branch. After that, RcppParallel binaries ship their own oneTBB and are self-contained. ## Also found, not fixed here - The `uvr lock failed ... GLIBC_2.29 not found` errors in the same log are the `-gnu` uvr artifact on el8's glibc 2.28; fixed in build-env-images. - `build-env-redhat:8` R 4.5.3/4.6.0 cannot load `stats` (`libRlapack.so: undefined symbol: dgemmtr_`): the el8 R RPM symlinks `libRblas.so` to openblas 0.3.15, which predates that symbol. R 4.4.3 and el9 are fine. Belongs in the R RPM build. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/145 --- .pre-commit-config.yaml | 9 ++++ README.md | 2 +- .../RcppParallel/bundled-tbb-link-order.patch | 46 +++++++++++++++++++ local/patches/RcppParallel/system-tbb.patch | 19 -------- local/patches/registry.json | 30 ++---------- 5 files changed, 61 insertions(+), 45 deletions(-) create mode 100644 local/patches/RcppParallel/bundled-tbb-link-order.patch delete mode 100644 local/patches/RcppParallel/system-tbb.patch diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 140ae88..80650cc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,12 +7,20 @@ exclude: | benchmark/| docker/reprex/ ) +# The `^local/patches/.*\.patch$` excludes below keep unified diffs byte-exact: +# a context line for a blank line is a single space, and stripping it (or +# appending a newline) makes `git apply` reject the patch, which surfaces as +# "patch did not apply cleanly" at build time rather than as a lint failure +# here. The exclusions are per-hook, not global, so `validate patch registry` +# still runs when a patch changes. repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: - id: end-of-file-fixer + exclude: ^local/patches/.*\.patch$ - id: trailing-whitespace + exclude: ^local/patches/.*\.patch$ args: - --markdown-linebreak-ext=md - repo: https://github.com/DavidAnson/markdownlint-cli2 @@ -31,6 +39,7 @@ repos: rev: v3.8.0 hooks: - id: editorconfig-checker + exclude: ^local/patches/.*\.patch$ - repo: https://github.com/adrienverge/yamllint.git rev: v1.38.0 hooks: diff --git a/README.md b/README.md index 28541a1..538df34 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ For every package+tag combination: ## Patching packages Some CRAN packages fail to compile on specific platforms due to compiler- or OS-specific issues unrelated to the package itself. -The canonical example is `RcppParallel`, whose bundled TBB sources fail on musl (Alpine) and newer compiler/OS combinations. +The canonical example is `RcppParallel`, whose bundled TBB is linked in a way that lets a system TBB on the build host shadow it, so the published binary depends on a library the consumer does not have. Because such packages are often transitive dependencies of many others, a single failure cascades: all dependents fail even though nothing is wrong with the dependent itself. To address this, frequently-failing packages can be "patched" before they are installed — whether as a direct build target or a transitive dependency pulled in by `pak`. diff --git a/local/patches/RcppParallel/bundled-tbb-link-order.patch b/local/patches/RcppParallel/bundled-tbb-link-order.patch new file mode 100644 index 0000000..45114a8 --- /dev/null +++ b/local/patches/RcppParallel/bundled-tbb-link-order.patch @@ -0,0 +1,46 @@ +diff --git a/tools/config/configure.R b/tools/config/configure.R +index 6293fe1..2f84337 100644 +--- a/tools/config/configure.R ++++ b/tools/config/configure.R +@@ -186,12 +186,23 @@ define( + ) + + # set PKG_LIBS ++# ++# bincraft patch: the library directories below are passed as plain '-L', not ++# '-Wl,-L'. gcc expands its own search dirs (/usr/lib64, /usr/lib/) ++# into explicit '-L' options ahead of anything forwarded verbatim with '-Wl,', ++# so with '-Wl,-L' a system libtbb.so wins over the one named here: on a build ++# host with a distro TBB installed, '-ltbb' resolves to that library and ++# RcppParallel.so records its SONAME (libtbb.so.12, or libtbb.so.2 for the ++# classic Intel TBB) instead of the bundled 'libtbb.so'. The binary then loads ++# the system TBB rather than the copy shipped in RcppParallel/lib, and fails ++# outright on a machine that has no system TBB. gcc places a plain '-L' before ++# its built-in dirs, so the intended library is found first. + pkgLibs <- if (!is.na(tbbLib)) { + + # a TBB supplied via TBB_LIB / TBB_ROOT. an rpath is meaningless on Windows, + # where the loader has no equivalent -- see R/zzz.R for how we resolve there + c( +- "-Wl,-L\"$(TBB_LIB)\"", ++ "-L\"$(TBB_LIB)\"", + if (.Platform$OS.type != "windows") + sprintf("-Wl,-rpath,%s", shQuote(tbbLib)), + "-l$(TBB_NAME)", +@@ -201,14 +212,14 @@ pkgLibs <- if (!is.na(tbbLib)) { + } else if (R.version$os == "emscripten") { + + c( +- "-Wl,-Ltbb/build/lib_release", ++ "-Ltbb/build/lib_release", + "-l$(TBB_NAME)" + ) + + } else { + + c( +- "-Wl,-Ltbb/build/lib_release", ++ "-Ltbb/build/lib_release", + "-l$(TBB_NAME)", + "-l$(TBB_MALLOC_NAME)" + ) diff --git a/local/patches/RcppParallel/system-tbb.patch b/local/patches/RcppParallel/system-tbb.patch deleted file mode 100644 index 263a593..0000000 --- a/local/patches/RcppParallel/system-tbb.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff --git a/src/Makevars.in b/src/Makevars.in -index be8445f..7cb6c9e 100644 ---- a/src/Makevars.in -+++ b/src/Makevars.in -@@ -60,7 +60,13 @@ else - endif - - ifeq ($(UNAME), Linux) -- USE_TBB=Linux -+ # bincraft patch: link the system oneTBB (installed in the build-env images) -+ # instead of building the bundled Intel TBB, which fails on musl (Alpine) and -+ # newer toolchains (g++ 15). Leaving USE_TBB unset skips the bundled build; -+ # -DRCPP_PARALLEL_USE_TBB=1 keeps the TBB backend so dependents (rstan, ...) -+ # link TBB, and -ltbb/-ltbbmalloc pull the system library from default paths. -+ PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -DTBB_INTERFACE_NEW -+ PKG_LIBS += -ltbb -ltbbmalloc - endif - - ifeq ($(UNAME), SunOS) diff --git a/local/patches/registry.json b/local/patches/registry.json index 99b80e3..fe0d387 100644 --- a/local/patches/registry.json +++ b/local/patches/registry.json @@ -1,42 +1,22 @@ [ { "package": "RcppParallel", - "versions": "*", - "platforms": [ - "alpine", - "ubuntu", - "redhat" - ], + "versions": ">=6.0.0", + "platforms": ["*"], "env": {}, "configure_args": [], "makevars": {}, - "patch": "RcppParallel/system-tbb.patch", - "reason": "RcppParallel bundles an old Intel TBB whose build fails on musl and modern toolchains (g++ 8-15 + modern make); link the system oneTBB (2021+) instead, keeping the TBB backend so dependents (rstan, ...) link TBB. All build-env platforms now provide oneTBB 2021+: native on alpine/ubuntu/el10, built from source into /usr/local on el8/el9 (their stock TBB is classic 2018/2020, too old)." + "patch": "RcppParallel/bundled-tbb-link-order.patch", + "reason": "RcppParallel 6.x bundles oneTBB 2022 and builds it with cmake, which works on musl and g++ 8-15, so the system-TBB workaround needed for 5.x is gone. What remains broken is the link order: configure.R passes the TBB directory as '-Wl,-L', and gcc expands its own search dirs (/usr/lib64, /usr/lib/) into '-L' options ahead of anything forwarded with '-Wl,'. On a build host with a distro TBB installed, '-ltbb' therefore resolves to the system library and RcppParallel.so records its SONAME (libtbb.so.12, or libtbb.so.2 for the classic Intel TBB on el8/el9) instead of the bundled 'libtbb.so'. The published binary then loads the system TBB rather than the copy in RcppParallel/lib and fails to dyn.load on a consumer machine without one, the same way fs did with libuv. Passing a plain '-L' puts the bundled build dir ahead of gcc's defaults; verified on alpine 3.24, el8 and ubuntu noble to produce NEEDED libtbb.so + RPATH $ORIGIN/../lib, loading with every system libtbb removed." }, { "package": "fs", "versions": "*", - "platforms": [ - "*" - ], + "platforms": ["*"], "env": {}, "configure_args": [], "makevars": {}, "patch": "fs/force-vendored-libuv.patch", "reason": "fs 2.x configure links system libuv whenever pkg-config finds libuv-devel (installed as a build-time sysreq), producing an fs.so with NEEDED libuv.so.1. That binary fails to dyn.load on consumer machines lacking runtime libuv, because install.packages/renv do not install SystemRequirements (only pak does, and only in the build container). The patch short-circuits configure to copy src/Makevars.vendor and build the bundled static libuv (needs cmake) so the binary is self-contained on every platform. An env/pkg-config override was tried first but the rebuilt binary still linked libuv.so.1, so a source patch is used instead." - }, - { - "package": "rstan", - "versions": "*", - "platforms": [ - "*" - ], - "env": {}, - "configure_args": [], - "makevars": { - "CPPFLAGS": "-DTBB_INTERFACE_NEW -I/usr/local/include" - }, - "patch": null, - "reason": "StanHeaders' init_threadpool_tbb.hpp unconditionally includes the legacy (removed in oneTBB 2021+) for version detection, breaking compilation of Module.cpp against the bundled oneTBB. Pre-defining TBB_INTERFACE_NEW skips that include and selects the modern tbb/global_control.h + tbb/task_arena.h path that the bundled TBB provides (-I/usr/local/include preserves the default CPPFLAGS the override replaces)" } ] From fe2289af56e4724200cd1ebc41e06e67f5c9cb71 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 31 Jul 2026 09:48:41 +0000 Subject: [PATCH 24/53] fix(patches): force RcppParallel to use its bundled oneTBB (#146) ## Why `RcppParallel` binaries built on ubuntu 22.04 still record `NEEDED libtbb.so.12` and cannot `dyn.load` without the distro TBB, although #145 landed the link-order patch and build-env-images dropped `TBB_INC`/`TBB_LIB` the same morning. The link-order fix does not survive a build image that exports those variables, and the published images still do: `.crow/images.yaml` in build-env-images triggers on `cron`/`manual` only, so every image in the registry is still the 2026-07-21 build. With `TBB_LIB` set, `configure.R` never reaches the bundled-oneTBB branch at all, `install.libs.R` fills `RcppParallel/lib` with absolute symlinks into the image's library dir, and the plain `-L` from #145 just points at the system TBB instead of the bundled one. Nothing on the pipeline side can undo this: R reads `~/.Renviron` **after** the process environment, so neither a Crow `environment:` block nor the registry `env` field wins. ``` # the image, not the Containerfile docker run --rm reg.devxy.io/rpkgs/build-env-ubuntu:jammy sh -lc 'grep TBB ~/.Renviron' TBB_INC=/usr/include/oneapi TBB_LIB=/usr/lib/x86_64-linux-gnu ``` Rather than couple correctness to image freshness for a third round-trip, the patch now forces the bundled TBB itself. ## Changes - `local/patches/RcppParallel/bundled-tbb-link-order.patch` -> `local/patches/RcppParallel/force-bundled-tbb.patch`. Keeps the `-Wl,-L` -> `-L` link-order hunk (the bundled branch has the same problem when a distro libtbb is installed) and adds an opt-out, `BINCRAFT_ALLOW_SYSTEM_TBB=TRUE`, for the ambient `TBB_ROOT`/`TBB_LIB`/`TBB_INC`. - All four read sites have to move together; patching only `configure.R` builds the bundled TBB and then **segfaults R on the post-install load test**: - `tools/config/configure.R`: branch selection. - `src/install.libs.R`: `R CMD INSTALL` runs it outside the `tbb` rule in `src/Makevars` that passes the configured values, so at install time it still sees the image environment. - `R/tbb.R` `tbbLibraryPath()`: run time. `.onLoad()` would `dyn.load` the system TBB into the global scope next to the bundled one that `RcppParallel.so` needs - two copies of the same symbols, hence the segfault. - `R/tbb.R` `tbbCxxFlags()` / `tbbLdFlags()`: otherwise dependents such as `rstan` get the system TBB handed back to them. - `local/patches/registry.json`: new patch path and a `reason` describing both failure modes. ## Verification Built through `bincraft:::prepare_patched_repo()` on the **current, unfixed** images (all three still export `TBB_INC`/`TBB_LIB`), with bincraft v5.0.1, i.e. what CI deploys: | image | `NEEDED` | rpath | `RcppParallel/lib` | load, all system `libtbb*` moved away | | --- | --- | --- | --- | --- | | `build-env-ubuntu:jammy` | `libtbb.so` | `$ORIGIN/../lib` | real `libtbb.so.2`, 5.0 MB | OK, 12 threads | | `build-env-redhat:9` | `libtbb.so` | `$ORIGIN/../lib` | real `libtbb.so.2`, 5.1 MB | OK, 12 threads | | `build-env-alpine:3.24` | `libtbb.so` | `$ORIGIN/../lib` | real `libtbb.so.2`, 4.7 MB | OK, 12 threads | For contrast, the same jammy build without this change: ``` NEEDED libtbb.so.12 RUNPATH /usr/lib/x86_64-linux-gnu:$ORIGIN/../lib lib/ libtbb.so.12.5 -> /usr/lib/x86_64-linux-gnu/libtbb.so.12.5 (dangling off the image) load libtbb.so.12: cannot open shared object file: No such file or directory ``` With `TBB_LIB` still exported, `RcppParallel::tbbLibraryPath()` resolves to the package's own `lib`, and `CxxFlags()` emits the package's own `include` plus `-DTBB_INTERFACE_NEW` - not `/usr/include/oneapi`. ## Behaviour change Published `RcppParallel` binaries carry their own oneTBB on every platform, whichever image version CI pulls. The patch content changed, so the patched-binary cache key changes with it and no stale entry is reused. The build-env-images fix is still worth rolling out (those images also carry the broken el8 `uvr` and uvr 0.4.1), but RcppParallel no longer waits on it. ## Follow-up, not in this PR The binaries already in B2 are the broken ones; they need a rebuild, and a Bunny `/purge` does not evict Perma-Cache. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/146 --- .../RcppParallel/bundled-tbb-link-order.patch | 46 ------ .../RcppParallel/force-bundled-tbb.patch | 154 ++++++++++++++++++ local/patches/registry.json | 4 +- 3 files changed, 156 insertions(+), 48 deletions(-) delete mode 100644 local/patches/RcppParallel/bundled-tbb-link-order.patch create mode 100644 local/patches/RcppParallel/force-bundled-tbb.patch diff --git a/local/patches/RcppParallel/bundled-tbb-link-order.patch b/local/patches/RcppParallel/bundled-tbb-link-order.patch deleted file mode 100644 index 45114a8..0000000 --- a/local/patches/RcppParallel/bundled-tbb-link-order.patch +++ /dev/null @@ -1,46 +0,0 @@ -diff --git a/tools/config/configure.R b/tools/config/configure.R -index 6293fe1..2f84337 100644 ---- a/tools/config/configure.R -+++ b/tools/config/configure.R -@@ -186,12 +186,23 @@ define( - ) - - # set PKG_LIBS -+# -+# bincraft patch: the library directories below are passed as plain '-L', not -+# '-Wl,-L'. gcc expands its own search dirs (/usr/lib64, /usr/lib/) -+# into explicit '-L' options ahead of anything forwarded verbatim with '-Wl,', -+# so with '-Wl,-L' a system libtbb.so wins over the one named here: on a build -+# host with a distro TBB installed, '-ltbb' resolves to that library and -+# RcppParallel.so records its SONAME (libtbb.so.12, or libtbb.so.2 for the -+# classic Intel TBB) instead of the bundled 'libtbb.so'. The binary then loads -+# the system TBB rather than the copy shipped in RcppParallel/lib, and fails -+# outright on a machine that has no system TBB. gcc places a plain '-L' before -+# its built-in dirs, so the intended library is found first. - pkgLibs <- if (!is.na(tbbLib)) { - - # a TBB supplied via TBB_LIB / TBB_ROOT. an rpath is meaningless on Windows, - # where the loader has no equivalent -- see R/zzz.R for how we resolve there - c( -- "-Wl,-L\"$(TBB_LIB)\"", -+ "-L\"$(TBB_LIB)\"", - if (.Platform$OS.type != "windows") - sprintf("-Wl,-rpath,%s", shQuote(tbbLib)), - "-l$(TBB_NAME)", -@@ -201,14 +212,14 @@ pkgLibs <- if (!is.na(tbbLib)) { - } else if (R.version$os == "emscripten") { - - c( -- "-Wl,-Ltbb/build/lib_release", -+ "-Ltbb/build/lib_release", - "-l$(TBB_NAME)" - ) - - } else { - - c( -- "-Wl,-Ltbb/build/lib_release", -+ "-Ltbb/build/lib_release", - "-l$(TBB_NAME)", - "-l$(TBB_MALLOC_NAME)" - ) diff --git a/local/patches/RcppParallel/force-bundled-tbb.patch b/local/patches/RcppParallel/force-bundled-tbb.patch new file mode 100644 index 0000000..c46a05e --- /dev/null +++ b/local/patches/RcppParallel/force-bundled-tbb.patch @@ -0,0 +1,154 @@ +diff --git a/R/aaa.R b/R/aaa.R +index 568a2aa..bfdab4c 100644 +--- a/R/aaa.R ++++ b/R/aaa.R +@@ -5,4 +5,21 @@ TBB_LIB <- "" + TBB_INC <- "" + + TBB_NAME <- "tbb" +-TBB_MALLOC_NAME <- "tbbmalloc" +\ No newline at end of file ++TBB_MALLOC_NAME <- "tbbmalloc" ++ ++# bincraft patch: our build images (and plenty of user environments) export ++# TBB_ROOT / TBB_LIB / TBB_INC. A binary we publish always carries its own ++# oneTBB in RcppParallel/lib -- see the companion changes in ++# tools/config/configure.R and src/install.libs.R -- so honouring those ++# variables at run time is actively harmful: .onLoad() would dyn.load() a ++# second, unrelated TBB into the process next to the bundled one (two copies ++# of the same symbols in the global scope, which segfaults R on load), and ++# RcppParallelLibs() / CxxFlags() would hand that system TBB to dependents ++# such as rstan, putting NEEDED libtbb.so.12 back into their binaries. Read ++# the variables only when explicitly opted back in. ++bincraftGetenv <- function(name, unset = "") { ++ if (Sys.getenv("BINCRAFT_ALLOW_SYSTEM_TBB", unset = "FALSE") == "TRUE") ++ Sys.getenv(name, unset = unset) ++ else ++ unset ++} +\ No newline at end of file +diff --git a/R/tbb.R b/R/tbb.R +index 6f6a745..e407986 100644 +--- a/R/tbb.R ++++ b/R/tbb.R +@@ -17,7 +17,7 @@ tbbLibraryPath <- function(name = NULL) { + sysname <- Sys.info()[["sysname"]] + + # find root for TBB install +- tbbRoot <- Sys.getenv("TBB_LIB", unset = tbbRoot()) ++ tbbRoot <- bincraftGetenv("TBB_LIB", unset = tbbRoot()) + if (is.null(name)) + return(tbbRoot) + +@@ -58,7 +58,7 @@ tbbCxxFlags <- function() { + flags <- c("-DRCPP_PARALLEL_USE_TBB=1") + + # if TBB_INC is set, apply those library paths +- tbbInc <- Sys.getenv("TBB_INC", unset = TBB_INC) ++ tbbInc <- bincraftGetenv("TBB_INC", unset = TBB_INC) + if (!file.exists(tbbInc)) { + tbbInc <- system.file("include", package = "RcppParallel") + } +@@ -117,7 +117,7 @@ tbbLdFlags <- function() { + } + + # shortcut if TBB_LIB defined +- tbbLib <- Sys.getenv("TBB_LINK_LIB", Sys.getenv("TBB_LIB", unset = TBB_LIB)) ++ tbbLib <- bincraftGetenv("TBB_LINK_LIB", bincraftGetenv("TBB_LIB", unset = TBB_LIB)) + if (nzchar(tbbLib)) { + if (R.version$os == "emscripten") { + fmt <- "-L%1$s -l%2$s" +diff --git a/src/install.libs.R b/src/install.libs.R +index 3b3cfda..c0e6f3e 100644 +--- a/src/install.libs.R ++++ b/src/install.libs.R +@@ -477,6 +477,18 @@ prependFlags <- function(prependFlags, toFlags) { + tbbLib <- Sys.getenv("TBB_LIB") + tbbInc <- Sys.getenv("TBB_INC") + ++# bincraft patch: the companion change in tools/config/configure.R stops an ++# ambient TBB_LIB / TBB_INC from selecting a system TBB, but this script is ++# also run directly by `R CMD INSTALL` (not only through the `tbb` rule in ++# src/Makevars, which passes the configured values), so at install time it ++# still sees the image's environment and would symlink the system libraries ++# into RcppParallel/lib. Drop them here for the same reason, under the same ++# opt-out. ++if (Sys.getenv("BINCRAFT_ALLOW_SYSTEM_TBB", unset = "FALSE") != "TRUE") { ++ tbbLib <- "" ++ tbbInc <- "" ++} ++ + args <- commandArgs(trailingOnly = TRUE) + if (identical(args, "build")) { + if (nzchar(tbbLib) && nzchar(tbbInc)) { +diff --git a/tools/config/configure.R b/tools/config/configure.R +index 6293fe1..eae4aaa 100644 +--- a/tools/config/configure.R ++++ b/tools/config/configure.R +@@ -40,6 +40,24 @@ tbbRoot <- Sys.getenv("TBB_ROOT", unset = NA) + tbbLib <- Sys.getenv("TBB_LIB", unset = NA) + tbbInc <- Sys.getenv("TBB_INC", unset = NA) + ++# bincraft patch: ignore an ambient TBB_ROOT / TBB_LIB / TBB_INC. Several of ++# our build images export these (a leftover from RcppParallel 5.x, whose ++# bundled Intel TBB would not build on musl or with modern g++), and any of ++# them switches the branches below to a system TBB. The published binary then ++# records NEEDED libtbb.so.12 (or libtbb.so.2 for the classic Intel TBB) and ++# gets a RcppParallel/lib full of absolute symlinks into the image's library ++# dir, so it cannot dyn.load on a consumer machine without that exact TBB. ++# 6.x bundles oneTBB 2022 and builds it with cmake on every platform we ship, ++# so the bundled copy is always the right choice here; forcing it in the ++# package rather than relying on the image environment keeps the binary ++# correct whichever image version CI happens to pull. Set ++# BINCRAFT_ALLOW_SYSTEM_TBB=TRUE to restore the upstream behaviour. ++if (Sys.getenv("BINCRAFT_ALLOW_SYSTEM_TBB", unset = "FALSE") != "TRUE") { ++ tbbRoot <- NA ++ tbbLib <- NA ++ tbbInc <- NA ++} ++ + tbbName <- Sys.getenv("TBB_NAME", unset = "tbb") + tbbMallocName <- Sys.getenv("TBB_MALLOC_NAME", unset = "tbbmalloc") + +@@ -186,12 +204,23 @@ define( + ) + + # set PKG_LIBS ++# ++# bincraft patch: the library directories below are passed as plain '-L', not ++# '-Wl,-L'. gcc expands its own search dirs (/usr/lib64, /usr/lib/) ++# into explicit '-L' options ahead of anything forwarded verbatim with '-Wl,', ++# so with '-Wl,-L' a system libtbb.so wins over the one named here: on a build ++# host with a distro TBB installed, '-ltbb' resolves to that library and ++# RcppParallel.so records its SONAME (libtbb.so.12, or libtbb.so.2 for the ++# classic Intel TBB) instead of the bundled 'libtbb.so'. The binary then loads ++# the system TBB rather than the copy shipped in RcppParallel/lib, and fails ++# outright on a machine that has no system TBB. gcc places a plain '-L' before ++# its built-in dirs, so the intended library is found first. + pkgLibs <- if (!is.na(tbbLib)) { + + # a TBB supplied via TBB_LIB / TBB_ROOT. an rpath is meaningless on Windows, + # where the loader has no equivalent -- see R/zzz.R for how we resolve there + c( +- "-Wl,-L\"$(TBB_LIB)\"", ++ "-L\"$(TBB_LIB)\"", + if (.Platform$OS.type != "windows") + sprintf("-Wl,-rpath,%s", shQuote(tbbLib)), + "-l$(TBB_NAME)", +@@ -201,14 +230,14 @@ pkgLibs <- if (!is.na(tbbLib)) { + } else if (R.version$os == "emscripten") { + + c( +- "-Wl,-Ltbb/build/lib_release", ++ "-Ltbb/build/lib_release", + "-l$(TBB_NAME)" + ) + + } else { + + c( +- "-Wl,-Ltbb/build/lib_release", ++ "-Ltbb/build/lib_release", + "-l$(TBB_NAME)", + "-l$(TBB_MALLOC_NAME)" + ) diff --git a/local/patches/registry.json b/local/patches/registry.json index fe0d387..a7e29dd 100644 --- a/local/patches/registry.json +++ b/local/patches/registry.json @@ -6,8 +6,8 @@ "env": {}, "configure_args": [], "makevars": {}, - "patch": "RcppParallel/bundled-tbb-link-order.patch", - "reason": "RcppParallel 6.x bundles oneTBB 2022 and builds it with cmake, which works on musl and g++ 8-15, so the system-TBB workaround needed for 5.x is gone. What remains broken is the link order: configure.R passes the TBB directory as '-Wl,-L', and gcc expands its own search dirs (/usr/lib64, /usr/lib/) into '-L' options ahead of anything forwarded with '-Wl,'. On a build host with a distro TBB installed, '-ltbb' therefore resolves to the system library and RcppParallel.so records its SONAME (libtbb.so.12, or libtbb.so.2 for the classic Intel TBB on el8/el9) instead of the bundled 'libtbb.so'. The published binary then loads the system TBB rather than the copy in RcppParallel/lib and fails to dyn.load on a consumer machine without one, the same way fs did with libuv. Passing a plain '-L' puts the bundled build dir ahead of gcc's defaults; verified on alpine 3.24, el8 and ubuntu noble to produce NEEDED libtbb.so + RPATH $ORIGIN/../lib, loading with every system libtbb removed." + "patch": "RcppParallel/force-bundled-tbb.patch", + "reason": "RcppParallel 6.x bundles oneTBB 2022 and builds it with cmake on every platform we ship, so the system-TBB workaround needed for 5.x is gone, but two things still steer the build back to a system TBB. (1) Ambient TBB_ROOT/TBB_LIB/TBB_INC: several build images still export these (build-env-images dropped them, but the images are rebuilt only by cron/manual runs, so a stale image keeps them), and R reads ~/.Renviron *after* the process environment, so no pipeline-side env override can undo it. configure.R then takes the system-TBB branch, install.libs.R symlinks the image's libraries into RcppParallel/lib as absolute paths, and the binary records NEEDED libtbb.so.12 (libtbb.so.2 for the classic Intel TBB on el8/el9) -- it cannot dyn.load on a consumer machine without that exact TBB. Both files are patched to ignore those variables (opt out with BINCRAFT_ALLOW_SYSTEM_TBB=TRUE); install.libs.R needs it separately because R CMD INSTALL runs it outside the src/Makevars rule that passes the configured values. (2) Link order: the bundled branch passes its build dir as '-Wl,-Ltbb/build/lib_release', and gcc expands its own search dirs (/usr/lib64, /usr/lib/) into '-L' options ahead of anything forwarded with '-Wl,', so '-ltbb' would still resolve to a distro TBB when one is installed; a plain '-L' puts the bundled dir first. Verified on the current build-env-ubuntu:jammy image (which still exports TBB_INC/TBB_LIB): NEEDED libtbb.so, RUNPATH $ORIGIN/../lib, real libtbb.so.2 in RcppParallel/lib, and the package loads with every system libtbb moved away." }, { "package": "fs", From ee15c50f53996229451a44cfe12b2222853728e2 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 31 Jul 2026 12:19:26 +0000 Subject: [PATCH 25/53] refactor: migrate package installation from pak to uvr (#147) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit `bincraft` dropped pak in favour of uvr (5.0.x, "Dependencies and their system requirements are now installed with `uvr` instead of pak during `build_binary_package()`"), so the pipelines, helper scripts and images in this repo move with it. ## Approach uvr is project-scoped in a way pak is not: `uvr add` refuses to run outside a project and always installs into `.uvr/library/`, and only `uvr sync` honours `--library`. So there is no one-line `pak::pak(...)` equivalent. `local/uvr-install.sh` encapsulates the dance — bootstrap a pinned uvr, mint a throwaway project under `TMPDIR`, `uvr add --no-install`, then `uvr sync --library `. Keeping the project outside the checkout also keeps `uvr init`'s `.Rprofile` from hijacking `.libPaths()` for every other R call in the pipeline. This matches what bincraft itself does (`uvr sync --install-system-deps --library `), and bincraft requires `uvr` on `PATH`, which the bootstrap provides: every pipeline that calls `bincraft::` runs `install-bincraft.R` (and therefore the bootstrap) first. ## Changes | File | Change | | --- | --- | | `local/uvr-install.sh` | **New.** The single replacement for `pak::pak(...)`. Bootstraps uvr `v0.4.4`, resolves the R interpreter from `UVR_R_BIN`/`R_VERSION`/`PATH`, pins the manifest to that R's exact version, and syncs into `UVR_TARGET_LIB`/`R_LIBS_USER`. | | `local/install-bincraft.R` | Installs `forgejo::codefloe.com/rpkgs/bincraft@` instead of a `git::` URL; keeps the `git ls-remote` tag resolution. Exports `UVR_R_BIN`/`UVR_TARGET_LIB` from `R.home()`/`.libPaths()[1]` so the per-R-minor passes target their own R and library. | | `.crow/auto-apply-patches.yaml`, `.crow/weekly-patch-proposals.yaml`, `.crow/weekly-audit-missing.yaml`, `.crow/weekly-rebuild-missing.yaml`, `.crow/build-all-versions-install-deps.yaml` | `pak::pak(...)` → `UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh ...`. The explicit `UVR_R_BIN` matters in `build-all-versions-install-deps.yaml`, which has no `R_VERSION` in its step environment. | | `.crow/build-all-versions.yaml`, `.crow/process-updates.yaml`, `.crow/weekly-rebuild-missing.yaml` | `R_PKG_CACHE_DIR` → `UVR_CACHE_DIR` + `UVR_PACKAGES_DIR` on the same `/mnt/cache` volume, preserving the amd64-off/arm64-on split. Drops the `rm -rf .../pkgcache/_metadata/...` cleanup. | | `local/r-minor-helpers.R`, `local/build-all.R`, `local/tests/test-trim-pkgcache.R` | Removes `trim_pkgcache_metadata()`, its every-25-packages call and its tests. uvr's cache does not mint a fresh ~70 MB snapshot per `PACKAGES` change. | | `.crow/build-all-versions-install-deps.yaml` | Drops `pak::sysreqs_db_update()`; uvr resolves sysreqs from its vendored `r-system-requirements` rules via `--install-system-deps`. | | `docker/Containerfile-shiny-app` | Bootstraps uvr and drives both dependency installs through one uvr project with `UVR_LIBRARY` pointed at the image's R library. | | `docker/build-one.Dockerfile` | Ships `uvr-install.sh` at `/work/local/` so `install-bincraft.R` finds it. | | `docker/reprex/alpine.sh` | Replaces `pak::local_install_deps()` with DESCRIPTION parsing + `uvr add`. | | `local/test-package-loading.R` | Installs via the helper instead of `pak::pkg_install()`. | | `README.md` | Documents uvr for sysreq inference, archived-version installs and cache clearing. | | `renovate.json` | Tracks the `UVR_PIN` in `uvr-install.sh` via `github-releases`. | ## Behaviour notes - **`weekly-audit-missing` still takes bincraft from the default branch**, not the latest release tag, matching what the `git::` pak call did. Called out in a comment rather than silently changed. - **The uvr pin is repo-wide.** bincraft resolves `uvr` from `PATH` and pins no version of its own, so `UVR_PIN` in `uvr-install.sh` governs the whole pipeline. - **Persistent caches now also benefit bincraft**, which reads `UVR_CACHE_DIR`/`UVR_PACKAGES_DIR` from the inherited pipeline environment. - **`uvr sync` will not prune the shared library.** Pruning is disabled whenever `--library` is passed (`do_prune = prune && library_override.is_none()`), so `/mnt/cache/R-pkgs` keeps bincraft and its dependencies. The wipe-on-ABI-mismatch path is *not* similarly guarded, which is why the helper pins the manifest to the active R's exact version. - **`plans/` and `specs/` are untouched** — they are dated records of decisions made in June 2026 and describe bincraft's then-pak-based internals; rewriting them would misstate history. ## Verification `shellcheck`, all pre-commit hooks (on this commit's file range) and the `local/tests/` suite (100 assertions) pass. Not yet exercised in CI: the build-env images do not ship `uvr`, so the per-step `curl install.sh` bootstrap is untested against a real image. Worth a manual `build-all-versions-install-deps` run before merging. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/147 --- .crow/auto-apply-patches.yaml | 2 +- .crow/build-all-versions-install-deps.yaml | 33 ++++---- .crow/build-all-versions.yaml | 64 ++++++++------- .crow/process-updates.yaml | 46 +++++------ .crow/weekly-audit-missing.yaml | 3 +- .crow/weekly-patch-proposals.yaml | 2 +- .crow/weekly-rebuild-missing.yaml | 7 +- README.md | 19 ++--- build-all-versions-install-deps.yaml | 10 +-- docker/Containerfile-shiny-app | 22 +++++- docker/build-one.Dockerfile | 3 + docker/reprex/alpine.sh | 24 ++++-- local/build-all.R | 31 ++++---- local/install-bincraft.R | 47 +++++++++-- local/packages-to-build.R | 15 ++-- local/r-minor-helpers.R | 39 ---------- local/test-package-loading.R | 32 ++++---- local/tests/test-trim-pkgcache.R | 68 ---------------- local/uvr-install.sh | 90 ++++++++++++++++++++++ renovate.json | 14 +++- 20 files changed, 326 insertions(+), 245 deletions(-) delete mode 100644 local/tests/test-trim-pkgcache.R create mode 100755 local/uvr-install.sh diff --git a/.crow/auto-apply-patches.yaml b/.crow/auto-apply-patches.yaml index b9c8697..0076353 100644 --- a/.crow/auto-apply-patches.yaml +++ b/.crow/auto-apply-patches.yaml @@ -45,7 +45,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/R-pkgs - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))' + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite - /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-pr --limit $PATCH_LIMIT backend_options: kubernetes: diff --git a/.crow/build-all-versions-install-deps.yaml b/.crow/build-all-versions-install-deps.yaml index e0cca86..448cff3 100644 --- a/.crow/build-all-versions-install-deps.yaml +++ b/.crow/build-all-versions-install-deps.yaml @@ -10,22 +10,22 @@ variables: - arm64 default: amd64 OS: - description: "Base OS image name." + description: 'Base OS image name.' options: - alpine - redhat - ubuntu default: alpine OS_VERSION: - description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)." + description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).' options: - - "3.24" - - "8" - - "9" - - "10" - - "jammy" - - "noble" - default: "3.24" + - '3.24' + - '8' + - '9' + - '10' + - 'jammy' + - 'noble' + default: '3.24' R_VERSION: description: 'Primary R version under /opt/R.' options: @@ -66,23 +66,24 @@ steps: from_secret: B2_S3_SECRET_KEY PGPASS: from_secret: PGPASS - R_PKG_CACHE_DIR: /mnt/cache/pkgcache R_LIBS_USER: /mnt/cache/R-pkgs + # Keep uvr's downloads and extracted-package entries on the persistent + # volume instead of the container-local ~/.uvr default. + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages CCACHE_DIR: /mnt/cache/ccache volumes: - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache commands: # one-time full wipe to fix corrupted .so files from previous failed builds # - rm -rf /mnt/cache/R-pkgs - # Clear churny pkgcache metadata left by a prior crashed run (the "patched" - # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*). - # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs. - - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true - - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages + - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . # Pin the same bincraft version the build steps use, so the precomputed # snapshot and the per-agent library stay consistent across the pipeline. - - /opt/R/$R_VERSION/bin/R -q -e 'pak::sysreqs_db_update(); source("local/install-bincraft.R"); pak::pak(c("RPostgres", "s3fs", "data.table", "future", "jsonlite")); packageVersion("bincraft")' + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres s3fs data.table future jsonlite + - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))" backend_options: docker: diff --git a/.crow/build-all-versions.yaml b/.crow/build-all-versions.yaml index 3932811..9ab888a 100644 --- a/.crow/build-all-versions.yaml +++ b/.crow/build-all-versions.yaml @@ -11,25 +11,25 @@ variables: - arm64 default: amd64 OS: - description: "Base OS image name." + description: 'Base OS image name.' options: - alpine - redhat - ubuntu default: alpine OS_VERSION: - description: "OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble)." + description: 'OS image tag. Must match OS (alpine: 3.24; redhat: 8/9/10; ubuntu: jammy/noble).' options: - - "3.22" - - "3.23" - - "3.24" - - "8" - - "9" - - "10" - - "jammy" - - "noble" - - "resolute" - default: "3.24" + - '3.22' + - '3.23' + - '3.24' + - '8' + - '9' + - '10' + - 'jammy' + - 'noble' + - 'resolute' + default: '3.24' R_VERSION: description: 'Primary R version under /opt/R.' options: @@ -47,38 +47,49 @@ labels: platform: linux/${ARCH} group: rpkgs-${ARCH} +# Empty UVR_CACHE_DIR/UVR_PACKAGES_DIR fall back to uvr's container-local +# ~/.uvr defaults; amd64 deliberately does not persist them (as with the +# pkgcache dir it replaces), arm64 does. matrix: include: - ARCH: amd64 - R_PKG_CACHE_DIR: '' + UVR_CACHE_DIR: '' + UVR_PACKAGES_DIR: '' SPLIT_INTO: 4 SPLIT_INDEX: 1 - ARCH: amd64 - R_PKG_CACHE_DIR: '' + UVR_CACHE_DIR: '' + UVR_PACKAGES_DIR: '' SPLIT_INTO: 4 SPLIT_INDEX: 2 - ARCH: amd64 - R_PKG_CACHE_DIR: '' + UVR_CACHE_DIR: '' + UVR_PACKAGES_DIR: '' SPLIT_INTO: 4 SPLIT_INDEX: 3 - ARCH: amd64 - R_PKG_CACHE_DIR: '' + UVR_CACHE_DIR: '' + UVR_PACKAGES_DIR: '' SPLIT_INTO: 4 SPLIT_INDEX: 4 - ARCH: arm64 - R_PKG_CACHE_DIR: /mnt/cache/pkgcache + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages SPLIT_INTO: 4 SPLIT_INDEX: 1 - ARCH: arm64 - R_PKG_CACHE_DIR: /mnt/cache/pkgcache + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages SPLIT_INTO: 4 SPLIT_INDEX: 2 - ARCH: arm64 - R_PKG_CACHE_DIR: /mnt/cache/pkgcache + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages SPLIT_INTO: 4 SPLIT_INDEX: 3 - ARCH: arm64 - R_PKG_CACHE_DIR: /mnt/cache/pkgcache + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages SPLIT_INTO: 4 SPLIT_INDEX: 4 @@ -107,8 +118,10 @@ steps: from_secret: GITHUB_PAT # normal env vars GIT_USER: pat-s - # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves - R_PKG_CACHE_DIR: ${R_PKG_CACHE_DIR} + # set the location of uvr's caches, which persist the R package + # dependencies needed to install the packages themselves + UVR_CACHE_DIR: ${UVR_CACHE_DIR} + UVR_PACKAGES_DIR: ${UVR_PACKAGES_DIR} R_LIBS_USER: /mnt/cache/R-pkgs CCACHE_DIR: /mnt/cache/ccache NCPUS: 2 @@ -116,12 +129,7 @@ steps: - ${ARCH}-binaries-r-dep-cache-${OS}-${OS_VERSION//./}:/mnt/cache commands: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - # Clear churny pkgcache metadata left by a prior crashed run (the "patched" - # repo mints a new hash per PACKAGES change -> unbounded pkgs-*.rds/patched-*). - # Keep pkg/ downloads and the stable CRAN/BioC/INLA repo dirs. Within-run - # growth is bounded separately by trim_pkgcache_metadata() in build-all.R. - - rm -rf /mnt/cache/pkgcache/R/pkgcache/_metadata/patched-* /mnt/cache/pkgcache/R/pkgcache/_metadata/pkgs-*.rds || true - - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages + - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # The primary pass must not rely on build-all-versions-install-deps having # run on *this* agent: depends_on only orders the steps, but the cache # volume is per-agent, so a job landing on an agent where install-deps did diff --git a/.crow/process-updates.yaml b/.crow/process-updates.yaml index 59b1c26..1e4833c 100644 --- a/.crow/process-updates.yaml +++ b/.crow/process-updates.yaml @@ -49,109 +49,109 @@ matrix: R_VERSION: 4.5.3 IMG: alpine:3.22 OS_ID: alpine322 - PROCESS_NEW: "FALSE" + PROCESS_NEW: 'FALSE' - OS: alpine-322 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.23 OS_ID: alpine322 - PROCESS_NEW: "FALSE" + PROCESS_NEW: 'FALSE' - OS: alpine-323 ARCH: amd64 R_VERSION: 4.5.3 IMG: alpine:3.23 OS_ID: alpine323 - PROCESS_NEW: "FALSE" + PROCESS_NEW: 'FALSE' - OS: alpine-323 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.23 OS_ID: alpine323 - PROCESS_NEW: "FALSE" + PROCESS_NEW: 'FALSE' - OS: alpine-324 ARCH: amd64 R_VERSION: 4.5.3 IMG: alpine:3.24 OS_ID: alpine324 - PROCESS_NEW: "FALSE" + PROCESS_NEW: 'FALSE' - OS: alpine-324 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.24 OS_ID: alpine324 - PROCESS_NEW: "FALSE" + PROCESS_NEW: 'FALSE' - OS: redhat-8 ARCH: amd64 R_VERSION: 4.4.3 IMG: redhat:8 OS_ID: rhel8 - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: redhat-8 ARCH: arm64 R_VERSION: 4.4.3 IMG: redhat:8 OS_ID: rhel8 - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: redhat-9 ARCH: amd64 R_VERSION: 4.4.3 IMG: redhat:9 OS_ID: rhel9 - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: redhat-9 ARCH: arm64 R_VERSION: 4.4.3 IMG: redhat:9 OS_ID: rhel9 - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: redhat-10 ARCH: amd64 R_VERSION: 4.5.3 IMG: redhat:10 OS_ID: rhel10 - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: redhat-10 ARCH: arm64 R_VERSION: 4.5.3 IMG: redhat:10 OS_ID: rhel10 - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: ubuntu-2204 ARCH: amd64 R_VERSION: 4.4.3 IMG: ubuntu:jammy OS_ID: jammy - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: ubuntu-2204 ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:jammy OS_ID: jammy - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: ubuntu-2404 ARCH: amd64 R_VERSION: 4.4.3 IMG: ubuntu:noble OS_ID: noble - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: ubuntu-2404 ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:noble OS_ID: noble - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: ubuntu-2604 ARCH: amd64 R_VERSION: 4.5.3 IMG: ubuntu:resolute OS_ID: resolute - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' - OS: ubuntu-2604 ARCH: arm64 R_VERSION: 4.5.3 IMG: ubuntu:resolute OS_ID: resolute - PROCESS_NEW: "TRUE" + PROCESS_NEW: 'TRUE' steps: - name: 'Processing Updates' @@ -182,8 +182,10 @@ steps: NTFY_AUTH: TRUE NTFY_PASSWORD: from_secret: ntfy_token - # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves - R_PKG_CACHE_DIR: /mnt/cache/pkgcache + # set the location of uvr's caches, which persist the R package + # dependencies needed to install the packages themselves + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages R_LIBS_USER: /mnt/cache/R-pkgs R_VERSION: ${R_VERSION} CCACHE_DIR: /mnt/cache/ccache @@ -194,10 +196,10 @@ steps: INTERVAL: lubridate::interval(lubridate::today() - 6, lubridate::today() - 3) commands: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/R-pkgs/pkgcache /mnt/cache/pkgcache/R/pkgcache + - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft + - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise diff --git a/.crow/weekly-audit-missing.yaml b/.crow/weekly-audit-missing.yaml index d66a37b..4efe409 100644 --- a/.crow/weekly-audit-missing.yaml +++ b/.crow/weekly-audit-missing.yaml @@ -142,7 +142,8 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/packages /mnt/cache/R-pkgs - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("git::https://codefloe.com/rpkgs/bincraft.git", "httr2", "jsonlite"))' + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite - /opt/R/$R_VERSION/bin/R -q -e 'source("local/weekly-missing-binaries-audit.R")' backend_options: docker: diff --git a/.crow/weekly-patch-proposals.yaml b/.crow/weekly-patch-proposals.yaml index 0284e93..027d41c 100644 --- a/.crow/weekly-patch-proposals.yaml +++ b/.crow/weekly-patch-proposals.yaml @@ -35,7 +35,7 @@ steps: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/R-pkgs - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak(c("httr2", "jsonlite"))' + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 jsonlite - /opt/R/$R_VERSION/bin/Rscript local/propose-patches.R --open-issue - /opt/R/$R_VERSION/bin/Rscript local/proposal-tracking.R --open-issue backend_options: diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index 53f178f..03a13f9 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -141,7 +141,8 @@ steps: FORGEJO_TOKEN: from_secret: FORGEJO_TOKEN GIT_USER: pat-s - R_PKG_CACHE_DIR: /mnt/cache/pkgcache + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages R_LIBS_USER: /mnt/cache/R-pkgs R_VERSION: ${R_VERSION} CCACHE_DIR: /mnt/cache/ccache @@ -150,12 +151,12 @@ steps: NCPUS: 2 commands: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages + - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - rm -rf /mnt/cache/R-pkgs/00LOCK-* - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("httr2")' + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")' - $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1 backend_options: diff --git a/README.md b/README.md index 538df34..989069e 100644 --- a/README.md +++ b/README.md @@ -112,9 +112,9 @@ Processing updates with an existing database file takes around 5 minutes. ### Inferring System Dependencies -R package dependencies and their system dependencies are installed through {pak}. -{pak} allows for parallel downloads and installation, significantly speeding up package installation compared to `install.packages()`. -Additionally, it automatically infers package dependencies using JSON rules from [rstudio/r-system-requirements](https://github.com/rstudio/r-system-requirements). +R package dependencies and their system dependencies are installed through [uvr](https://github.com/nbafrank/uvr). +`uvr` allows for parallel downloads and installation, significantly speeding up package installation compared to `install.packages()`. +Additionally, it automatically infers package dependencies using JSON rules vendored from [rstudio/r-system-requirements](https://github.com/rstudio/r-system-requirements). Not all R packages specify required system dependencies in their DESCRIPTION file, and not all listed dependencies have existing rules in `rstudio/r-system-requirements`. For Alpine, no rules existed until recently, establishing a foundation for semi-automated package installation on Alpine Linux. @@ -152,12 +152,13 @@ A Shiny dashboard providing a search functionality of the database and grouped s Is supported by writing `Meta/archive.rds` during each package index update, listing all available archived packages. -### `pak::pak(package@version)` +### `uvr add package@version` -`pak` searches for `Archive/` and can install all versions it finds. +Clients that resolve archived versions search for `Archive/` and can install all versions they find. +This holds for `uvr` as well as for older `pak`-based clients. Ensure to use a clean cache if other repositories have been used previously. -If in doubt or when testing, call `pak::meta_clean(force = TRUE)`. +If in doubt or when testing, call `uvr cache clean`. ## Lessons Learned @@ -180,7 +181,7 @@ If in doubt or when testing, call `pak::meta_clean(force = TRUE)`. ## URL Composition and Platform Identifiers -Platform identifiers have been aligned with those used in to ensure proper recognition by the automatic syslib dependency installer of `pak`, specifically via the environment variable `PKG_SYSREQS_PLATFORM`: +Platform identifiers have been aligned with those used in , which `uvr` vendors and uses for its automatic syslib dependency installer (`uvr sync --install-system-deps`): - redhat-9 - redhat-8 @@ -237,8 +238,8 @@ internal error 1 in memDecompress Solution: ```sh -rm -rf /mnt/cache/R-pkgs/pak /mnt/cache/pkgcache/ /root/.cache/R/ -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))' +uvr cache clean +rm -rf /mnt/cache/uvr /root/.cache/R/ ``` diff --git a/build-all-versions-install-deps.yaml b/build-all-versions-install-deps.yaml index 926d550..dd02e8a 100644 --- a/build-all-versions-install-deps.yaml +++ b/build-all-versions-install-deps.yaml @@ -30,8 +30,9 @@ # from_secret: HETZNER_S3_SECRET_KEY_K3S # # normal env vars # GIT_USER: pat-s -# # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves -# # R_PKG_CACHE_DIR: /mnt/cache/pkgcache +# # set the location of uvr's caches, which persist the R package dependencies needed to install the packages themselves +# # UVR_CACHE_DIR: /mnt/cache/uvr/cache +# # UVR_PACKAGES_DIR: /mnt/cache/uvr/packages # R_LIBS_USER: /mnt/cache/R-pkgs # CCACHE_DIR: /mnt/cache/ccache # volumes: @@ -39,9 +40,8 @@ # commands: # - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . # - mkdir -p /mnt/cache/R-pkgs -# - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/pkgcache -# - /opt/R/$R_VERSION/bin/R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' -# - /opt/R/$R_VERSION/bin/R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraft.git", dependencies = TRUE)' +# - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft /mnt/cache/uvr +# - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh forgejo::codefloe.com/rpkgs/bincraft # - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' # # - /opt/R/$R_VERSION/bin/R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine322', 'amd64'); saveRDS(pkgs, '/mnt/cache/pkgs_amd64.rds')" # - /opt/R/$R_VERSION/bin/R -q -e "future::plan('multisession', workers = 6L); pkgs = bincraft::query_packages_without_historic_versions('alpine323', 'arm64'); saveRDS(pkgs, '/mnt/cache/pkgs_arm64.rds')" diff --git a/docker/Containerfile-shiny-app b/docker/Containerfile-shiny-app index 7c7994f..4b0bd6c 100644 --- a/docker/Containerfile-shiny-app +++ b/docker/Containerfile-shiny-app @@ -1,7 +1,15 @@ FROM devxygmbh/r-alpine:4.4-3.20 AS build # ARG GITHUB_PAT -RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$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="" diff --git a/docker/build-one.Dockerfile b/docker/build-one.Dockerfile index 5bc107a..8e61ebd 100644 --- a/docker/build-one.Dockerfile +++ b/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 diff --git a/docker/reprex/alpine.sh b/docker/reprex/alpine.sh index 94806e5..851a9cc 100644 --- a/docker/reprex/alpine.sh +++ b/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")) }) - - diff --git a/local/build-all.R b/local/build-all.R index 1df1f83..37fc593 100644 --- a/local/build-all.R +++ b/local/build-all.R @@ -27,7 +27,9 @@ package_cache_files <- c( "/mnt/cache/packages/s3_cache.rds" ) if (!all(file.exists(package_cache_files))) { - message("Package snapshot missing from cache; recomputing via packages-to-build.R") + message( + "Package snapshot missing from cache; recomputing via packages-to-build.R" + ) dir.create("/mnt/cache/packages", showWarnings = FALSE, recursive = TRUE) save_rds_atomic <- function(obj, path) { tmp <- paste0(path, ".tmp.", Sys.getpid()) @@ -36,7 +38,10 @@ if (!all(file.exists(package_cache_files))) { } source(file.path("local", "packages-to-build.R")) save_rds_atomic(pkgs, "/mnt/cache/packages/pkgs_to_build.rds") - save_rds_atomic(pkgs[r_minor_sensitive == TRUE], "/mnt/cache/packages/r_minor_sensitive_pkgs.rds") + save_rds_atomic( + pkgs[r_minor_sensitive == TRUE], + "/mnt/cache/packages/r_minor_sensitive_pkgs.rds" + ) message("Package snapshot recomputed.") } @@ -112,20 +117,22 @@ built <- DBI::dbGetQuery( ) DBI::dbDisconnect(con) before <- nrow(chunk) -chunk <- chunk[!paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag), ] -sprintf("Skipped %d already-attempted package versions; %d remaining for this job", before - nrow(chunk), nrow(chunk)) +chunk <- chunk[ + !paste(chunk$Package, chunk$Version) %in% paste(built$name, built$tag), +] +sprintf( + "Skipped %d already-attempted package versions; %d remaining for this job", + before - nrow(chunk), + nrow(chunk) +) # Read pre-computed S3 listing from install-deps step # This avoids loading s3fs/reticulate/Python in the build container, -# saving significant memory for pak subprocess forks +# saving significant memory for the dependency-installer subprocesses s3_cache <- readRDS("/mnt/cache/packages/s3_cache.rds") sprintf("S3 cache: %s files", length(s3_cache)) n <- nrow(chunk) -# Every `trim_every` packages, bound the pkgcache _metadata dir so a full-platform -# run does not accumulate thousands of ~70 MB snapshots and fill the host disk. -# No-op on amd64 (R_PKG_CACHE_DIR is empty / cache not persisted). -trim_every <- 25L mapply( function(pkg, ver, sens, i) { cat(sprintf("[%d/%d] %s_%s (r_minor_sensitive=%s)\n", i, n, pkg, ver, sens)) @@ -151,12 +158,6 @@ mapply( upload = TRUE, store_build_metadata = TRUE ) - if (i %% trim_every == 0L) { - removed <- trim_pkgcache_metadata() - if (removed > 0L) { - cat(sprintf(" [pkgcache trim] removed %d stale _metadata entries\n", removed)) - } - } }, chunk$Package, chunk$Version, diff --git a/local/install-bincraft.R b/local/install-bincraft.R index 4665b3b..e39cb4f 100644 --- a/local/install-bincraft.R +++ b/local/install-bincraft.R @@ -11,10 +11,11 @@ # # How it works: list the remote tags with `git ls-remote` (no token needed for # the public repo), keep the `vX.Y.Z` release tags, pick the highest version, -# and install it with pak. pak is idempotent on the git ref, so re-running keeps -# the package when it is already current and only updates when a newer tag ships. -# Filtering/sorting is done in R (not via git's `--sort`/refspec) so behaviour is -# identical across git versions and `system2()` argument handling. +# and install it with uvr via `local/uvr-install.sh`. uvr is idempotent on the +# git ref, so re-running keeps the package when it is already current and only +# updates when a newer tag ships. Filtering/sorting is done in R (not via git's +# `--sort`/refspec) so behaviour is identical across git versions and +# `system2()` argument handling. repo_url <- Sys.getenv( "BINCRAFT_GIT_URL", @@ -44,7 +45,43 @@ latest <- tags[order(package_version(sub("^v", "", tags)), decreasing = TRUE)][ ] message(sprintf("Installing latest bincraft release: %s", latest)) -pak::pak(sprintf("git::%s@%s", repo_url, latest)) + +# uvr addresses Forgejo repos as `forgejo::host/owner/repo@ref` rather than as a +# git URL, so drop the scheme and the trailing `.git` from `repo_url`. +spec <- sprintf( + "forgejo::%s@%s", + sub("\\.git$", "", sub("^[a-z]+://", "", repo_url)), + latest +) + +# `local/uvr-install.sh` when run from the repo root, `/work/local/` in the +# build-one image, which copies the two scripts into a flatter layout. +helper <- Sys.getenv("UVR_INSTALL_SH", unset = "") +if (!nzchar(helper)) { + candidates <- c("local/uvr-install.sh", "/work/local/uvr-install.sh") + found <- candidates[file.exists(candidates)] + if (length(found) == 0L) { + stop("Could not locate uvr-install.sh; set UVR_INSTALL_SH", call. = FALSE) + } + helper <- found[1L] +} + +# Point uvr at the R running this script and at the library it would install +# into, so the per-R-minor passes in the build pipelines (which call a different +# Rscript with R_LIBS_USER pointed elsewhere) target their own R and library. +Sys.setenv( + UVR_R_BIN = file.path(R.home("bin"), "R"), + UVR_TARGET_LIB = .libPaths()[1L] +) + +status <- system2(helper, shQuote(spec)) +if (!identical(status, 0L)) { + stop( + sprintf("uvr failed to install %s (exit %s)", spec, status), + call. = FALSE + ) +} + message(sprintf( "bincraft %s installed (%s)", as.character(utils::packageVersion("bincraft")), diff --git a/local/packages-to-build.R b/local/packages-to-build.R index 7a3652d..887952d 100644 --- a/local/packages-to-build.R +++ b/local/packages-to-build.R @@ -15,15 +15,15 @@ suppressPackageStartupMessages(library(data.table)) # Sys.setenv("OS_VERSION" = "3.22") # Sys.setenv("ARCH" = "arm64") -arch = Sys.getenv("ARCH") +arch <- Sys.getenv("ARCH") # target: alpine-322, ubuntu-2404, redhat-9, etc. -platform = paste( +platform <- paste( Sys.getenv("OS"), gsub("[.]", "", Sys.getenv("OS_VERSION")), sep = "-" ) # Use bincraft's codename detection for S3 paths (e.g. "rhel10" not "redhat10") -codename = bincraft::set_codename(NULL) +codename <- bincraft::set_codename(NULL) con <- DBI::dbConnect( RPostgres::Postgres(), @@ -35,8 +35,8 @@ con <- DBI::dbConnect( sslmode = "require" ) -cran_archive = tools::CRAN_archive_db() -cran_release = tools::CRAN_package_db() +cran_archive <- tools::CRAN_archive_db() +cran_release <- tools::CRAN_package_db() # Subset cran_archive to only those packages cran_archive_in_release <- cran_archive[ names(cran_archive) %in% cran_release$Package @@ -84,13 +84,14 @@ s3fs::s3_file_system( region_name = "eu-central-003", refresh = TRUE ) -s3_pkgs = s3fs::s3_dir_ls( +s3_pkgs <- s3fs::s3_dir_ls( sprintf("devxy-rpkgs-binaries/%s/%s/latest/src/contrib", arch, codename), recurse = TRUE ) # Save the raw S3 file listing for the build step to use as s3_package_cache -# This avoids loading s3fs/reticulate in the build container, saving memory for pak forks +# This avoids loading s3fs/reticulate in the build container, saving memory for +# the dependency-installer subprocesses saveRDS(basename(s3_pkgs), "/mnt/cache/packages/s3_cache.rds") file_names <- basename(s3_pkgs) diff --git a/local/r-minor-helpers.R b/local/r-minor-helpers.R index 6f01c29..65aafdf 100644 --- a/local/r-minor-helpers.R +++ b/local/r-minor-helpers.R @@ -31,42 +31,3 @@ parse_build_args <- function(args) { ncpus = as.integer(pos[3L]) ) } - -# Bound the {pkgcache} metadata dir, which otherwise grows without limit: the -# "patched" repo mints a new content hash on every PACKAGES change, so each build -# writes a fresh ~70 MB _metadata/pkgs-.rds (+ patched-/) that is -# never reused. Keep the `keep` newest entries by mtime; only remove entries -# older than `min_age_secs`, so a concurrent split-job's in-flight files are -# never deleted (each build uses a unique hash, so aged entries are -# unreferenced). Stable repo dirs (CRAN-*, BioC*, INLA-*) and pkg/ downloads are -# not matched and thus preserved. Returns the number of entries removed. -trim_pkgcache_metadata <- function(cache_dir = Sys.getenv("R_PKG_CACHE_DIR"), - keep = 20L, - min_age_secs = 600) { - meta <- file.path(cache_dir, "R", "pkgcache", "_metadata") - if (!nzchar(cache_dir) || !dir.exists(meta)) { - return(0L) - } - entries <- c( - Sys.glob(file.path(meta, "patched-*")), - Sys.glob(file.path(meta, "pkgs-*.rds")) - ) - if (length(entries) == 0L) { - return(0L) - } - info <- file.info(entries) - order_new_first <- order(info$mtime, decreasing = TRUE) - ranked <- entries[order_new_first] - ranked_mtime <- info$mtime[order_new_first] - if (length(ranked) <= keep) { - return(0L) - } - candidates <- ranked[(keep + 1L):length(ranked)] - candidate_age <- as.numeric(Sys.time()) - as.numeric(ranked_mtime[(keep + 1L):length(ranked)]) - removable <- candidates[candidate_age >= min_age_secs] - if (length(removable) == 0L) { - return(0L) - } - unlink(removable, recursive = TRUE, force = TRUE) - length(removable) -} diff --git a/local/test-package-loading.R b/local/test-package-loading.R index 26a2e82..a3b7a28 100644 --- a/local/test-package-loading.R +++ b/local/test-package-loading.R @@ -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 diff --git a/local/tests/test-trim-pkgcache.R b/local/tests/test-trim-pkgcache.R deleted file mode 100644 index 1a5b418..0000000 --- a/local/tests/test-trim-pkgcache.R +++ /dev/null @@ -1,68 +0,0 @@ -source(file.path("..", "r-minor-helpers.R")) - -# Build a fake _metadata dir under a temp R_PKG_CACHE_DIR. Each entry's mtime is -# set to `age_secs` in the past so we can exercise the age gate deterministically. -make_meta <- function(patched = 0L, pkgs = 0L, keep_repos = TRUE, age_secs = 3600) { - root <- tempfile("pkgcache-") - meta <- file.path(root, "R", "pkgcache", "_metadata") - dir.create(meta, recursive = TRUE) - old <- Sys.time() - age_secs - mk_dir <- function(p) { dir.create(p); Sys.setFileTime(p, old); p } - mk_file <- function(p) { writeLines("x", p); Sys.setFileTime(p, old); p } - for (i in seq_len(patched)) mk_dir(file.path(meta, sprintf("patched-%03d", i))) - for (i in seq_len(pkgs)) mk_file(file.path(meta, sprintf("pkgs-%03d.rds", i))) - if (keep_repos) { - mk_dir(file.path(meta, "CRAN-075c426938")) - mk_dir(file.path(meta, "BioCsoft-1ac964ed6c")) - mk_file(file.path(meta, "bioc-sysreqs.dcf.gz")) - mk_dir(file.path(root, "R", "pkgcache", "pkg")) # downloads, must survive - } - root -} - -n_churn <- function(root) { - meta <- file.path(root, "R", "pkgcache", "_metadata") - length(Sys.glob(file.path(meta, "patched-*"))) + - length(Sys.glob(file.path(meta, "pkgs-*.rds"))) -} - -test_that("empty cache_dir is a no-op", { - expect_identical(trim_pkgcache_metadata("", keep = 5L, min_age_secs = 0), 0L) -}) - -test_that("missing _metadata dir is a no-op", { - expect_identical( - trim_pkgcache_metadata(tempfile("absent-"), keep = 5L, min_age_secs = 0), - 0L - ) -}) - -test_that("fewer than keep entries removes nothing", { - root <- make_meta(patched = 2L, pkgs = 2L) - expect_identical(trim_pkgcache_metadata(root, keep = 20L, min_age_secs = 0), 0L) - expect_identical(n_churn(root), 4L) -}) - -test_that("trims down to keep newest, leaving churn == keep", { - root <- make_meta(patched = 30L, pkgs = 30L) # 60 churn entries, all old - removed <- trim_pkgcache_metadata(root, keep = 20L, min_age_secs = 0) - expect_identical(removed, 40L) - expect_identical(n_churn(root), 20L) -}) - -test_that("entries younger than min_age_secs are protected", { - root <- make_meta(patched = 30L, pkgs = 0L, keep_repos = FALSE, age_secs = 60) - # keep=5 would drop 25, but all are 60s old < 600s gate -> nothing removed - expect_identical(trim_pkgcache_metadata(root, keep = 5L, min_age_secs = 600), 0L) - expect_identical(n_churn(root), 30L) -}) - -test_that("stable repo dirs and pkg downloads are never touched", { - root <- make_meta(patched = 30L, pkgs = 30L) - trim_pkgcache_metadata(root, keep = 0L, min_age_secs = 0) - meta <- file.path(root, "R", "pkgcache", "_metadata") - expect_true(dir.exists(file.path(meta, "CRAN-075c426938"))) - expect_true(dir.exists(file.path(meta, "BioCsoft-1ac964ed6c"))) - expect_true(file.exists(file.path(meta, "bioc-sysreqs.dcf.gz"))) - expect_true(dir.exists(file.path(root, "R", "pkgcache", "pkg"))) -}) diff --git a/local/uvr-install.sh b/local/uvr-install.sh new file mode 100755 index 0000000..e1c4d0f --- /dev/null +++ b/local/uvr-install.sh @@ -0,0 +1,90 @@ +#!/bin/sh +# Install R packages into the CI library with uvr (https://github.com/nbafrank/uvr). +# +# Usage: +# local/uvr-install.sh httr2 jsonlite +# local/uvr-install.sh forgejo::codefloe.com/rpkgs/bincraft@v4.4.3 +# +# Replaces `pak::pak(...)`. uvr is project-scoped: `uvr add` refuses to run +# outside a project and always writes to `.uvr/library/`, and only +# `uvr sync --library` can target an existing library. The project is therefore +# minted in a scratch directory under TMPDIR and thrown away afterwards; that +# also keeps `uvr init`'s `.Rprofile` out of the repo checkout, where it would +# hijack `.libPaths()` for every other R call in the pipeline. +# +# Pruning is a no-op here: uvr disables it whenever `--library` is passed, +# precisely because such a target may be shared (`/mnt/cache/R-pkgs` holds +# bincraft and its dependencies alongside whatever this script installs). +# +# System dependencies come from uvr's vendored r-system-requirements rules, so +# `pak::sysreqs_db_update()` and `PKG_SYSREQS_PLATFORM` are no longer needed. +# +# Environment: +# UVR_R_BIN R interpreter to install for; set by install-bincraft.R so +# the per-R-minor passes target their own R, not the primary +# R_VERSION fallback interpreter selector (/opt/R//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: $0 ..." >&2 + exit 2 +fi + +# The build images keep R under /opt/R/ and off PATH. uvr resolves the +# interpreter via PATH and never downloads one unless `uvr r install` is run, so +# put the requested R first. +r_bin="${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 diff --git a/renovate.json b/renovate.json index 8c8e208..7b2c3b3 100644 --- a/renovate.json +++ b/renovate.json @@ -1,7 +1,12 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", "extends": ["local>devxy/renovate-config"], - "ignorePaths": ["docker/**", ".crow/process-updates.yaml", ".crow/build-all-versions.yaml", ".crow/weekly-rebuild-missing.yaml"], + "ignorePaths": [ + "docker/**", + ".crow/process-updates.yaml", + ".crow/build-all-versions.yaml", + ".crow/weekly-rebuild-missing.yaml" + ], "customManagers": [ { "customType": "regex", @@ -14,6 +19,13 @@ "packageNameTemplate": "https://codefloe.com/rpkgs/bincraft.git", "datasourceTemplate": "git-tags", "extractVersionTemplate": "^v?(?.+)$" + }, + { + "customType": "regex", + "fileMatch": ["^local/uvr-install\\.sh$"], + "matchStrings": [ + "# renovate: datasource=(?\\S+) depName=(?\\S+)\\s+UVR_PIN=\"(?[^\"]+)\"" + ] } ] } From e02be7518fa4789688a44b5d56280fff5d3fd765 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Tue, 4 Aug 2026 02:32:01 +0000 Subject: [PATCH 26/53] chore(deps): update dependency nbafrank/uvr to v0.4.5 --- local/uvr-install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/local/uvr-install.sh b/local/uvr-install.sh index e1c4d0f..14b7f78 100755 --- a/local/uvr-install.sh +++ b/local/uvr-install.sh @@ -30,7 +30,7 @@ set -eu # renovate: datasource=github-releases depName=nbafrank/uvr -UVR_PIN="v0.4.4" +UVR_PIN="v0.4.5" if [ "$#" -eq 0 ]; then echo "usage: $0 ..." >&2 From 02dd5a695dc1a1816a8f815a7f5471deed99d2b3 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Wed, 5 Aug 2026 00:32:29 +0000 Subject: [PATCH 27/53] chore(deps): update terraform bunnynet to ~> 0.17 --- .terraform.lock.hcl | 72 ++++++++++++++++++++++----------------------- provider.tf | 2 +- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index fdf41e1..aca8ce1 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -38,43 +38,43 @@ provider "registry.opentofu.org/hashicorp/http" { } provider "registry.terraform.io/bunnyway/bunnynet" { - version = "0.16.0" - constraints = "~> 0.16" + version = "0.17.0" + constraints = "~> 0.17" hashes = [ - "h1:+7y/HM0f4/cm7dpL5RulSZ3k5EDokVaIutfuanc1hhA=", - "h1:/4n/gUEzVa7LArNrNbZa4RyGC3+MRCCYTuqRqF36Z7U=", - "h1:4cSbrSalUxXnG0RVwrQG51NNleZNFU9GJxWCLK1M9WM=", - "h1:AlidPvq+LqsveQVhc9JYa7OKf4mcR+DjCzMomoBcmkw=", - "h1:Beny1tSl5O/jM7sSP7qYv+NEVTTyS/BGtSxvMFsII/o=", - "h1:E50kVGCtxWYoJgOLtdat1JFc9KCIeMByk65XSIpuaB0=", - "h1:ErNz5hzwf70NouW7a1DAknWI/0/BFUEX53hQ4BnUxWg=", - "h1:GTB8ugjpBEsRZpdVmKJw70IF2B1/fd1Gwven6XKghpk=", - "h1:JEEDgEc2gwjwfvnDwWO2ZHaf9T5WHtb7A6ABx6rQqhE=", - "h1:OVd3EgjJDuyMBFQ4XZYrs09NNEtFw4jGAbwyeos2H3M=", - "h1:U/9QeqZ+Q2MQ7eNfD1eWomLFlbYGwpliHcD/UTFe/D0=", - "h1:VPUe+m5Fx31TAR7udJPGGzk3EpCNizf0TmnKplOJyRM=", - "h1:YkJwUFpUemqi6bwRIEJW4xSpI7CAEXirqhyjl6Rmm68=", - "h1:a/15E8lijUcqvhUGxtqKmJT6jYGmQW9z7yBoOjusDm8=", - "h1:hii960NFcNpr0eZ/dcbnYOf2oZuo2IZl+z1IMTwh5YA=", - "h1:mq/KWNt6PPZLdNpO1ekzrn6EfWz6l8sTHG74dgy07nI=", - "h1:vso6Er2XV/MsUTMtXIlz0AhIFx0TZnK73YNSZfA/9ZY=", - "zh:1f581ed8bc8b676f0127af7c018912ca82972e9348370d9f4dbe5b44005bb0ec", - "zh:1fa5b9c01ffbc7fdc507bbcffc177a1f1deb9f56f3d27183c6d92a11ea3208f8", - "zh:42b6524a9658df7093199b65eb210b3246a9f9822c8778a77e2d00a222441c03", - "zh:4c4f17fe2ae86087626dfd1055b0faea6a23fe3a12aabb2a7de3b9b2df6e3e41", - "zh:5346bb67d7154a8bc8c887b4b86bef95b3e92857d4304f55afea6d56ed152932", - "zh:591df2c3d4552f6f613415c900023d43e73e00e90312b7b1a666fe567219120f", - "zh:7156849aa03348c7556b746d3d9956293678de4a9e30c80480358dcdacb2a7fa", - "zh:75dee86262352f061ad072a5b873d3b3eabbb124ab0f20a803cfd44a87a31067", - "zh:7c33954aff1878bec78a50742897fae78dd2fbd19abeaeaca0c560ccc8f78810", - "zh:7d9cf36633dd991b41891d1c91b45b5c803852a902705453d6be4513524a574c", + "h1:+qDt35lVSK7acw6a1xHuPYrqmZEcHSmtd+6n1TxNuYw=", + "h1:1dCu2l4DhPBjizVAH/WwAjT1Xbo52K4PMvHoD5zUhuU=", + "h1:Dvn46Auwuel4jqrqZXs2D7kdujNhs17LEmqhuY0k4/4=", + "h1:M5eDL3m2uSEr1XATJW0foHzKl8pFhCtgKuOM24bJRwU=", + "h1:PddaC7nM/gY4x9i3xy6TxOs9MAu2/6g58Xs/gv4DRV8=", + "h1:QVIKiZluI+NQAKu8NpFBl3Nvyx+d81vW9btEUdIQREc=", + "h1:S6TnzXHsRoGYvC1vJBkDiVEc0spceksY4n6x5WN5iYw=", + "h1:VcxZDWqCWMSjcUsC1K4sB6uYEoeoou+BC0ePoJXmf3A=", + "h1:W0y/agBVqls1cJlFGFYMu2VnqoPXFzxVHPIYe3OqfYQ=", + "h1:XmNd5fP9a0O77ve5BMQP2vARExgIa7rYl6KvyUYXPSs=", + "h1:e0EFKrWSQwaa/kGhnha4DXk4T68Av8QxP84mRSdWC9M=", + "h1:eM+/lUiU0pNSgQKoqKPgE3xJrJ0MHIpKG+yhaGB/P0M=", + "h1:fPWWA4T0/y7GX+tCGN23l1jODhZ3uCdR/MKgZDXYpAE=", + "h1:g+r2GVi4gVC4DuQg3PL70gW9BDskgWUzCBIMXTUq63A=", + "h1:gaZ8eALDtVHqykVDHav8004gHiMGaYR/3KwET0FUgao=", + "h1:kbqW25eaiv4N/N/z+sxLdJZ15yh5cgnRD/q6RclPMLc=", + "h1:rGjxue3mXRyQQqpywTXC4zK//JAtf0Cz7RP+uPMMJjw=", + "zh:05943fef14c2028f4722bf078aa1889229e94302f7678cc6f63adb669d8ea612", + "zh:26a163930a92a7408f7bbd0130064b84df8a232b500d8c6c3989952986308539", + "zh:41305feaaade55391447521ec309f3c038b631ca542907ad95132fab71a7e116", + "zh:606919a930f0299948504adbdcd0f239a8af5c418f85741c48f8add370a3d038", + "zh:66963d5b445639511939fc508513fd31da3ee1d4ee1a565ee396c9532897a349", + "zh:6c981ec0c8545556395c43e2511861ab65ee9ecf2a960480e7889c3af0d23af3", + "zh:7334a1bdb726ce1f1bf0a3155f30f84f65206980c229c832ff5f0b0718c44e0b", + "zh:75f6c86bf74511e605423332d113711c76c8028361a32282fb3359d6c7ecae9e", + "zh:7aebb1a01cfe8be54903853202ae06eba14ad99c37d230ed93ce7d6633e05e9b", "zh:890df766e9b839623b1f0437355032a3c006226a6c200cd911e15ee1a9014e9f", - "zh:9552ed1be3059b31544632d6293c2bfcd2474983e116c42702a6c408deb8e44d", - "zh:b3cb1f2bde0fd591d18109119f6235ff41c7ea6441777a356a64c348ee4ccdf7", - "zh:b5c1748403bf43274eba2574219cfa082351c8b1c1537a768acebef5cc5b2c0a", - "zh:c1b032e33aee40945770bbdf6002f777ee7b4ca541c00f4cf5eb23c09d32ef54", - "zh:d469680df9845fb506be27b2c838d39ccd8e98e26540b99936775f954299c35c", - "zh:dd59fa97fea4b10b901a6a749ebff81895f54126a2f08b4cd8f5baf6cfbbd854", - "zh:fb142d8ea02909587a4858374fe33d8609347150f4d32b7e15423320ffbd07b1", + "zh:9041d0e20c9ceea532de6eebf5cb3a27dad0bb49d3f5b5154be2a08d68fbbf1f", + "zh:a6bbf65431a02be4df0ebb1cbe01185ad357ff6e33c01bd0558f59bed90c8f36", + "zh:c6d075a31096f080c388dfe46036f451c0cc114c3311a4f46ab8dbe1938a202f", + "zh:dd8703f7b55b8bc8e10f8718bea889781100b18e932b04898995b63178c3d36e", + "zh:dd92a5cd4e133a4000e7e5bc8cce876ae0ed803543cedd2f3d590661ba244d04", + "zh:e024fdf121bebc48c1e6debea344c6d4f174117f3ae605fca6e13b9705d92d22", + "zh:ee0e80c31b438e35fa1608f6a2f5824d2806db1e5e8b9f7a90986585c7bcb895", + "zh:fc2d4b705411b48f8c045981f9368a3ea2f74969dd6302008c31ff0bedd51f0a", ] } diff --git a/provider.tf b/provider.tf index c22ce2d..badbbc1 100644 --- a/provider.tf +++ b/provider.tf @@ -2,7 +2,7 @@ terraform { required_providers { bunnynet = { source = "registry.terraform.io/BunnyWay/bunnynet" - version = "~> 0.16" + version = "~> 0.17" } } } From 0da29ab3f6ae2e5548ce22a6e886b3ec62cd79d0 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 7 Aug 2026 09:15:04 +0000 Subject: [PATCH 28/53] fix(index): add a slot repair for a broken Built stamp and retire alpine 3.21 (#150) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem `arm64/alpine321` and `arm64/alpine322` advertise a broken stamp: ``` arm64/alpine321 :: 22930 Built: R 4.4.0; NA; 2026-07-31 13:35:52 UTC; unix arm64/alpine322 :: 24696 Built: R 4.5.0; NA; 2026-07-31 13:51:54 UTC; unix ``` The per-minor sub-slots (`contrib/4.4`, `4.5`, `4.6`) are affected too. All 18 other slots are correct. uvr matches the stamp's platform triple plus R minor to pick binary over source, so nothing matches `NA` and both slots silently serve as source-only, which is exactly the regression bincraft#85 added the stamp to prevent. `install.packages()` is unaffected, since it reads `Built:` from each tarball's own `DESCRIPTION`. The tarballs are fine (`arm64/alpine322/.../dress.graph_0.8.3.tar.gz` carries `aarch64-unknown-linux-musl`), and so is the R that built them (`r-4.5.0_1_aarch64.apk` ships `R_PLATFORM='aarch64-unknown-linux-musl'`). Only the index is wrong. bincraft#96 stops a stamp like this being written again, but it cannot repair what is already there. ## Why not just re-run the index update `upload_package_index()` reuses the slot's remote `PACKAGES.db`, and cranlike's `update_db()` only reparses files whose md5 changed, so entries already in the database keep the stamp they were written with. Dropping `PACKAGES.db` to force a full reparse does work, and it is what bincraft#85's rollout note suggested, but for an S3 repo cranlike reads each package's metadata from the CRAN *source* mirror on GitHub. A 25k-entry slot is then 25k requests to raw.githubusercontent.com, with a real risk of being rate-limited part-way through and leaving the slot half-written. Only the `Built` column is wrong, so this corrects it in place instead: patch the column in `PACKAGES.db`, put the database 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. ## Change - `local/repair-built-stamp.R` — repairs the generic slot plus every per-minor sub-slot. Dry-run by default; `--apply` writes. The replacement comes from `bincraft::built_stamp()` under the R running the script, so it is exactly what a healthy run would have written, and bincraft#96's guard makes a broken build image fail rather than write a second bad stamp. - `.crow/repair-built-stamp.yaml` — manual pipeline, routed by `target_arch` to the matching agent group and platform image, with `dry_run` defaulting to `true`. - `.crow/archive-missed-packages.yaml` — drop the two `alpine321` matrix entries. Alpine 3.21 is EOL: the website advertises only 3.23/3.24 and `process-updates.yaml` already dropped it, so that slot is retired rather than repaired. ## Verification `crow lint .crow/` passes on all nine pipelines. `air format` and `jarl check` are clean; the script parses, and the `/opt/R` minor-version derivation was checked against `4.4.3 / 4.5.3 / 4.6.0 / current` → `4.4 4.5 4.6`. The repair itself is unrun by design — it needs B2 credentials and an arm64 agent. ## Rollout 1. Cut a bincraft release so `local/install-bincraft.R` picks up #96 (it resolves the latest `vX.Y.Z` tag, and #96 is only on `main`). 2. Run this pipeline with `target_arch=arm64`, `OS=alpine`, `OS_VERSION=3.22`, `R_VERSION=4.5.3`, `dry_run=true` and check the reported counts. 3. Re-run with `dry_run=false`. 4. Confirm: `curl -sS https://cran.devxy.io/arm64/alpine322/latest/src/contrib/PACKAGES | grep '^Built:' | sort | uniq -c` `arm64/alpine321` is deliberately left alone. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/150 --- .crow/archive-missed-packages.yaml | 4 - .crow/repair-built-stamp.yaml | 97 ++++++++++++++++ local/repair-built-stamp.R | 175 +++++++++++++++++++++++++++++ 3 files changed, 272 insertions(+), 4 deletions(-) create mode 100644 .crow/repair-built-stamp.yaml create mode 100644 local/repair-built-stamp.R diff --git a/.crow/archive-missed-packages.yaml b/.crow/archive-missed-packages.yaml index 71f808b..bd127d6 100644 --- a/.crow/archive-missed-packages.yaml +++ b/.crow/archive-missed-packages.yaml @@ -28,10 +28,6 @@ matrix: ARCH: amd64 - CODENAME: redhat-10 ARCH: arm64 - - CODENAME: alpine321 - ARCH: amd64 - - CODENAME: alpine321 - ARCH: arm64 - CODENAME: alpine322 ARCH: amd64 - CODENAME: alpine322 diff --git a/.crow/repair-built-stamp.yaml b/.crow/repair-built-stamp.yaml new file mode 100644 index 0000000..12e2644 --- /dev/null +++ b/.crow/repair-built-stamp.yaml @@ -0,0 +1,97 @@ +### Manual repair of a slot whose PACKAGES index advertises a broken `Built` +### stamp (e.g. `Built: R 4.5.0; NA; ...`). +# +# uvr matches the stamp's platform triple plus R minor to decide binary vs +# source, so an unusable triple turns a whole slot source-only. See +# local/repair-built-stamp.R for why this patches PACKAGES.db in place instead +# of forcing a full reparse. +# +# Run with `dry_run: true` first: it reports how many entries are broken per +# slot and changes nothing. Pick the R version the slot should advertise, which +# is the R_VERSION its entry in .crow/process-updates.yaml uses. +variables: + target_arch: + description: 'Architecture of the slot to repair.' + options: + - amd64 + - arm64 + default: arm64 + OS: + description: 'Base OS image name.' + options: + - alpine + - redhat + - ubuntu + default: alpine + OS_VERSION: + description: 'OS image tag. Must match OS (alpine: 3.22/3.23/3.24; redhat: 8/9/10; ubuntu: jammy/noble/resolute).' + options: + - '3.22' + - '3.23' + - '3.24' + - '8' + - '9' + - '10' + - 'jammy' + - 'noble' + - 'resolute' + default: '3.22' + R_VERSION: + description: 'R version whose stamp the slot should advertise.' + options: + - 4.5.3 + - 4.4.3 + default: 4.5.3 + dry_run: + description: 'Report what would change without writing anything.' + options: + - 'true' + - 'false' + default: 'true' + +when: + - event: manual + evaluate: 'target_arch == "${ARCH}"' + +skip_clone: true + +labels: + platform: linux/${ARCH} + group: rpkgs-${ARCH} + +matrix: + include: + - ARCH: amd64 + - ARCH: arm64 + +steps: + - name: 'Repair Built stamp' + image: 'reg.devxy.io/rpkgs/build-env-${OS}:${OS_VERSION}' + pull: true + environment: + B2_S3_ACCESS_KEY: + from_secret: B2_S3_ACCESS_KEY + B2_S3_SECRET_KEY: + from_secret: B2_S3_SECRET_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + GIT_USER: pat-s + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' + - | + if [ "$dry_run" = "false" ]; then + /opt/R/$R_VERSION/bin/Rscript local/repair-built-stamp.R "$ARCH" --apply + else + /opt/R/$R_VERSION/bin/Rscript local/repair-built-stamp.R "$ARCH" + fi + backend_options: + docker: + resources: + requests: + memory: 2Gi + cpu: 1000m + limits: + memory: 8Gi + cpu: 2000m diff --git a/local/repair-built-stamp.R b/local/repair-built-stamp.R new file mode 100644 index 0000000..06f73be --- /dev/null +++ b/local/repair-built-stamp.R @@ -0,0 +1,175 @@ +#!/usr/bin/env Rscript + +### Rewrite a broken `Built` stamp across one arch/codename slot. +### +### A slot's index can end up advertising a stamp whose platform triple is +### unusable, e.g. `Built: R 4.5.0; NA; ...`. uvr picks binary vs source by +### matching that triple plus the R minor, so no client matches it and the whole +### slot silently reverts to source-only, which makes uvr compile everything and +### fail wherever a system `-dev` library is missing. +### +### Rewriting it is not a matter of re-running the normal index update. +### `upload_package_index()` reuses the slot's remote `PACKAGES.db`, and +### cranlike's `update_db()` only reparses files whose md5 changed, so entries +### already in the database keep the stamp they were written with. 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 through. +### +### Only the `Built` column is wrong, so correct it in place instead: patch the +### column in `PACKAGES.db`, put the database 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. +### +### The replacement comes from `bincraft::built_stamp()` under the R running +### this script, so run it under the R version the slot should advertise (the +### `R_VERSION` its entry in `.crow/process-updates.yaml` uses). That is what a +### healthy `upload_package_index()` run would have written. +### +### Usage, inside the platform's build image: +### Rscript local/repair-built-stamp.R [--apply] +### +### Without `--apply` it reports what it would change and touches nothing. + +suppressPackageStartupMessages({ + library(bincraft) +}) + +args <- commandArgs(trailingOnly = TRUE) +arch <- args[1L] +apply_changes <- "--apply" %in% args + +if (is.na(arch) || !nzchar(arch)) { + stop( + "Usage: Rscript local/repair-built-stamp.R [--apply]", + call. = FALSE + ) +} + +bucket <- "devxy-rpkgs-binaries" +endpoint <- "https://s3.eu-central-003.backblazeb2.com" +region <- "eu-central-003" + +codename <- bincraft::set_codename(NULL) +if (is.null(codename) || is.na(codename) || !nzchar(codename)) { + stop( + "Could not detect a codename from /etc/os-release; run this in a build image.", + call. = FALSE + ) +} + +# built_stamp() refuses an unusable platform, so a broken build image fails here +# rather than writing a second bad stamp over the first one. +stamp <- bincraft::built_stamp() +message(sprintf("Slot: %s/%s", arch, codename)) +message(sprintf("New stamp: %s", stamp)) + +s3fs::s3_file_system( + aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + aws_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), + endpoint = endpoint, + region_name = region, + refresh = TRUE +) + +base_dir <- file.path(bucket, arch, codename, "latest", "src", "contrib") + +# A stamp is broken when its platform component is absent or literally "NA". +broken_stamp_where <- paste( + "Built IS NULL", + "OR Built LIKE '%; NA;%'", + "OR Built LIKE '%; ;%'" +) + +# The generic slot plus every per-minor sub-slot, which carry the same stamp and +# are poisoned by the same run. +r_minors <- sub( + "^.*/R/([0-9]+\\.[0-9]+)\\.[0-9]+$", + "\\1", + list.dirs("/opt/R", recursive = FALSE) +) +r_minors <- unique(grep("^[0-9]+\\.[0-9]+$", r_minors, value = TRUE)) +slots <- c(base_dir, file.path(base_dir, r_minors)) + +repair_slot <- function(slot) { + db_remote <- file.path(slot, "PACKAGES.db") + if (!s3fs::s3_file_exists(db_remote)) { + message(sprintf(" %s: no PACKAGES.db, skipping", slot)) + return(invisible(NULL)) + } + + db_local <- tempfile(fileext = ".db") + s3fs::s3_file_download(db_remote, db_local, overwrite = TRUE) + + con <- DBI::dbConnect(RSQLite::SQLite(), db_local) + on.exit(DBI::dbDisconnect(con), add = TRUE) + + total <- DBI::dbGetQuery(con, "SELECT COUNT(*) AS n FROM packages")$n + broken <- DBI::dbGetQuery( + con, + sprintf("SELECT COUNT(*) AS n FROM packages WHERE %s", broken_stamp_where) + )$n + + message(sprintf(" %s: %s entries, %s broken", slot, total, broken)) + if (broken == 0L) { + return(invisible(NULL)) + } + if (!apply_changes) { + message(" (dry run, pass --apply to rewrite)") + return(invisible(NULL)) + } + + DBI::dbExecute( + con, + sprintf("UPDATE packages SET Built = ? WHERE %s", broken_stamp_where), + params = list(stamp) + ) + DBI::dbDisconnect(con) + on.exit() + + s3fs::s3_file_upload(db_local, db_remote, overwrite = TRUE) + message(sprintf(" rewrote %s entries and uploaded PACKAGES.db", broken)) + invisible(NULL) +} + +invisible(lapply(slots, repair_slot)) + +if (!apply_changes) { + message("Dry run complete; nothing was changed.") + quit(save = "no") +} + +# Re-emit PACKAGES/PACKAGES.gz/PACKAGES.rds from the corrected database. Nothing +# is reparsed, because no tarball's md5 changed. +message("Re-emitting index files from the corrected database...") +bincraft::upload_package_index( + codename = codename, + s3_endpoint = endpoint, + s3_region = region, + s3_bucket = bucket, + s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY") +) +for (minor in r_minors) { + try( + bincraft::upload_package_index( + codename = codename, + r_minor = minor, + s3_endpoint = endpoint, + s3_region = region, + s3_bucket = bucket, + s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY") + ), + silent = FALSE + ) +} + +message("Done. Verify with:") +message(sprintf( + " curl -sS https://cran.devxy.io/%s/%s/latest/src/contrib/PACKAGES | grep '^Built:' | sort | uniq -c", + arch, + codename +)) From 77ce1d212dfdf791be19c768931b75ddd3991e09 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 7 Aug 2026 09:41:53 +0000 Subject: [PATCH 29/53] fix(ci): gate the Built-stamp repair on its own variable (#151) ## Problem `repair-built-stamp.yaml` gated on `target_arch`: ```yaml when: - event: manual evaluate: 'target_arch == "${ARCH}"' ``` That is the same variable `build-all-versions.yaml` and `build-all-versions-install-deps.yaml` gate on. A manual run passing `target_arch=arm64` to reach the repair therefore matched all three, so triggering a dry-run repair also queued a full arm64 rebuild. I hit this triggering the alpine 3.22 dry run (pipeline 10706), which I killed. `crow pipeline ps` renders empty states on this version, so I could not confirm from the CLI whether the rebuild workflows started before the kill or only sat queued behind the running cron jobs; no output was attributable to them. ## Change Gate on `repair_built_stamp` instead. Every other pipeline here already gates on a variable named after itself (`process_cran_updates`, `weekly_audit_missing`, `weekly_rebuild_missing`), and `target_arch` was the odd one out being shared by two. The header now records the collision and the exact invocation, so the next pipeline added here does not repeat it. ## Verification `crow lint` passes; `prek` clean. Grep of every trigger condition in `.crow/` confirms `repair_built_stamp` is unique and that no other pipeline gates on `OS`, `OS_VERSION`, `R_VERSION` or `dry_run` alone: ``` archive-missed-packages.yaml: task == "archive-missed-packages" build-all-versions.yaml: target_arch == "${ARCH}" build-all-versions-install-deps.yaml: target_arch == "${ARCH}" weekly-audit-missing.yaml: weekly_audit_missing == ... repair-built-stamp.yaml: repair_built_stamp == "${ARCH}" process-updates.yaml: process_cran_updates == ... weekly-rebuild-missing.yaml: weekly_rebuild_missing == ... ``` ## Note for whoever runs it `crow pipeline create` against this instance returned HTTP 504 while still creating the pipeline. Retrying on that error duplicates the run: I created four before noticing. Verify with `pipeline ls` rather than trusting the exit status. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/151 --- .crow/repair-built-stamp.yaml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/.crow/repair-built-stamp.yaml b/.crow/repair-built-stamp.yaml index 12e2644..83821e9 100644 --- a/.crow/repair-built-stamp.yaml +++ b/.crow/repair-built-stamp.yaml @@ -9,9 +9,18 @@ # Run with `dry_run: true` first: it reports how many entries are broken per # slot and changes nothing. Pick the R version the slot should advertise, which # is the R_VERSION its entry in .crow/process-updates.yaml uses. +# +# The gate variable is `repair_built_stamp`, not `target_arch`: `target_arch` is +# what build-all-versions and build-all-versions-install-deps gate on, so a +# manual run passing it would start a full rebuild alongside this repair. Every +# pipeline here gates on a variable named after itself for exactly that reason. +# +# crow pipeline create --branch main \ +# --var repair_built_stamp=arm64 --var OS=alpine --var OS_VERSION=3.22 \ +# --var R_VERSION=4.5.3 --var dry_run=true devxy/build-cran-binaries variables: - target_arch: - description: 'Architecture of the slot to repair.' + repair_built_stamp: + description: 'Architecture of the slot to repair. Also gates this pipeline.' options: - amd64 - arm64 @@ -51,7 +60,7 @@ variables: when: - event: manual - evaluate: 'target_arch == "${ARCH}"' + evaluate: 'repair_built_stamp == "${ARCH}"' skip_clone: true From 2f732457d2af605415b1768a0992db7d9a17c1cf Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 7 Aug 2026 14:12:22 +0000 Subject: [PATCH 30/53] feat(edge): route PACKAGES requests to the per-R-minor slot (#152) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem `install.packages("curl")` fails in `reg.devxy.io/r/r-alpine:4.5-3.24` with "package 'curl' is not available for this version of R", on both arches. `curl` is not missing from the repo: it is in `…/latest/src/contrib/4.5/` and `…/4.6/`, the per-minor slots that base R cannot address. The image's repo URL resolves to `…/latest/src/contrib`, whose index does not list it. On `amd64/alpine324` that is 2 886 packages invisible to `install.packages()` (23 on `amd64/noble`) — what issue #63 records as "missing binaries". Two further findings while investigating: - The middleware only ever rewrote the bare `cran.rpkgs.com/src/contrib/…` form, and that form was broken for every Linux client on a stock R user agent: `ALPINE_REGEX`/`UBUNTU_REGEX`/`RHEL_REGEX` need a Posit-style UA that carries the distro, so stock R fell through to `extractOs()` and got redirected to `/amd64/linux-musl/latest/…`, a slot that does not exist. - `PACKAGES*` is served `cdn-cache: BYPASS` (bincraft uploads it `no-store`), so the middleware sees every index request and no purge is needed for routing changes to take effect. ## What this changes **`edge/rpkgs-router.ts`** — the middleware, now a reviewed file in this repo rather than dashboard state. It routes `PACKAGES`, `PACKAGES.gz` and `PACKAGES.rds` into `…/src/contrib//` for slots listed in `UNION_SLOTS`, and nothing else. Tarballs are deliberately left alone. R keeps the `contriburl` it *asked for*, not the one the redirect served it, so every tarball URL is resolved against the flat directory and the union index steers the per-minor ones with a `Path: ` field. Rewriting a tarball request here would send flat-slot packages into a directory that does not hold them. Also in the script: the phantom `linux-gnu`/`linux-musl` fallback is gone (an unidentifiable distro goes to CRAN, as an unparseable UA already did), and every redirect carries `Cache-Control: no-store` since its target depends on the User-Agent. The macOS branches are unchanged. **`cdn.tf`** — `bunnynet_compute_script.rpkgs_router` with `content = file("edge/rpkgs-router.ts")`, the `UNION_SLOTS` variable, and `middleware_script` pointing at the resource instead of the literal `29277`. `UNION_SLOTS` is empty, so merging and applying this changes no client's behaviour. A slot is added only once bincraft has republished its per-minor index as a union (rpkgs/bincraft#97); routing to a raw per-minor index would hide every package it does not carry. Rolling back is a variable edit, not a deploy. **`specs/`, `plans/`** — the design and the implementation plan, including the two approaches that were rejected (edge-side merge, moving the minor up the path) and why. ## Verification `just edge-test` runs 13 routing cases against the SDK's local server, so what is tested is the artifact that gets deployed; pass-through cases proxy to the real origin. All pass. End to end, with the middleware in front of a locally built union index for `amd64/alpine324` (31 507 records), inside the runtime image: ``` curl: 7.1.0 -> …/latest/src/contrib/4.5 -> curl_7.1.0.tar.gz 717 725 B jsonlite: 2.0.0 -> …/latest/src/contrib -> jsonlite_2.0.0.tar.gz 1 055 849 B ``` `tofu validate` passes. `tofu plan` has not been run: no `BUNNYNET_API_KEY` available in this environment. ## Before applying The script pre-dates this configuration, so it must be adopted, not created: ```sh tofu import bunnynet_compute_script.rpkgs_router 29277 tofu plan ``` The plan should show an in-place `content` update and no replacement of the pull zone. Without the import, tofu creates a second script and repoints the zone at it. Note that `name = "rpkgs-router"` will rename the existing script on apply. ## Not fixed here `install.packages("curl")` on `alpine324` will now *resolve*, then fail to build: that slot's tarballs are byte-identical CRAN **source** tarballs (no `Meta/`, no `Built:` in DESCRIPTION) which the index nevertheless stamps `Built: R 4.5.3; …-linux-musl`. Sampled: `amd64/alpine324` 3/12 binary, `arm64/alpine324` 13/30, `amd64/noble` 12/12, `amd64/alpine323` 17/20. That slot needs a rebuild, tracked separately. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/152 --- cdn.tf | 25 +- edge/rpkgs-router.test.ts | 160 ++++++++++++ edge/rpkgs-router.ts | 235 ++++++++++++++++++ justfile | 14 ++ plans/2026-08-07-per-minor-edge-routing.md | 166 +++++++++++++ ...026-08-07-per-minor-edge-routing-design.md | 174 +++++++++++++ 6 files changed, 773 insertions(+), 1 deletion(-) create mode 100644 edge/rpkgs-router.test.ts create mode 100644 edge/rpkgs-router.ts create mode 100644 plans/2026-08-07-per-minor-edge-routing.md create mode 100644 specs/2026-08-07-per-minor-edge-routing-design.md diff --git a/cdn.tf b/cdn.tf index 8a950f5..fe1b25f 100644 --- a/cdn.tf +++ b/cdn.tf @@ -52,6 +52,29 @@ ### cran.rpkgs.com +# The edge middleware that resolves the bare cran.rpkgs.com form to an +# / slot and routes PACKAGES* to the per-R-minor slot. The source of +# truth is edge/rpkgs-router.ts; `tofu apply` publishes a new release. +# +# The script pre-dates this configuration, so it is adopted rather than created: +# tofu import bunnynet_compute_script.rpkgs_router 29277 +resource "bunnynet_compute_script" "rpkgs_router" { + type = "middleware" + name = "rpkgs-router" + content = file("${path.module}/edge/rpkgs-router.ts") +} + +# Slots ("/", comma separated) whose per-minor index bincraft has +# already republished as a union of the per-minor and flat slots. Routing to a +# slot that is not listed here would hide every package the per-minor index does +# not carry, so this stays empty until a slot has been backfilled. +resource "bunnynet_compute_script_variable" "rpkgs_router_union_slots" { + script = bunnynet_compute_script.rpkgs_router.id + name = "UNION_SLOTS" + default_value = "" + required = false +} + resource "bunnynet_pullzone" "cran_rpkgs_com" { name = "cran-rpkgs" @@ -64,7 +87,7 @@ resource "bunnynet_pullzone" "cran_rpkgs_com" { origin { type = "OriginUrl" url = "https://devxy-rpkgs-binaries.s3.eu-central-003.backblazeb2.com" - middleware_script = 29277 + middleware_script = bunnynet_compute_script.rpkgs_router.id } routing { diff --git a/edge/rpkgs-router.test.ts b/edge/rpkgs-router.test.ts new file mode 100644 index 0000000..553185d --- /dev/null +++ b/edge/rpkgs-router.test.ts @@ -0,0 +1,160 @@ +/** + * Routing matrix for `edge/rpkgs-router.ts`. + * + * The script is exercised through the SDK's local server rather than by + * importing its internals, so what is tested is the artifact that gets + * deployed. Requests that the script passes through are proxied to the real + * origin, which keeps the "no redirect" cases honest: they assert that the + * client reached the flat slot, not merely that no `Location` was set. + * + * Run with `just edge-test`. + */ +import { assertEquals } from 'jsr:@std/assert@1'; + +const SCRIPT = new URL('./rpkgs-router.ts', import.meta.url).pathname; +const BASE = 'http://127.0.0.1:8080'; +const UNION_SLOTS = 'amd64/alpine324'; + +const UA_R45_MUSL = 'R (4.5.3 x86_64-pc-linux-musl x86_64 linux-musl)'; +const UA_R46_MUSL = 'R (4.6.0 x86_64-pc-linux-musl x86_64 linux-musl)'; +const UA_R45_ALPINE = 'R/4.5.3 R (4.5.3 x86_64-pc-linux-musl x86_64 linux-musl) Alpine Linux 3.24'; +const UA_R45_DARWIN = 'R (4.5.1 aarch64-apple-darwin20 aarch64 darwin20)'; +const UA_CURL = 'curl/8.0.1'; + +const SLOT = '/amd64/alpine324/latest/src/contrib'; +const OTHER_SLOT = '/amd64/noble/latest/src/contrib'; + +interface Probe { + status: number; + location: string | null; + cacheControl: string | null; +} + +async function probe(path: string, userAgent: string): Promise { + const res = await fetch(BASE + path, { + headers: { 'User-Agent': userAgent }, + redirect: 'manual', + }); + await res.body?.cancel(); + return { + status: res.status, + location: res.headers.get('location'), + cacheControl: res.headers.get('cache-control'), + }; +} + +/** Kill tolerantly: the child has already exited if the script failed to load. */ +async function stopServer(child: Deno.ChildProcess): Promise { + try { + child.kill(); + } catch { + // already gone + } + await child.status; +} + +async function startServer(): Promise { + const child = new Deno.Command(Deno.execPath(), { + args: ['run', '-A', SCRIPT], + env: { UNION_SLOTS }, + stdout: 'null', + stderr: 'inherit', + }).spawn(); + + for (let attempt = 0; attempt < 150; attempt++) { + try { + const res = await fetch(`${BASE}/`, { + headers: { 'User-Agent': UA_CURL }, + redirect: 'manual', + }); + await res.body?.cancel(); + return child; + } catch { + await new Promise((resolve) => setTimeout(resolve, 200)); + } + } + + await stopServer(child); + throw new Error('edge script did not start listening on ' + BASE); +} + +Deno.test('rpkgs-router', async (t) => { + const server = await startServer(); + + try { + await t.step("routes an index request to the client's R minor", async () => { + const res = await probe(`${SLOT}/PACKAGES.gz`, UA_R45_MUSL); + assertEquals(res.status, 302); + assertEquals(res.location, `https://cran.rpkgs.com${SLOT}/4.5/PACKAGES.gz`); + }); + + await t.step('routes R 4.6 to its own slot', async () => { + const res = await probe(`${SLOT}/PACKAGES.gz`, UA_R46_MUSL); + assertEquals(res.location, `https://cran.rpkgs.com${SLOT}/4.6/PACKAGES.gz`); + }); + + await t.step('routes PACKAGES and PACKAGES.rds too', async () => { + for (const file of ['PACKAGES', 'PACKAGES.rds']) { + const res = await probe(`${SLOT}/${file}`, UA_R45_MUSL); + assertEquals(res.location, `https://cran.rpkgs.com${SLOT}/4.5/${file}`, `expected ${file} to be routed`); + } + }); + + await t.step('marks the redirect uncacheable', async () => { + const res = await probe(`${SLOT}/PACKAGES.gz`, UA_R45_MUSL); + assertEquals(res.cacheControl, 'no-store'); + }); + + await t.step('leaves a slot outside UNION_SLOTS alone', async () => { + const res = await probe(`${OTHER_SLOT}/PACKAGES.gz`, UA_R45_MUSL); + assertEquals(res.location, null); + assertEquals(res.status, 200); + }); + + await t.step('never routes a tarball', async () => { + const res = await probe(`${SLOT}/jsonlite_2.0.0.tar.gz`, UA_R45_MUSL); + assertEquals(res.location, null); + assertEquals(res.status, 200); + }); + + await t.step('does not redirect a path already under a minor', async () => { + const res = await probe(`${SLOT}/4.5/PACKAGES.gz`, UA_R45_MUSL); + assertEquals(res.location, null); + assertEquals(res.status, 200); + }); + + await t.step('leaves a client without an R version alone', async () => { + const res = await probe(`${SLOT}/PACKAGES.gz`, UA_CURL); + assertEquals(res.location, null); + assertEquals(res.status, 200); + }); + + await t.step('resolves the bare root to slot and minor', async () => { + const res = await probe('/src/contrib/PACKAGES.gz', UA_R45_ALPINE); + assertEquals(res.location, `https://cran.rpkgs.com${SLOT}/4.5/PACKAGES.gz`); + }); + + await t.step('sends an unidentifiable distro to CRAN', async () => { + const res = await probe('/src/contrib/PACKAGES.gz', UA_R45_MUSL); + assertEquals(res.location, 'https://cran.r-project.org/src/contrib/PACKAGES.gz'); + }); + + await t.step('keeps the macOS rewrite', async () => { + const res = await probe('/src/contrib/foo_1.0.tar.gz', UA_R45_DARWIN); + assertEquals(res.location, 'https://cran.rpkgs.com/bin/macosx/big-sur-arm64/contrib/4.5/foo_1.0.tar.gz'); + }); + + await t.step('keeps the macOS binary passthrough to CRAN', async () => { + const path = '/bin/macosx/big-sur-arm64/contrib/4.5/foo_1.0.tar.gz'; + const res = await probe(path, UA_R45_DARWIN); + assertEquals(res.location, `https://cran.r-project.org${path}`); + }); + + await t.step('collapses duplicate slashes before matching', async () => { + const res = await probe(`/amd64/alpine324//latest/src/contrib//PACKAGES.gz`, UA_R45_MUSL); + assertEquals(res.location, `https://cran.rpkgs.com${SLOT}/4.5/PACKAGES.gz`); + }); + } finally { + await stopServer(server); + } +}); diff --git a/edge/rpkgs-router.ts b/edge/rpkgs-router.ts new file mode 100644 index 0000000..9cd410b --- /dev/null +++ b/edge/rpkgs-router.ts @@ -0,0 +1,235 @@ +/** + * Edge middleware for cran.rpkgs.com. + * + * Two jobs: + * + * 1. Resolve the bare `https://cran.rpkgs.com` form to a concrete + * `/` slot from the User-Agent, or send the client to CRAN when + * the distro cannot be identified. + * 2. Route `PACKAGES*` requests to the per-R-minor slot + * (`…/latest/src/contrib//`), so a stock `install.packages()` sees the + * packages that only exist there. + * + * Only index files are routed. Tarballs are deliberately left alone: R keeps + * the contrib URL it asked for, not the one it was redirected to, so every + * tarball URL is resolved against the flat directory and the union index steers + * the per-minor ones with a `Path: ` field. Rewriting a tarball request + * here would send flat-slot packages into a directory that does not hold them. + * + * Routing is gated on UNION_SLOTS. The raw per-minor index holds only the + * ABI-sensitive subset of a slot; it is safe to route to it only once bincraft + * has republished it as a union of the per-minor and flat slots. + * + * Deployed by OpenTofu from this file (`bunnynet_compute_script.rpkgs_router`). + * Test with `just edge-test`. + */ +import * as BunnySDK from 'https://esm.sh/@bunny.net/edgescript-sdk@0.12'; + +const PUBLIC_CDN_ORIGIN = 'https://cran.rpkgs.com'; +const CRAN_ORIGIN = 'https://cran.r-project.org'; + +/** Slots ("/", comma separated) whose per-minor index is a union. */ +const UNION_SLOTS = new Set( + (Deno.env.get('UNION_SLOTS') ?? '') + .split(',') + .map((slot) => slot.trim()) + .filter((slot) => slot.length > 0), +); + +/** `///latest/src/contrib[/]` */ +const SLOT_PATH_REGEX = /^\/(amd64|arm64)\/([a-z0-9._-]+)\/latest\/src\/contrib\/?(.*)$/; + +/** A path that already sits in a per-minor slot, e.g. `4.5/PACKAGES.gz`. */ +const MINOR_DIR_REGEX = /^\d+\.\d+\//; + +/** The only files this script routes. */ +const INDEX_FILE_REGEX = /^PACKAGES(\.gz|\.rds)?$/; + +const SRC_CONTRIB_REGEX = /^\/src\/contrib\/(.+)$/; + +const MACOS_BIN_REGEX = + /^\/bin\/macosx\/(big-sur-arm64|big-sur-x86_64|monterey-arm64|monterey-x86_64)\/contrib\/([0-9.]+)\/(.+)$/; + +const RHEL_REGEX = /(almalinux|rocky)[^\d]*(\d+)/i; + +const UBUNTU_REGEX = /Ubuntu ([\d.]+)/i; +const UBUNTU_CODENAMES: Record = { + '24.04': 'noble', + '22.04': 'jammy', +}; + +const ALPINE_REGEX = /(?:Alpine Linux(?:\s+VERSION_ID=)?|alpine-)\s*(\d+)\.(\d+)/i; + +/** + * R's own User-Agent is `R (4.5.3 x86_64-pc-linux-musl …)`; the Posit-style one + * some sites configure is `R/4.5.3 R (…)`. Both carry the minor, which is why + * per-minor routing works without the distro being identifiable. + */ +const R_MINOR_REGEXES = [/\bR\/(\d+)\.(\d+)/, /\bR \((\d+)\.(\d+)/]; + +function normalizePathname(pathname: string): string { + return pathname.replace(/\/{2,}/g, '/'); +} + +function redirectTo(location: string, status = 302): Response { + return new Response(null, { + status, + headers: { + Location: location, + // The target depends on the User-Agent, so the redirect itself must + // never be cached; only its target is a cacheable, UA-independent URL. + 'Cache-Control': 'no-store', + 'X-Via': 'MyMiddleware', + 'X-Rewritten-By': 'rpkgs-edge-middleware', + }, + }); +} + +function extractRMinor(userAgent: string): string | null { + for (const regex of R_MINOR_REGEXES) { + const match = userAgent.match(regex); + if (match) { + return `${match[1]}.${match[2]}`; + } + } + return null; +} + +function mapArch(arch: string): string { + if (arch === 'aarch64') return 'arm64'; + if (arch === 'x86_64') return 'amd64'; + return arch; +} + +function extractArch(userAgent: string): string { + const match = userAgent.match(/(x86_64|aarch64|arm64|i386|i686)/); + return match ? mapArch(match[1]) : ''; +} + +/** + * Identify the `/` slot from the User-Agent, or null. + * + * A stock R User-Agent carries only `linux-gnu` / `linux-musl`, which are not + * slot names: returning them produced redirects into slots that do not exist + * (`/amd64/linux-musl/latest/…`, a guaranteed 404). An unidentifiable distro + * is reported as such so the caller can fall back to CRAN. + */ +function parseSlot(userAgent: string): string | null { + const arch = extractArch(userAgent); + if (!arch) { + return null; + } + + const rhel = userAgent.match(RHEL_REGEX); + if (rhel) { + return `${arch}/rhel${rhel[2]}`; + } + + const ubuntu = userAgent.match(UBUNTU_REGEX); + if (ubuntu) { + const codename = UBUNTU_CODENAMES[ubuntu[1]]; + if (codename) { + return `${arch}/${codename}`; + } + } + + const alpine = userAgent.match(ALPINE_REGEX); + if (alpine) { + return `${arch}/alpine${alpine[1]}${alpine[2]}`; + } + + return null; +} + +function parseMacUserAgent(userAgent: string): { os: string; arch: string; rver: string } | null { + const rverMatch = userAgent.match(/R \((\d+)\.(\d+)/); + const archMatch = userAgent.match(/(aarch64|arm64|x86_64)/); + const osMatch = userAgent.match(/darwin(\d+)/); + + if (!rverMatch || !archMatch || !osMatch) { + return null; + } + + const arch = archMatch[1] === 'aarch64' ? 'arm64' : archMatch[1]; + const darwinVer = parseInt(osMatch[1], 10); + const os = darwinVer >= 21 && darwinVer < 22 ? `monterey-${arch}` : `big-sur-${arch}`; + + return { os, arch, rver: `${rverMatch[1]}.${rverMatch[2]}` }; +} + +/** + * The contrib path a request should be served from, relative to the slot. + * + * Returns the per-minor path for an index file when the slot is known to carry + * a union index and the client's R minor is known; otherwise the flat path, + * which is what every client sees today. + */ +function contribPath(slot: string, rest: string, userAgent: string): string { + const flat = rest ? `/${slot}/latest/src/contrib/${rest}` : `/${slot}/latest/src/contrib`; + + if (!INDEX_FILE_REGEX.test(rest) || !UNION_SLOTS.has(slot)) { + return flat; + } + + const rMinor = extractRMinor(userAgent); + return rMinor ? `/${slot}/latest/src/contrib/${rMinor}/${rest}` : flat; +} + +BunnySDK.net.http + .servePullZone({ url: 'https://cran.rpkgs.com/' }) + .onOriginRequest((ctx) => { + const url = new URL(ctx.request.url); + const path = normalizePathname(url.pathname); + const userAgent = ctx.request.headers.get('User-Agent') || ''; + + // macOS clients are served from CRAN's own binary tree. + const srcContrib = path.match(SRC_CONTRIB_REGEX); + if (srcContrib && /darwin/.test(userAgent)) { + const mac = parseMacUserAgent(userAgent); + if (mac) { + return Promise.resolve( + redirectTo(`${PUBLIC_CDN_ORIGIN}/bin/macosx/${mac.os}/contrib/${mac.rver}/${srcContrib[1]}`), + ); + } + } + + if (MACOS_BIN_REGEX.test(path)) { + return Promise.resolve(redirectTo(`${CRAN_ORIGIN}${path}`)); + } + + // Already-qualified slot URLs: what the runtime images have baked in. + const slotPath = path.match(SLOT_PATH_REGEX); + if (slotPath) { + const slot = `${slotPath[1]}/${slotPath[2]}`; + const rest = slotPath[3]; + + // Never rewrite a request that is already in a per-minor slot, or the + // redirect would chase its own tail. + if (MINOR_DIR_REGEX.test(rest)) { + return Promise.resolve(ctx.request); + } + + const target = contribPath(slot, rest, userAgent); + if (target === path) { + return Promise.resolve(ctx.request); + } + return Promise.resolve(redirectTo(`${PUBLIC_CDN_ORIGIN}${target}`)); + } + + // The bare `https://cran.rpkgs.com` form, resolved from the User-Agent. + if (path === '/' || path === '/src/contrib' || path.startsWith('/src/contrib/')) { + const slot = parseSlot(userAgent); + if (!slot) { + return Promise.resolve(redirectTo(`${CRAN_ORIGIN}${path}`)); + } + + const rest = srcContrib ? srcContrib[1] : ''; + return Promise.resolve(redirectTo(`${PUBLIC_CDN_ORIGIN}${contribPath(slot, rest, userAgent)}`)); + } + + return Promise.resolve(ctx.request); + }) + .onOriginResponse((ctx) => { + ctx.response.headers.append('X-Via', 'MyMiddleware'); + return Promise.resolve(ctx.response); + }); diff --git a/justfile b/justfile index a9a705e..6c75b13 100644 --- a/justfile +++ b/justfile @@ -73,3 +73,17 @@ rebuild os tag arch package *versions: --build-arg CACHEBUST="$(date +%s)" \ -f docker/build-one.Dockerfile \ local + +# run the edge middleware routing matrix (uses a local deno, else the deno image) +edge-test: + #!/usr/bin/env bash + set -euo pipefail + if command -v deno >/dev/null 2>&1; then + deno test -A edge/rpkgs-router.test.ts + else + docker run --rm \ + -v "$PWD:/w" -w /w \ + -v deno-cache:/deno-dir \ + denoland/deno:latest \ + deno test -A edge/rpkgs-router.test.ts + fi diff --git a/plans/2026-08-07-per-minor-edge-routing.md b/plans/2026-08-07-per-minor-edge-routing.md new file mode 100644 index 0000000..3c3e320 --- /dev/null +++ b/plans/2026-08-07-per-minor-edge-routing.md @@ -0,0 +1,166 @@ +# Per-R-minor edge routing implementation plan + +Spec: `specs/2026-08-07-per-minor-edge-routing-design.md` + +**Goal:** let a stock `install.packages()` see the per-minor packages by routing `PACKAGES*` requests to `…/src/contrib//`, where `bincraft` publishes a union index. + +**Architecture:** the union is built in `bincraft`; the edge script only redirects index requests, gated on a `UNION_SLOTS` script variable; the script lives in this repo and is applied by OpenTofu. + +**Tech stack:** Deno / TypeScript (Bunny Edge Scripting, SDK 0.12), OpenTofu with `BunnyWay/bunnynet` 0.17, R (bincraft). + +## Global constraints + +- Redirect only `PACKAGES`, `PACKAGES.gz` and `PACKAGES.rds`; never a tarball, because the union index already carries the correct tarball URL for both classes of package. +- Every redirect carries `Cache-Control: no-store`; redirect targets stay UA-independent. +- `UNION_SLOTS` is empty by default, so deploying the script is a no-op until a slot is backfilled. +- A slot is `/`, e.g. `amd64/alpine324`. +- Verified prerequisites: `PACKAGES*` is served `cdn-cache: BYPASS`, so the script sees every index request; `Deno.env.get()` reads script variables; the SDK local server listens on `127.0.0.1:8080`. + +--- + +## Task 1: Edge script and its test matrix + +**Files:** + +- Create: `edge/rpkgs-router.ts` +- Create: `edge/rpkgs-router.test.ts` +- Modify: `justfile` (add `edge-test`) + +**Produces:** a single-file script deployable as `bunnynet_compute_script.content`, reading `UNION_SLOTS` from the environment. + +- [ ] **Step 1: write the test matrix first** + +`edge/rpkgs-router.test.ts` spawns `deno run -A edge/rpkgs-router.ts` with `UNION_SLOTS=amd64/alpine324`, waits for `127.0.0.1:8080`, and issues requests with `redirect: "manual"`. + +Cases, asserted on the `location` header (or its absence): + +| # | path | User-Agent | expectation | +| --- | ------------------------------------------------------ | --------------------------------------------- | ------------------------------------------------------------ | +| 1 | `/amd64/alpine324/latest/src/contrib/PACKAGES.gz` | `R (4.5.3 x86_64-pc-linux-musl …)` | 302 → `…/src/contrib/4.5/PACKAGES.gz` | +| 2 | same | `R (4.6.0 …)` | 302 → `…/src/contrib/4.6/PACKAGES.gz` | +| 3 | same, but slot `amd64/noble` | `R (4.5.3 …)` | no redirect (slot not in `UNION_SLOTS`) | +| 4 | `…/src/contrib/curl_7.1.0.tar.gz` | `R (4.5.3 …)` | no redirect | +| 5 | `…/src/contrib/4.5/PACKAGES.gz` | `R (4.5.3 …)` | no redirect (loop guard) | +| 6 | `…/src/contrib/PACKAGES.gz` | `curl/8.0` | no redirect (no R minor) | +| 7 | `/src/contrib/PACKAGES.gz` | alpine UA with `Alpine Linux … 3.24` | 302 → `/amd64/alpine324/latest/src/contrib/4.5/PACKAGES.gz` | +| 8 | `/src/contrib/PACKAGES.gz` | `R (4.5.3 x86_64-pc-linux-musl …)`, no distro | 302 → `cran.r-project.org`, **not** a `linux-musl` slot | +| 9 | `/src/contrib/foo_1.0.tar.gz` | `R (4.5.1 aarch64-apple-darwin20 …)` | 302 → `/bin/macosx/big-sur-arm64/contrib/4.5/foo_1.0.tar.gz` | +| 10 | `/bin/macosx/big-sur-arm64/contrib/4.5/foo_1.0.tar.gz` | any | 302 → `cran.r-project.org` | +| 11 | any redirect above | — | `cache-control: no-store` | + +- [ ] **Step 2: run the tests and watch them fail** + +`just edge-test` → every case fails, because `edge/rpkgs-router.ts` does not exist. + +- [ ] **Step 3: write `edge/rpkgs-router.ts`** + +Order of evaluation in `onOriginRequest`: + +1. normalise `//` runs in the path +2. darwin `/src/contrib/*` → `/bin/macosx//contrib//` +3. `/bin/macosx/**` → CRAN +4. `/{arch}/{os}/latest/src/contrib/`: pass through if `rest` already starts with `/`, or is not an index file, or the slot is not in `UNION_SLOTS`, or the UA has no R minor; otherwise redirect into `/` +5. `/`, `/src/contrib`, `/src/contrib/**`: resolve arch+os from the UA, redirect to CRAN when the distro is unidentifiable, otherwise redirect to the qualified path, adding `/` under the same index-file rule +6. anything else: pass through + +The R minor comes from either `R/4.5.3` or `R (4.5.3 …)`, so a stock UA is enough. The `linux-gnu` / `linux-musl` fallback in `parseUserAgent` is deleted: those are not slot names. + +- [ ] **Step 4: run the tests until they pass** + +`just edge-test` + +- [ ] **Step 5: commit** + +```bash +git add edge/rpkgs-router.ts edge/rpkgs-router.test.ts justfile +git commit -m "feat(edge): route PACKAGES requests to the per-R-minor slot" +``` + +--- + +## Task 2: Manage the script from OpenTofu + +**Files:** + +- Modify: `cdn.tf` + +**Consumes:** `edge/rpkgs-router.ts` from Task 1. + +- [ ] **Step 1: add the resources** + +```terraform +resource "bunnynet_compute_script" "rpkgs_router" { + type = "middleware" + name = "rpkgs-router" + content = file("${path.module}/edge/rpkgs-router.ts") +} + +resource "bunnynet_compute_script_variable" "rpkgs_router_union_slots" { + script = bunnynet_compute_script.rpkgs_router.id + name = "UNION_SLOTS" + default_value = "" + required = false +} +``` + +and replace `middleware_script = 29277` with `middleware_script = bunnynet_compute_script.rpkgs_router.id`. + +- [ ] **Step 2: validate** + +`tofu init -backend=false && tofu validate` + +- [ ] **Step 3: import the existing script (needs `BUNNYNET_API_KEY`)** + +```bash +tofu import bunnynet_compute_script.rpkgs_router 29277 +tofu plan +``` + +The plan must show an in-place `content` update and **no** replacement of the pull zone. A replacement means the import did not take. + +- [ ] **Step 4: commit** + +```bash +git add cdn.tf +git commit -m "feat(cdn): manage the edge middleware script from this repo" +``` + +--- + +## Task 3: Union index writer in bincraft + +**Files (repo `codefloe.com/rpkgs/bincraft`):** + +- Modify: `R/package_index.R` +- Test: `tests/testthat/test-package_index.R` + +**Produces:** `write_union_index(flat_records, minor_records)` returning the merged records, called from `upload_package_index()` when `r_minor` is set. + +- [ ] **Step 1: write the failing tests** + +- a package present in both slots keeps the per-minor record, with `Path = "4.5"` +- a package only in the flat slot survives with no `Path` +- a package only in the per-minor slot survives with `Path = "4.5"` +- a union smaller than the flat input raises an error rather than returning + +- [ ] **Step 2: run them and watch them fail** + +`Rscript -e 'testthat::test_file("tests/testthat/test-package_index.R")'` + +- [ ] **Step 3: implement `write_union_index()` and call it from `upload_package_index()`** + +After `update_PACKAGES()` has written the per-minor index, read the flat slot's `PACKAGES.rds`, set `Path = ` on the per-minor records, drop the flat records for packages the per-minor slot already has, and rewrite `PACKAGES`, `PACKAGES.gz` and `PACKAGES.rds` in the per-minor slot. + +- [ ] **Step 4: run the tests until they pass** + +- [ ] **Step 5: commit and open the PR against bincraft** + +--- + +## Task 4: Roll out slot by slot + +- [ ] Re-index one slot (`amd64/alpine324`, R 4.5) and confirm the union index lists both `curl` (per-minor, `Path: 4.5`) and `jsonlite` (flat, no `Path`). +- [ ] Set `UNION_SLOTS = "amd64/alpine324"` and confirm in `reg.devxy.io/r/r-alpine:4.5-3.24` that `available.packages()` returns the union count and `"curl" %in% rownames(...)`. +- [ ] Add `arm64/alpine324`, then the remaining slots. + +`install.packages("curl")` will still fail to build on `alpine324` until that slot's source tarballs are replaced with real binaries. That is tracked separately. diff --git a/specs/2026-08-07-per-minor-edge-routing-design.md b/specs/2026-08-07-per-minor-edge-routing-design.md new file mode 100644 index 0000000..b55812c --- /dev/null +++ b/specs/2026-08-07-per-minor-edge-routing-design.md @@ -0,0 +1,174 @@ +# Design: Routing clients to per-R-minor binary slots + +Date: 2026-08-07 +Status: Approved (pending spec review) + +## Problem + +`bincraft` routes ABI-"risky" packages to a per-minor slot `…/latest/src/contrib//` and indexes every directory independently (`upload_package_index()` calls `cranlike::update_PACKAGES()` on one prefix at a time). +Nothing unions those indices, and `contrib.url()` only ever yields `/src/contrib`, so no value of `options(repos)` can address a per-minor slot. +Only `uvr` resolves per-minor URLs, which means the per-minor slots are invisible to `install.packages()` by construction. + +Measured on 2026-08-07: + +| slot | flat `src/contrib` | `src/contrib/4.5` | unique packages only in the per-minor slot | +| ----------------- | ------------------ | ----------------- | ------------------------------------------ | +| `amd64/alpine324` | 21 640 | 3 310 | 2 886 | +| `amd64/noble` | 24 495 | 398 | 23 | + +This is what issue #63 records as "missing binaries" on `alpine324`. +The packages are not missing; they are in a directory base R cannot reach. +The user-visible symptom in `reg.devxy.io/r/r-alpine:4.5-3.24` is: + +``` +> install.packages("curl") +Warning message: +package 'curl' is not available for this version of R +``` + +A second, unrelated defect exists on the same slot and is **out of scope here**: many `alpine324` tarballs are byte-identical CRAN _source_ tarballs that the index nevertheless stamps `Built: R 4.5.3; …-linux-musl`. +Routing exposes `curl`; only a rebuild of that slot makes it install. + +## Goal + +Let a stock `install.packages()` see one complete package list for its own R minor, without duplicating tarballs and without an R-version-varying cache key anywhere in the CDN. + +## Key constraint that drives the design + +R resolves a package's download URL from the index, not from the request path, and it keeps the `contriburl` it _asked for_ rather than the one it was redirected to. +Measured with `options(repos = …/latest)` against a middleware that redirects the index into `4.5/`: + +``` +curl available: TRUE +curl repo: …/latest/src/contrib # the flat URL, not the 4.5 one it was served from +``` + +So the union index is always addressed relative to the **flat** directory, whatever path it was fetched from. +`available.packages()` honours a `Path:` field and folds it into the `Repository` column, which gives the whole routing for free: + +- a per-minor record carries `Path: `, so its tarball is fetched from `…/src/contrib//` +- a flat record carries no `Path`, so its tarball is fetched from `…/src/contrib/` + +Verified end to end against the live CDN with a locally built union index for `amd64/alpine324` (31 507 records): + +``` +curl: 7.1.0 -> …/latest/src/contrib/4.5 -> curl_7.1.0.tar.gz 717 725 B +jsonlite: 2.0.0 -> …/latest/src/contrib -> jsonlite_2.0.0.tar.gz 1 055 849 B +``` + +The corollary is that the edge script must **not** rewrite tarball requests: every tarball URL is already correct when it leaves the client, and redirecting one into `/` would break exactly the flat packages the union is meant to preserve. + +The complementary trick does not work: R's `gzcon()` reads only the first member of a concatenated gzip stream (10 291 of an expected 31 931 records), so an edge-side merge would have to fully decompress and recompress both indices and additionally 404 `PACKAGES.rds` to stop R preferring it. +That is why the union is produced in `bincraft`, not at the edge. + +## Approaches considered + +| Approach | Where the union lives | Verdict | +| ----------------------------------------------------------- | ------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------- | +| **A. Union index written by `bincraft` (chosen)** | per-minor `PACKAGES*`, per-minor entries carry `Path: ` | Edge does one redirect; `PACKAGES.rds` stays correct; no duplication | +| B. Merge at the edge | middleware fetches both indices, recompresses | ~2 MB decompress/recompress per cache fill, cache key must include the R minor, breaks R's `.rds` fast path | +| C. Move the minor up the path (`latest//src/contrib/`) | addressable by `options(repos)` directly | No edge logic at all, but a full layout migration and breaks the published URL contract | + +Chosen: **A**. + +## Architecture + +### bincraft: union index (separate PR) + +After writing a per-minor index, republish it as a union of that slot and the flat slot: + +1. Read the flat slot's `PACKAGES.rds` and the per-minor slot's own records. +2. Set `Path: ` on every per-minor record, so its tarball resolves into the per-minor directory. +3. Drop every flat record whose package is already present in the per-minor slot, so the per-minor build always wins, and leave the survivors without a `Path`. +4. Write the merged `PACKAGES`, `PACKAGES.gz` and `PACKAGES.rds` into `…/src/contrib//`. + +Guard: refuse to publish a union with fewer records than the flat index it was built from. +A truncated union is worse than no union, because it silently removes packages from every client on that minor. + +### Edge script (this repo) + +The script routes `PACKAGES`, `PACKAGES.gz` and `PACKAGES.rds` requests, and nothing else. + +``` +normalize path +parseClient(UA) -> { rMinor, arch, os } # rMinor from "R (4.5.3 …)" or "R/4.5.3" +darwin branches # unchanged +if path is /{arch}/{os}/latest/src/contrib/PACKAGES* + already under // ? pass through # loop guard + rMinor known && slot in UNION_SLOTS ? 302 -> …/src/contrib//PACKAGES* + else pass through # flat slot, today's behaviour +if path is /src/contrib/… # bare root + resolve arch + os; unknown -> 302 to CRAN + then apply the same PACKAGES* rule +else pass through +``` + +Redirects carry `Cache-Control: no-store`. +Every cacheable URL is therefore UA-independent, and no cache key has to vary by R version. + +### Repaired bare-root detection + +The bare `https://cran.rpkgs.com` form is currently broken for every Linux client that uses a stock R user agent. +`ALPINE_REGEX`, `UBUNTU_REGEX` and `RHEL_REGEX` only match a Posit-style user agent the user has to set by hand; stock R never carries the distro, so the script falls through to `extractOs()` and redirects to a slot that does not exist: + +``` +UA: R (4.5.3 x86_64-pc-linux-musl …) -> 302 /amd64/linux-musl/latest/… (404) +UA: R (4.5.3 x86_64-pc-linux-gnu …) -> 302 /amd64/linux-gnu/latest/… (404) +``` + +The fallback to a phantom `linux-musl` / `linux-gnu` slot is removed. +An unidentifiable distro redirects to CRAN, which is the existing behaviour for an unparseable user agent. +The R _minor_ is always present in a stock user agent, so per-minor routing itself does not depend on distro detection. + +### Rollout gate + +`UNION_SLOTS` is a `bunnynet_compute_script_variable` listing the slots whose per-minor index is already a union. +It is empty by default, so deploying the script changes nothing until `bincraft` has backfilled a slot, and a rollback is a variable edit rather than a code deploy. +All slots currently carry `4.4`, `4.5` and `4.6`; a client on any other minor falls through to the flat slot. + +### Deployment from this repo + +The script is a file in the repo, applied by the existing OpenTofu configuration: + +``` +edge/rpkgs-router.ts # the script +edge/rpkgs-router.test.ts # UA x path -> expected Location matrix +cdn.tf # bunnynet_compute_script + _variable +``` + +Provider `BunnyWay/bunnynet` v0.17.0 (already pinned) ships `bunnynet_compute_script` with `content` loadable via `file()`, plus `bunnynet_compute_script_variable`. +`middleware_script = bunnynet_compute_script.rpkgs_router.id` replaces the hard-coded `29277`, after a one-time `tofu import` of the existing script. + +## Error handling + +- Unknown R minor, or a slot not listed in `UNION_SLOTS`: pass through to the flat slot. + The client sees exactly today's behaviour. +- Unparseable distro on the bare-root form: redirect to CRAN. +- A request already under `…/src/contrib//`: pass through, so a redirect can never loop. +- A per-minor slot that does not exist for a listed minor: the client gets the origin's 404. + `UNION_SLOTS` is the operator's assertion that the slot is ready, so this is a configuration error, not a runtime condition to paper over. + +## Testing + +Local, before any apply: `deno run -A edge/rpkgs-router.ts` serves the middleware against the real origin, so `edge/rpkgs-router.test.ts` drives the whole matrix against that local server. + +- User agent matrix: R 4.4 / 4.5 / 4.6 on musl and gnu, both arches, Posit-style and stock forms, plus a darwin UA and a non-R UA. +- Path matrix: `PACKAGES`, `PACKAGES.gz`, `PACKAGES.rds`, a tarball, a path already under `4.5/`, and `/src/contrib/…` on the bare root. +- Assertion is the `Location` header (or its absence), not the body. + +After apply, a smoke test against `cran.rpkgs.com`: + +- `available.packages()` inside `reg.devxy.io/r/r-alpine:4.5-3.24` returns the union count, and `"curl" %in% rownames(...)` is `TRUE`. +- A flat-slot package still downloads from `…/src/contrib/`, and a per-minor package downloads from `…/src/contrib//`. + +## Out of scope + +- `Meta/archive.rds` stays flat-only, so `remotes::install_version()` does not see per-minor archives. +- The `alpine324` source-tarball defect: that slot serves CRAN sources stamped as binaries, and needs a rebuild independent of this work. +- Any change to how `uvr` resolves per-minor URLs; it already addresses the slots directly. + +## Split of work + +1. `bincraft`: union index writer plus its guard, and a re-index of one slot to validate. +2. This repo: `edge/rpkgs-router.ts`, its test matrix, and the `cdn.tf` resources with `UNION_SLOTS` empty. +3. Enable `UNION_SLOTS` slot by slot as `bincraft` backfills them. From 6bc8213a2f7e229e1d953e170c987023a04dfcd3 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Sat, 8 Aug 2026 00:32:07 +0000 Subject: [PATCH 31/53] chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.10.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 80650cc..2334bd5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -36,7 +36,7 @@ repos: hooks: - id: air-format - repo: https://github.com/editorconfig-checker/editorconfig-checker - rev: v3.8.0 + rev: v3.10.0 hooks: - id: editorconfig-checker exclude: ^local/patches/.*\.patch$ From 4cb8b692ab4d38b10e785a0f947e83dd3c098bd7 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Sun, 9 Aug 2026 00:32:28 +0000 Subject: [PATCH 32/53] chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.11.1 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2334bd5..82461cb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -36,7 +36,7 @@ repos: hooks: - id: air-format - repo: https://github.com/editorconfig-checker/editorconfig-checker - rev: v3.10.0 + rev: v3.11.1 hooks: - id: editorconfig-checker exclude: ^local/patches/.*\.patch$ From 1e843523a0312f3943fd11aca8f64e0117f7eca9 Mon Sep 17 00:00:00 2001 From: pat-s Date: Sun, 9 Aug 2026 10:02:05 +0000 Subject: [PATCH 33/53] fix(ci): gate the three ungated pipelines on their own variable (#155) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem A manual `crow pipeline create` instantiates **every** pipeline in `.crow/`, and each one decides for itself whether to run. Three had nothing to decide with — their only manual condition was a bare `event: manual`: - `auto-apply-patches` — pushes to `auto/registry-patch-proposals` and opens/updates a PR - `weekly-patch-proposals` — posts and edits two Forgejo issues - `trial-build-registry` — starts a build per matrix row, on both arches So they fired on *any* manual trigger in this repo, whatever it was for. That is how they came to run alongside a manual `process-updates` run for `alpine-324-arm64` (#10723), which is also why that pipeline is marked failure. `repair-built-stamp.yaml` already documents the rule this breaks: > The gate variable is `repair_built_stamp`, not `target_arch` … Every pipeline here gates on a variable named after itself for exactly that reason. ## What this changes Each of the three gets a gate variable named after the pipeline, `evaluate`d on the manual event, defaulting to off: ```yaml variables: auto_apply_patches: description: 'Run the auto-patch proposer. Also gates this pipeline.' options: ['true', 'false'] default: 'false' when: - event: manual evaluate: 'auto_apply_patches == "true"' - event: cron cron: auto-apply-patches ``` Cron triggers are untouched, so the scheduled runs behave exactly as before. The run-manually comments in all three headers were also stale: they documented `--var task=` with `woodpecker-cli`, and no pipeline evaluates a `task` variable. They now show the real invocation. ## Note on the sibling pipelines The already-gated pipelines use `default: all` (e.g. `weekly_rebuild_missing`). If Crow applies a declared default to a variable that an API-created pipeline never passed, those would match on an unrelated manual run too — `weekly-rebuild-missing` would be an expensive way to find out. I could not settle that from #10723 because its step logs have since expired, so I left them alone rather than guess. The three fixed here default to `'false'`, which is safe under either semantics. ## Verification `crow lint .crow/` passes. Auditing every pipeline that accepts a manual event now reports a gate on all ten: ``` build-all-versions-install-deps.yaml: gated auto-apply-patches.yaml: gated weekly-patch-proposals.yaml: gated weekly-audit-missing.yaml: gated repair-built-stamp.yaml: gated archive-missed-packages.yaml: gated weekly-rebuild-missing.yaml: gated trial-build-registry.yaml: gated build-all-versions.yaml: gated process-updates.yaml: gated ``` Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/155 --- .crow/auto-apply-patches.yaml | 15 ++++++++++++++- .crow/trial-build-registry.yaml | 16 ++++++++++++++-- .crow/weekly-patch-proposals.yaml | 18 ++++++++++++++++++ 3 files changed, 46 insertions(+), 3 deletions(-) diff --git a/.crow/auto-apply-patches.yaml b/.crow/auto-apply-patches.yaml index 0076353..7c33c5b 100644 --- a/.crow/auto-apply-patches.yaml +++ b/.crow/auto-apply-patches.yaml @@ -9,14 +9,27 @@ # FORGEJO_TOKEN is used for both the branch push and opening the PR (no separate # write-scoped secret needed). Register the `auto-apply-patches` cron in the crow # UI, or run manually: -# woodpecker-cli pipeline create --var task=auto-apply-patches --branch=main 7 +# crow pipeline create --branch main \ +# --var auto_apply_patches=true devxy/build-cran-binaries +# +# The gate variable is `auto_apply_patches`, named after the pipeline: a manual +# run instantiates every pipeline in `.crow/`, so one without its own gate runs +# on *any* manual trigger in this repo. This one pushes a branch and opens a PR, +# so it must stay off unless it is what was asked for. variables: + auto_apply_patches: + description: 'Run the auto-patch proposer. Also gates this pipeline.' + options: + - 'true' + - 'false' + default: 'false' patch_limit: description: 'Max candidates to propose per run (top by failure volume).' default: '10' when: - event: manual + evaluate: 'auto_apply_patches == "true"' - event: cron cron: auto-apply-patches diff --git a/.crow/trial-build-registry.yaml b/.crow/trial-build-registry.yaml index 73856a1..2195423 100644 --- a/.crow/trial-build-registry.yaml +++ b/.crow/trial-build-registry.yaml @@ -7,15 +7,27 @@ # # The repo uses no `pull_request` triggers, so this runs manually against the # branch (or on a cron); point it at the auto-patch branch via `patch_branch`: -# woodpecker-cli pipeline create --var task=trial-build-registry \ -# --var patch_branch=auto/registry-patch-proposals --branch=main 7 +# crow pipeline create --branch main --var trial_build_registry=true \ +# --var patch_branch=auto/registry-patch-proposals devxy/build-cran-binaries +# +# The gate variable is `trial_build_registry`, named after the pipeline: a +# manual run instantiates every pipeline in `.crow/`, so one without its own +# gate runs on *any* manual trigger in this repo. This one starts a build per +# matrix row on both arches, which is far too expensive to fire by accident. variables: + trial_build_registry: + description: 'Trial-build the branch new registry entries. Also gates this pipeline.' + options: + - 'true' + - 'false' + default: 'false' patch_branch: description: 'Branch whose new registry entries to trial-build.' default: auto/registry-patch-proposals when: - event: manual + evaluate: 'trial_build_registry == "true"' - event: cron cron: trial-build-registry diff --git a/.crow/weekly-patch-proposals.yaml b/.crow/weekly-patch-proposals.yaml index 027d41c..712e87d 100644 --- a/.crow/weekly-patch-proposals.yaml +++ b/.crow/weekly-patch-proposals.yaml @@ -8,8 +8,26 @@ # Global across platforms (the classifier groups over all of single_builds), so # a single job -- no matrix. Clones read-only; the only writes are the two # Forgejo issues via FORGEJO_TOKEN. +# +# Run manually with: +# crow pipeline create --branch main \ +# --var weekly_patch_proposals=true devxy/build-cran-binaries +# +# The gate variable is `weekly_patch_proposals`, named after the pipeline: a +# manual run instantiates every pipeline in `.crow/`, so one without its own +# gate runs on *any* manual trigger in this repo. This one posts and edits +# Forgejo issues, so an unrelated manual run must not fire it. +variables: + weekly_patch_proposals: + description: 'Run the weekly failure triage. Also gates this pipeline.' + options: + - 'true' + - 'false' + default: 'false' + when: - event: manual + evaluate: 'weekly_patch_proposals == "true"' - event: cron cron: weekly-patch-proposals From 0c86b2692d07e18decc55b4738a3cfa2562ab892 Mon Sep 17 00:00:00 2001 From: pat-s Date: Sun, 9 Aug 2026 10:08:40 +0000 Subject: [PATCH 34/53] fix(cdn): declare the User-Agent cache vary instead of dropping it (#156) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem `tofu plan` after importing the middleware script shows: ``` ~ resource "bunnynet_pullzone" "cran_rpkgs_com" { ~ cache_vary_headers = [ - "User-Agent", ] ``` The zone carries `cache_vary_headers = ["User-Agent"]`, set before this configuration existed. `cdn.tf` never declared it, so the first apply of the managed middleware would remove it — as a side effect of an unrelated change, with no decision recorded anywhere. ## What this changes Declares the attribute with its current value, so the pull zone is a no-op in that plan. ## Why keep it rather than let it go On paper the router makes it redundant. The only UA-dependent responses it produces are redirects, and those carry `Cache-Control: no-store`; their targets are concrete per-slot, per-minor URLs whose content depends only on the path. Dropping the vary would also be a genuine win, since otherwise every distinct R version string (`R (4.5.3 x86_64-pc-linux-musl …)`) keys its own copy of every tarball. It stays anyway, for now: - it is the second line of defence against the one failure mode that would be quiet and confusing — an R 4.6 client served the 4.5 index - Bunny honouring `no-store` on an edge-script response has been confirmed for today's redirects (`cdn-cache: BYPASS` on `max-age=0`), but not for the new script in production - keeping it is the status quo, so it cannot regress anything Removing it is worth doing on its own, once per-minor routing is confirmed live and the redirects can be observed bypassing cache — not as a side effect of enabling that routing. ## Verification `tofu validate` passes. Re-planning after this merges should leave `bunnynet_pullzone.cran_rpkgs_com` unchanged, reducing the plan to the script `content` update and the new `UNION_SLOTS` variable. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/156 --- cdn.tf | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/cdn.tf b/cdn.tf index fe1b25f..5e8899d 100644 --- a/cdn.tf +++ b/cdn.tf @@ -105,6 +105,21 @@ resource "bunnynet_pullzone" "cran_rpkgs_com" { request_coalescing_enabled = true block_post_requests = true + # Set on the zone since before this configuration existed; declared here so + # `tofu apply` stops silently removing it. + # + # The router makes it redundant on paper: the only UA-dependent responses it + # produces are redirects, and those carry `Cache-Control: no-store`, while + # their targets are concrete per-slot, per-minor URLs whose content depends + # only on the path. Dropping it would also be a real win, because otherwise + # every distinct R version string keys its own copy of every tarball. + # + # It stays for now anyway: it is the second line of defence against the one + # failure that would be quiet and confusing (an R 4.6 client served the 4.5 + # index), and removing it is worth doing on its own once per-minor routing is + # confirmed live, not as a side effect of enabling that routing. + cache_vary_headers = ["User-Agent"] + limit_requests = 5000 limit_connections = 1000 From 070396908819b9365e5cf824e3f387ee875993bf Mon Sep 17 00:00:00 2001 From: pat-s Date: Sun, 9 Aug 2026 10:37:41 +0000 Subject: [PATCH 35/53] fix(audit): count a source fallback as a missing binary (#157) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem The audit's definition of "missing" was `missing_dt <- cran_dt[!s3_dt]`, where `s3_dt` came from listing the bucket. But an object being present does not mean a binary was built: when a build fails, bincraft publishes the CRAN source tarball in its place so the package stays installable, and a listing cannot tell the two apart. So every failed build looked done. On `amd64/alpine324` that is 13 547 of 24 134 comparable objects (56%) — all CRAN sources from the June 2026 bootstrap, none ever reported here, so `weekly-rebuild-missing` never retried any of them. `amd64/noble` sits at 4.6% for comparison. ## What this changes Reads the slot's own `PACKAGES` index instead of listing the bucket, and counts only records carrying a `Built` stamp. bincraft writes that stamp only for what it actually built (rpkgs/bincraft#105), so the index answers the question a listing cannot. Side effects of reading the index rather than the bucket: - the audit reports how many records the index holds and how many are served as source, so the gap is visible in the log - `s3fs` is no longer used, so the audit needs no B2 credentials - an object present but absent from the index is now counted as missing, which is correct: clients only see the index ## Sequencing This is inert until the matching bincraft change ships and a slot is re-indexed. A slot last indexed by an older bincraft carries `Built` on every record, including the fallbacks, so the audit reports exactly what it does today. Verified against the live indices: ``` amd64/alpine324: records=24152 built=24152 source-served=0 amd64/noble: records=24681 built=24681 source-served=0 ``` After a re-index those `source-served` counts become the real ones, and the packages behind them start appearing in issue #63 and getting rebuilt. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/157 --- local/weekly-missing-binaries-audit.R | 78 +++++++++++++++------------ 1 file changed, 43 insertions(+), 35 deletions(-) diff --git a/local/weekly-missing-binaries-audit.R b/local/weekly-missing-binaries-audit.R index 7b0b65d..e7ca776 100644 --- a/local/weekly-missing-binaries-audit.R +++ b/local/weekly-missing-binaries-audit.R @@ -7,7 +7,6 @@ options(error = function() { suppressPackageStartupMessages(library(data.table)) library(DBI, quietly = TRUE) library(RPostgres, quietly = TRUE) -library(s3fs, quietly = TRUE) library(jsonlite, quietly = TRUE) library(httr2, quietly = TRUE) @@ -50,8 +49,8 @@ cat(sprintf( )) # --------------------------------------------------------------------------- -# 1. Query PostgreSQL for known build failures (before s3fs init to avoid -# C++ pointer conflicts between s3fs/curl and RPostgres/libpq) +# 1. Query PostgreSQL for known build failures (before anything that uses curl, +# to avoid C++ pointer conflicts between curl and RPostgres/libpq) # --------------------------------------------------------------------------- cat("Connecting to PostgreSQL...\n") con <- DBI::dbConnect( @@ -97,62 +96,71 @@ cran_dt <- data.table( ) # --------------------------------------------------------------------------- -# 3. S3 tarballs +# 3. Published binaries # --------------------------------------------------------------------------- -cat("Connecting to S3...\n") -s3fs::s3_file_system( - aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), - aws_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), - endpoint = "https://s3.eu-central-003.backblazeb2.com", - region_name = "eu-central-003", - refresh = TRUE -) - -s3_path <- sprintf( - "devxy-rpkgs-binaries/%s/%s/latest/src/contrib", +# Read the slot's own index rather than listing the bucket. An object being +# present does not mean a binary was built: when a build fails, bincraft +# publishes the CRAN source tarball in its place so the package stays +# installable, and a bucket listing cannot tell the two apart. That is how +# amd64/alpine324 came to hold 13,547 CRAN sources that this audit never +# reported. bincraft stamps `Built` only on records it actually built, so the +# index answers the question a listing cannot. +# +# A slot last indexed by a bincraft that predates the source-fallback fix +# stamps `Built` on every record, including the fallbacks, so this reports +# exactly what it used to until that slot is re-indexed. +index_url <- sprintf( + "https://cran.rpkgs.com/%s/%s/latest/src/contrib/PACKAGES.gz", arch, s3_codename ) -cat(sprintf("Listing S3 path: %s\n", s3_path)) +cat(sprintf("Reading package index: %s\n", index_url)) -s3_pkgs <- tryCatch( - s3fs::s3_dir_ls(s3_path, recurse = FALSE), +index <- tryCatch( + { + con <- gzcon(url(index_url, open = "rb")) + on.exit(close(con), add = TRUE) + read.dcf(con, fields = c("Package", "Version", "Built")) + }, error = function(e) { cat(sprintf( - "WARNING: Could not list S3 path %s: %s\n", - s3_path, + "WARNING: Could not read %s: %s\n", + index_url, conditionMessage(e) )) - character(0) + NULL } ) -file_names <- basename(s3_pkgs) -matches <- regexec("^([A-Za-z0-9.]+)_([0-9][^/]*)\\.tar\\.gz$", file_names) -parts <- regmatches(file_names, matches) -parts <- parts[sapply(parts, length) == 3] -if (length(parts) == 0) { - s3_dt <- data.table(Package = character(0), Version = character(0)) +if (is.null(index) || nrow(index) == 0) { + binary_dt <- data.table(Package = character(0), Version = character(0)) } else { - s3_dt <- data.table( - Package = sapply(parts, `[`, 2), - Version = sapply(parts, `[`, 3) + built <- !is.na(index[, "Built"]) + binary_dt <- data.table( + Package = as.character(index[built, "Package"]), + Version = as.character(index[built, "Version"]) ) + cat(sprintf( + "Index holds %d records, %d of them built binaries (%d served as CRAN source)\n", + nrow(index), + sum(built), + sum(!built) + )) } cat(sprintf( - "S3 contains %d tarballs for %s/%s\n", - nrow(s3_dt), + "S3 contains %d binaries for %s/%s\n", + nrow(binary_dt), arch, s3_codename )) # --------------------------------------------------------------------------- -# 4. Find missing packages (CRAN release version not in S3) +# 4. Find missing packages (CRAN release version without a binary in S3) # --------------------------------------------------------------------------- setkey(cran_dt, Package, Version) -setkey(s3_dt, Package, Version) -missing_dt <- cran_dt[!s3_dt] +setkey(binary_dt, Package, Version) +missing_dt <- cran_dt[!binary_dt] cat(sprintf("%d CRAN release packages missing from S3\n", nrow(missing_dt))) # --------------------------------------------------------------------------- From f8e31af75b3ae418b858dca3d6baeda73e651834 Mon Sep 17 00:00:00 2001 From: pat-s Date: Sun, 9 Aug 2026 15:31:14 +0000 Subject: [PATCH 36/53] fix(ci): make every manual gate default to a value that matches nothing (#158) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem A manual `crow pipeline create` instantiates **every** file in `.crow/`, and a declared variable default is applied even when the run never passed that variable. A gate is therefore only a gate if its default matches nothing. #155 fixed the three pipelines that had no manual gate at all. It missed that a *permissive default* leaves a pipeline just as exposed. Demonstrated the expensive way: creating a pipeline with only ``` --var weekly_audit_missing=alpine-324-amd64 ``` also started `build-all-versions` — because its gate `target_arch` defaults to `amd64`, which matches its own amd64 matrix rows — and `process-updates` across every row, because that gate defaults to `all`. The run was killed before any `Upload package indexes` step produced output and both alpine324 indices were verified unchanged, but `build-all-versions` uploads binaries and rewrites indexes, so the next one might not be caught in time. Before: | pipeline | gate | default | fired on an unrelated manual run | | --- | --- | --- | --- | | `build-all-versions` | `target_arch` | `amd64` | amd64 rows — builds and uploads | | `build-all-versions-install-deps` | `target_arch` | `amd64` | amd64 rows | | `weekly-rebuild-missing` | `weekly_rebuild_missing` | `all` | every row | | `weekly-audit-missing` | `weekly_audit_missing` | `all` | every row | | `process-updates` | `process_cran_updates` | `all` | every row | | `repair-built-stamp` | `repair_built_stamp` | `arm64` | arm64 rows | `archive-missed-packages` was the one that behaved, because its gate variable is never declared and so matches nothing. That is the property this restores everywhere. ## What this changes Each of the six gets a `none` option on its gate variable and defaults to it, so a manual run has to name its target explicitly. The reason is recorded next to the default, where someone would go to change it. `none` is used rather than dropping the default so the expression always has a defined value to compare, instead of relying on undefined-variable semantics. Cron triggers are untouched — they match on the `cron:` name, not the variable. ## Verification `crow lint .crow/` reports all ten configs valid. Auditing every pipeline that accepts a manual event: ``` archive-missed-packages.yaml: gate=task default= auto-apply-patches.yaml: gate=auto_apply_patches default='false' build-all-versions-install-deps.yaml gate=target_arch default=none build-all-versions.yaml: gate=target_arch default=none process-updates.yaml: gate=process_cran_updates default=none repair-built-stamp.yaml: gate=repair_built_stamp default=none trial-build-registry.yaml: gate=trial_build_registry default='false' weekly-audit-missing.yaml: gate=weekly_audit_missing default=none weekly-patch-proposals.yaml: gate=weekly_patch_proposals default='false' weekly-rebuild-missing.yaml: gate=weekly_rebuild_missing default=none ``` Every gate now defaults to something that matches no matrix row. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/158 --- .crow/build-all-versions-install-deps.yaml | 8 ++++++-- .crow/build-all-versions.yaml | 8 ++++++-- .crow/process-updates.yaml | 8 ++++++-- .crow/repair-built-stamp.yaml | 8 ++++++-- .crow/weekly-audit-missing.yaml | 8 ++++++-- .crow/weekly-rebuild-missing.yaml | 8 ++++++-- 6 files changed, 36 insertions(+), 12 deletions(-) diff --git a/.crow/build-all-versions-install-deps.yaml b/.crow/build-all-versions-install-deps.yaml index 448cff3..2a6d9c2 100644 --- a/.crow/build-all-versions-install-deps.yaml +++ b/.crow/build-all-versions-install-deps.yaml @@ -3,12 +3,16 @@ # Variables are declared so the manual-run form exposes them (crow #1165); # they are merged with build-all-versions' identical declarations. variables: + # Gates this pipeline. A manual pipeline creation instantiates every file in + # .crow/, and a declared default is applied even when the run never passed + # this variable, so the default must be a value that matches no matrix row. target_arch: - description: 'Architecture to build.' + description: 'Architecture to build, or "none" to run nothing.' options: + - none - amd64 - arm64 - default: amd64 + default: none OS: description: 'Base OS image name.' options: diff --git a/.crow/build-all-versions.yaml b/.crow/build-all-versions.yaml index 9ab888a..fb1229d 100644 --- a/.crow/build-all-versions.yaml +++ b/.crow/build-all-versions.yaml @@ -4,12 +4,16 @@ # image and cache volume. Placement is via the group label (rpkgs-amd64/rpkgs-arm64). # Skip list lives in local/excluded-packages.json (read by local/build-all.R). variables: + # Gates this pipeline. A manual pipeline creation instantiates every file in + # .crow/, and a declared default is applied even when the run never passed + # this variable, so the default must be a value that matches no matrix row. target_arch: - description: 'Architecture to build.' + description: 'Architecture to build, or "none" to run nothing.' options: + - none - amd64 - arm64 - default: amd64 + default: none OS: description: 'Base OS image name.' options: diff --git a/.crow/process-updates.yaml b/.crow/process-updates.yaml index 1e4833c..7600876 100644 --- a/.crow/process-updates.yaml +++ b/.crow/process-updates.yaml @@ -7,9 +7,13 @@ # ("all" = every os/arch). # Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64). variables: + # Gates this pipeline. A manual pipeline creation instantiates every file in + # .crow/, and a declared default is applied even when the run never passed + # this variable, so the default must be a value that matches no matrix row. process_cran_updates: - description: "Manual run target: a specific -, or 'all' for every os/arch." + description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." options: + - none - all - alpine-322-amd64 - alpine-322-arm64 @@ -29,7 +33,7 @@ variables: - ubuntu-2404-arm64 - ubuntu-2604-amd64 - ubuntu-2604-arm64 - default: all + default: none when: - event: cron diff --git a/.crow/repair-built-stamp.yaml b/.crow/repair-built-stamp.yaml index 83821e9..e56e1e9 100644 --- a/.crow/repair-built-stamp.yaml +++ b/.crow/repair-built-stamp.yaml @@ -19,12 +19,16 @@ # --var repair_built_stamp=arm64 --var OS=alpine --var OS_VERSION=3.22 \ # --var R_VERSION=4.5.3 --var dry_run=true devxy/build-cran-binaries variables: + # Gates this pipeline. A manual pipeline creation instantiates every file in + # .crow/, and a declared default is applied even when the run never passed + # this variable, so the default must be a value that matches no matrix row. repair_built_stamp: - description: 'Architecture of the slot to repair. Also gates this pipeline.' + description: 'Architecture of the slot to repair, or "none" to run nothing.' options: + - none - amd64 - arm64 - default: arm64 + default: none OS: description: 'Base OS image name.' options: diff --git a/.crow/weekly-audit-missing.yaml b/.crow/weekly-audit-missing.yaml index 4efe409..3a9d98f 100644 --- a/.crow/weekly-audit-missing.yaml +++ b/.crow/weekly-audit-missing.yaml @@ -7,9 +7,13 @@ # ("all" = every os/arch). # Arch placement is via the group label (rpkgs-amd64, rpkgs-arm64). variables: + # Gates this pipeline. A manual pipeline creation instantiates every file in + # .crow/, and a declared default is applied even when the run never passed + # this variable, so the default must be a value that matches no matrix row. weekly_audit_missing: - description: "Manual run target: a specific -, or 'all' for every os/arch." + description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." options: + - none - all - alpine-322-amd64 - alpine-322-arm64 @@ -29,7 +33,7 @@ variables: - ubuntu-2404-arm64 - ubuntu-2604-amd64 - ubuntu-2604-arm64 - default: all + default: none when: - event: cron diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index 03a13f9..0353901 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -8,9 +8,13 @@ # single - to run just one. # Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64). variables: + # Gates this pipeline. A manual pipeline creation instantiates every file in + # .crow/, and a declared default is applied even when the run never passed + # this variable, so the default must be a value that matches no matrix row. weekly_rebuild_missing: - description: "Manual run target: a specific -, or 'all' for every os/arch." + description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." options: + - none - all - alpine-322-amd64 - alpine-322-arm64 @@ -30,7 +34,7 @@ variables: - ubuntu-2404-arm64 - ubuntu-2604-amd64 - ubuntu-2604-arm64 - default: all + default: none when: - event: cron From a126d74cd37422d2c0a9e8dec782173f945585eb Mon Sep 17 00:00:00 2001 From: pat-s Date: Sun, 9 Aug 2026 16:27:51 +0000 Subject: [PATCH 37/53] fix(build): keep source fallbacks out of the S3 package cache (#159) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem This is the gap flagged in rpkgs/bincraft#106. `build_binary_package()` has a fast path that compares against `s3_package_cache` instead of querying S3 per package, and that cache is produced here: ```r s3_pkgs <- s3fs::s3_dir_ls(".../latest/src/contrib", recurse = TRUE) saveRDS(basename(s3_pkgs), "/mnt/cache/packages/s3_cache.rds") ``` A raw bucket listing cannot tell a binary from a package whose build failed and was published as its CRAN source — the two occupy the same key. So every source fallback reads as "already built" and is skipped for good. That is how `alpine324` accumulated ~13.5k of them. The same listing feeds `s3_dt`, which is subtracted from the build list at line 194 (`pkgs <- pkgs_no_error[!s3_dt]`). That one matters more: it excludes the very packages that need building, before `build_binary_package()` is even called. ## What this changes Drops from the listing every object the slot's own index reports as served from source. bincraft leaves the `Built` stamp off exactly those records (rpkgs/bincraft#105), so the index already carries the answer and no credentials, downloads or extra API calls are needed. Both consumers are fixed: the saved cache and `s3_dt`. The cache stays a plain filename vector, so the build container still needs no `s3fs`/reticulate — that was the point of saving it in the first place. Two deliberately conservative edges: - archived objects have no index record, so they are kept. Unknown means binary, never "rebuild it". - if the index cannot be read, the full listing is kept and a warning is printed, so a CDN blip cannot mass-schedule a rebuild. ## Verification The script parses, and the new block run against the live indices: ``` amd64/alpine324: index=24235 source-served=13542 e.g. AATtools_0.0.3.tar.gz, ABCDscores_7.0.0.tar.gz amd64/noble: index=24681 source-served=0 ``` `alpine324` is re-indexed by bincraft 5.1.1, so 13 542 objects drop out and those packages become buildable. `noble` has not been re-indexed yet, so every record still carries `Built`, nothing is dropped, and its behaviour is exactly what it is today — the safe failure mode this relies on. The new log line makes it visible per run: ``` S3 cache: N objects, M served as CRAN source, K usable binaries ``` ## Sequencing Needs rpkgs/bincraft#106 (and a release) before a rebuild actually builds: this fixes the bulk build path's list, #106 fixes the per-package pre-build skip. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/159 --- local/packages-to-build.R | 59 +++++++++++++++++++++++++++++++++++---- 1 file changed, 53 insertions(+), 6 deletions(-) diff --git a/local/packages-to-build.R b/local/packages-to-build.R index 887952d..3b508fb 100644 --- a/local/packages-to-build.R +++ b/local/packages-to-build.R @@ -89,14 +89,61 @@ s3_pkgs <- s3fs::s3_dir_ls( recurse = TRUE ) -# Save the raw S3 file listing for the build step to use as s3_package_cache +file_names <- basename(s3_pkgs) + +# An object occupying a key is not proof a binary was built: a package whose +# build failed has its CRAN source published under exactly that name. Left in +# the cache, `build_binary_package()` reads it as "already built" and skips the +# package forever, which is how alpine324 accumulated ~13.5k source tarballs. +# +# bincraft stamps `Built` only on records it actually built, so the slot's own +# index distinguishes them. A slot last indexed by a bincraft that predates that +# fix stamps `Built` on everything, so the cache is then unchanged from before. +# Archived objects have no index record and are kept: unknown means binary, +# never "rebuild it". +index_url <- sprintf( + "https://cran.rpkgs.com/%s/%s/latest/src/contrib/PACKAGES.gz", + arch, + codename +) +source_served <- tryCatch( + { + con_idx <- gzcon(url(index_url, open = "rb")) + on.exit(close(con_idx), add = TRUE) + idx <- read.dcf(con_idx, fields = c("Package", "Version", "Built")) + sprintf( + "%s_%s.tar.gz", + idx[is.na(idx[, "Built"]), "Package"], + idx[is.na(idx[, "Built"]), "Version"] + ) + }, + error = function(e) { + cat(sprintf( + "WARNING: could not read %s (%s); keeping the full S3 cache\n", + index_url, + conditionMessage(e) + )) + character(0) + } +) + +binary_cache <- setdiff(file_names, source_served) +cat(sprintf( + "S3 cache: %d objects, %d served as CRAN source, %d usable binaries\n", + length(file_names), + length(file_names) - length(binary_cache), + length(binary_cache) +)) + +# Save the S3 file listing for the build step to use as s3_package_cache. # This avoids loading s3fs/reticulate in the build container, saving memory for # the dependency-installer subprocesses -saveRDS(basename(s3_pkgs), "/mnt/cache/packages/s3_cache.rds") - -file_names <- basename(s3_pkgs) -matches <- regexec("^([A-Za-z0-9.]+)_([0-9][^/]*)\\.tar\\.gz$", file_names) -parts <- regmatches(file_names, matches) +saveRDS(binary_cache, "/mnt/cache/packages/s3_cache.rds") +# Built from the filtered listing, not the raw one: `s3_dt` is subtracted from +# the build list below, so a source fallback left in here would exclude the very +# package that needs building. +matches <- regexec("^([A-Za-z0-9.]+)_([0-9][^/]*)\\.tar\\.gz$", binary_cache) +parts <- regmatches(binary_cache, matches) parts <- parts[sapply(parts, length) == 3] s3_dt <- data.table( Package = sapply(parts, `[`, 2), From 6372f0f928f81c76aaca3c3b6f71541a04a976d4 Mon Sep 17 00:00:00 2001 From: pat-s Date: Mon, 10 Aug 2026 06:30:25 +0000 Subject: [PATCH 38/53] fix(ci): refresh the apt index before uvr installs system dependencies (#161) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Unblocks the ubuntu 26.04 builds without waiting for an image rebuild. ## What broke ``` i Installing R package dependencies ! Error in installing dependencies for package huge with tag 2.0.1: uvr sync --install-system-deps --library /mnt/cache/R-pkgs-4.4 failed (exit 1) ! WARN Missing system dependencies for 1 package(s) igraph needs: libglpk-dev > Running: apt-get install -y libglpk-dev E: Unable to locate package libglpk-dev ``` Neither the package name nor the sysreq mapping is wrong. `libglpk-dev` is `5.0-2build1` in `universe`, which `ubuntu:resolute` enables by default. What is missing is the apt index: uvr v0.4.5 runs `apt-get install` with no `apt-get update` before it, and every ubuntu build image ends its apt layers with `rm -rf /var/lib/apt/lists/*`, so the shipped image has no index at all. Not specific to 26.04 — jammy and noble fail identically for any sysreq the image's preinstall line doesn't already cover. 26.04 surfaced it first, through `igraph` and everything depending on it (`huge` was the first to fail). ## Fix `apt-get update` before the sync in `local/uvr-install.sh`. That one site covers every pipeline: `build-all-versions`, `build-all-versions-install-deps`, `weekly-rebuild-missing`, `weekly-audit-missing`, `trial-build-registry`, `auto-apply-patches` and `weekly-patch-proposals` all reach it, either directly or through `install-bincraft.R`. The index it populates persists for the rest of the step, so the bincraft-driven `uvr sync` calls that follow are covered too. Guarded on `apt-get` and non-fatal: `apk add` fetches its index implicitly and dnf refreshes expired metadata on its own, so alpine and redhat are unaffected and skip it. ## Why here as well as in the image The real fix is upstream `e491b2e`, which refreshes the index before the auto-install. It landed one day after v0.4.5 was tagged, so no release carries it ([nbafrank/uvr#250](https://github.com/nbafrank/uvr/issues/250)); [build-env-images#23](https://codefloe.com/rpkgs/build-env-images/pulls/23) pins the ubuntu image to a commit that has it. That only reaches CI after an image rebuild is triggered. This change takes effect on the next pipeline run. It also stays useful afterwards: a baked index goes stale within weeks, and a stale index turns the same install into a 404 on the `.deb`. ## Verified In `ubuntu:resolute`, with the image state reproduced exactly (R installed, then `rm -rf /var/lib/apt/lists/*` to empty the index again): | Check | Result | |---|---| | `apt-get install -y libglpk-dev`, empty index | `E: Unable to locate package libglpk-dev` — the reported failure, reproduced | | Same container after `apt-get update` | `Candidate: 5.0-2build1`, `Components: main universe restricted multiverse` | | `igraph` + `UVR_INSTALL_SYSREQS=1 uvr sync`, empty index, uvr with the refresh | `Setting up libglpk-dev:amd64 (5.0-2build1)`, `System dependencies installed.`, `Installed 11 package(s)` | | `sh -n` and `shellcheck local/uvr-install.sh` | pass | ## Reverting Delete the guarded block. It is marked TEMPORARY with the upstream reference, and can go once the images ship a uvr above v0.4.5. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/161 --- local/uvr-install.sh | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/local/uvr-install.sh b/local/uvr-install.sh index 14b7f78..c5d37d3 100755 --- a/local/uvr-install.sh +++ b/local/uvr-install.sh @@ -87,4 +87,23 @@ cd "$project_dir" # --no-install: resolve and lock only. The install happens in the sync below, # which is the only command that honours --library. "$uvr_bin" add --no-install "$@" + +# TEMPORARY (drop once the images ship a uvr above v0.4.5): the sync below runs +# `apt-get install` for every resolved system dependency without refreshing the +# index first, and the ubuntu build images end their apt layers with +# `rm -rf /var/lib/apt/lists/*`. With no index apt cannot resolve a package that +# exists and is enabled, so `igraph needs: libglpk-dev` fails the whole build +# with `E: Unable to locate package libglpk-dev` on ubuntu 26.04. +# +# Fixed upstream in `e491b2e`, tagged one day after v0.4.5 (nbafrank/uvr#250), +# and the images pick it up via build-env-images#23 — but only after an image +# rebuild is triggered, which is why this runs here too. +# +# apt only: `apk add` fetches its index implicitly and dnf refreshes expired +# metadata on its own. Non-fatal, since a refresh failure still leaves whatever +# index is already there, and the install's own error is the more actionable one. +if command -v apt-get >/dev/null 2>&1; then + apt-get update -qq || echo "warning: apt-get update failed; continuing" >&2 +fi + "$uvr_bin" sync --library "$target_lib" --install-system-deps From 01b8ab43dfffee0e71bc63617275d5cffe5b2d88 Mon Sep 17 00:00:00 2001 From: pat-s Date: Mon, 10 Aug 2026 06:30:35 +0000 Subject: [PATCH 39/53] fix(rebuild): re-index and purge the CDN after a rebuild (#160) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem The rebuild now works — `AATtools 0.0.3` was detected as a source fallback, built, and published: ``` ℹ `upload_single_binary()`: Replacing the CRAN source published for AATtools 0.0.3 … with the binary. ✔ Successfully uploaded package AATtools with tag 0.0.3. ``` But clients still get the source, and will for about a year: ``` $ curl -sI .../src/contrib/AATtools_0.0.3.tar.gz etag: "ea8127d953ca6a2f118ea49441772af6" # CRAN's source MD5 cdn-cache: HIT cdn-cachedat: 08/09/2026 16:43:32 # predates the 18:12 upload ``` Two causes, both specific to a rebuild: 1. **The slot is never re-indexed.** `weekly-rebuild-missing` has no `upload_package_index` step, so the index keeps the old MD5 and — for anything that had been served from source — no `Built` stamp. This one self-heals at the next `process-updates` run. 2. **The tarball URL is never purged.** A normal update publishes new packages at *new* URLs, so `purge_cdn_cache.sh` only needs the five index files. A rebuild replaces an object *in place*, and the zone caches tarballs for `cache_expiration_time = 31919000` (~370 days). This does not self-heal. Nothing about a stale package looks wrong from the outside, which is what makes it worth fixing rather than documenting. ## What this changes **Re-index at the end of a rebuild**, flat and per-minor, mirroring the tail of `process-updates`. The codename is detected from the image's `/etc/os-release` (as `local/packages-to-build.R` already does) rather than adding `OS_ID` to all 18 matrix rows. **Purge the zone afterwards**, via a new `scripts/purge_cdn_zone.sh`. One call to `POST /pullzone/{id}/purgeCache` covers every replaced object, and all three hostnames — `cran.devxy.io`, `cran.allianceswisspass.devxy.io`, `cran.rpkgs.com` — share pull zone `3857050`, confirmed from the `cdn-pullzone` response header. Purging per URL was the alternative and is worse here: ~13.5k rate-limited calls per arch, where a single missed call leaves a package silently stale. The cost of the zone purge is a cold cache for everything else, which is why it stays out of the daily update path — `purge_cdn_cache.sh` is untouched. The purge runs on failure too (`when: status: [success, failure]`): a rebuild that died part-way still replaced objects, and those are exactly the ones a stale edge keeps hiding. ## Verification `crow lint .crow/` reports all ten configs valid; `bash -n` on the new script passes; prek hooks pass. Not yet exercised against Bunny — it needs `BUNNYNET_API_KEY`, which is a CI secret. The failure mode is explicit rather than silent: any status other than 200/204 prints the response body and exits non-zero. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/160 --- .crow/weekly-rebuild-missing.yaml | 33 ++++++++++++++++++++ scripts/purge_cdn_zone.sh | 52 +++++++++++++++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100755 scripts/purge_cdn_zone.sh diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index 0353901..c86fe5a 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -163,6 +163,17 @@ steps: - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")' - $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1 + # A rebuild replaces objects in place, so the slot's index still advertises + # the old MD5 and, for anything that had been served from source, no Built + # stamp. Re-index here rather than waiting for the next process-updates + # run, or the rebuilt binaries stay invisible to clients until then. + # The codename is detected from the image's /etc/os-release. + - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))' + - | + for RBIN in /opt/R/[0-9]*/bin/R; do + RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) + /opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true + done backend_options: docker: resources: @@ -172,3 +183,25 @@ steps: limits: memory: 18Gi cpu: 3000m + + - name: Purge CDN cache + image: reg.devxy.io/docker.io/library/alpine:3.24 + environment: + OTEL_R_TRACES_EXPORTER: none + OTEL_R_LOGS_EXPORTER: none + OTEL_R_METRICS_EXPORTER: none + BUNNYNET_API_KEY: + from_secret: BUNNYNET_API_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + # All hostnames on the zone share this id, so one purge covers + # cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com. + BUNNY_PULLZONE: '3857050' + commands: + - apk add --no-cache -q bash curl git + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE" + # A rebuild that died part-way still replaced objects, and those are exactly + # the ones a stale edge would keep hiding, so purge either way. + when: + - status: [success, failure] diff --git a/scripts/purge_cdn_zone.sh b/scripts/purge_cdn_zone.sh new file mode 100755 index 0000000..391a814 --- /dev/null +++ b/scripts/purge_cdn_zone.sh @@ -0,0 +1,52 @@ +#!/usr/bin/env bash +# +# Purge the entire BunnyCDN pull zone. +# +# `purge_cdn_cache.sh` purges the five index files by URL, which is right after +# a normal update: new packages arrive at new URLs, so only the index is stale. +# +# A rebuild is different. It replaces an object *in place*: a package whose +# build failed was published as its CRAN source, and the rebuilt binary takes +# exactly the same URL. The zone caches tarballs for ~370 days +# (`cache_expiration_time` in cdn.tf), so without a purge every client keeps +# receiving the source tarball for up to a year, and nothing about it looks +# wrong from the outside. +# +# Purging per URL would mean one API call per replaced package -- ~13.5k per +# arch against a rate-limited endpoint, where a single missed call leaves a +# silently stale package. One zone purge is a single call regardless of how many +# objects were replaced. The cost is a cold cache for everything else, which is +# why this is not used by the daily update path. +# +# All hostnames on the zone (cran.devxy.io, cran.allianceswisspass.devxy.io, +# cran.rpkgs.com) share pull zone 3857050, so one purge covers all of them. +# +# Usage: +# purge_cdn_zone.sh +# +set -euo pipefail + +if (($# < 2)); then + echo "usage: $0 " >&2 + exit 2 +fi + +api_key="$1" +zone_id="$2" + +echo "Purging BunnyCDN pull zone ${zone_id}" + +status=$( + curl -sS -o /tmp/purge_zone_response.txt -w '%{http_code}' -X POST \ + -H "AccessKey: ${api_key}" \ + -H "Content-Length: 0" \ + "https://api.bunny.net/pullzone/${zone_id}/purgeCache" +) + +if [[ "${status}" != "200" && "${status}" != "204" ]]; then + echo "Purge of pull zone ${zone_id} failed with HTTP ${status}:" >&2 + cat /tmp/purge_zone_response.txt >&2 + exit 1 +fi + +echo "Purged pull zone ${zone_id} (HTTP ${status})" From caf3276fb968c732f0a80792435e63973bf80c45 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Tue, 11 Aug 2026 00:31:56 +0000 Subject: [PATCH 40/53] chore(deps): update dependency nbafrank/uvr to v0.4.6 --- local/uvr-install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/local/uvr-install.sh b/local/uvr-install.sh index c5d37d3..1e25e47 100755 --- a/local/uvr-install.sh +++ b/local/uvr-install.sh @@ -30,7 +30,7 @@ set -eu # renovate: datasource=github-releases depName=nbafrank/uvr -UVR_PIN="v0.4.5" +UVR_PIN="v0.4.6" if [ "$#" -eq 0 ]; then echo "usage: $0 ..." >&2 From 4b7dc28cc83784fd350731b87f0d515df7c21299 Mon Sep 17 00:00:00 2001 From: pat-s Date: Wed, 12 Aug 2026 08:30:29 +0000 Subject: [PATCH 41/53] feat(rebuild): shard the weekly rebuild and make each shard resumable (#163) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ## Problem `weekly-rebuild-missing` runs one job per `-` and walks that slot's list serially in a single `R -q -e` argument. That was cheap while every source fallback was skipped as "already built". Since bincraft #105/#106/#107 and #159 the gate works, and the lists are large: 8 917 source-served records on `amd64/alpine324`, 15 023 on `amd64/resolute`. Pipeline 10910 (`weekly_rebuild_missing:alpine-324-amd64`) ran for two days, reached `[8692/23885] cholera`, and was killed there. Two failures follow from that shape: - **No parallelism.** The work is embarrassingly parallel across packages; one job does all of it. - **No resumability and no clean stopping point.** The loop ends only by exhausting the list, so the only way to stop it is a kill. A restart re-walks from the first entry, paying a CRAN version resolution and an S3 `HEAD` per package before reaching new work. And a kill matches neither `success` nor `failure`, so the `Purge CDN cache` step never ran: the ~4 600 binaries 10910 did publish stayed hidden behind stale edge copies. ## What this changes **Three shards per slot.** Each of the 18 `OS`/`ARCH` rows gains `SPLIT_INTO`/`SPLIT_INDEX`, mirroring `build-all-versions.yaml`. Cron and manual routing are unchanged: both filters already match on `${OS}-${ARCH}`, so they now match all three shards of a slot. **`local/rebuild-missing.R`** replaces the ~1 500-character inline one-liner. The slice is interleaved rather than contiguous, because the list is alphabetical and cost clusters by name (`Rcpp*`, `Bioc*`, `rstan*`). **Resume by re-deriving state from the bucket.** One `s3_dir_info()` listing gives ETags for the slot; a package is outstanding iff its object's ETag equals CRAN's published `MD5sum`, i.e. it is still byte-identical to CRAN's source. That is `check_s3_root_package()` evaluated in bulk. No progress file, no volume, no DB cursor, and correct when a sibling shard or a `process-updates` run completes something concurrently. It reads ETags rather than the index's `Built` field the way `packages-to-build.R` does, because the index is no longer rewritten until the dependent pipeline runs and so cannot reflect the current run's progress. Unknown always means "already a binary", never "rebuild it": a multipart ETag, an unreadable CRAN index or an empty listing can never mass-schedule work. **A 20 h wall-clock budget** per shard. It exits 0, so the re-index and purge always fire and the remainder is picked up next run with no bookkeeping. **`.crow/weekly-rebuild-reindex.yaml`** takes over re-indexing and the purge, with `depends_on: [weekly-rebuild-missing]` and `runs_on: [success, failure]`. Three shards writing one slot's `PACKAGES` concurrently would race: `update_PACKAGES()` lists the live bucket, so an early lister that uploads last publishes an index missing its siblings' work. ## Verification `crow lint .crow/` passes on all 11 pipelines. `prek run` passes. 19 assertions in `local/tests/test-rebuild-missing.R`, 0 failures, covering the partition (disjoint, covering, deterministic, short lists, out-of-range index) and the outstanding filter (source ETag kept, binary ETag dropped, absent object kept, multipart and missing-from-CRAN treated as built). One of those tests caught a real bug before it shipped: an empty ETag table indexed to zero length rather than to `NA`, which recycled the result away and reported "nothing to build" — the dangerous direction. Fixed with an explicit `lookup()`. The filter run against the live `amd64/alpine324` index, using its `MD5sum` column as the ETag (established to match the objects): ``` index packages: 24343 outstanding (filter): 8950 no Built stamp: 8917 filter vs no-Built agreement: 8917 of 8917 outstanding but stamped Built: 33 (version drift vs CRAN) shard sizes: 2984/2983/2983 (sum 8950, unique 8950) ``` It reproduces the source-served set exactly. The extra 33 are packages whose slot version differs from CRAN's current one, so no object exists at the CRAN version key: correctly outstanding. ## Notes for review - The 20 h budget is a chosen default, exposed as `REBUILD_BUDGET_HOURS` in the pipeline. - `depends_on` is file-level, not row-level, so on a full cron run no slot is re-indexed until the slowest of all 54 jobs finishes. The budget bounds that at roughly a day. - An explicit cancel still skips the re-index. Recovery is to trigger `weekly-rebuild-reindex` on its own. - The purge runs on every re-index row rather than one designated slot: a cron fires only its own slot's row, so gating on a named slot would leave every other slot unpurged. - Out of scope: `build-all-versions` still cannot rebuild source fallbacks, because `local/build-all.R:113-122` drops every version with any `single_builds` row, which is precisely the source-fallback set. Design: `specs/2026-08-12-shard-weekly-rebuild-design.md` Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/163 --- .crow/weekly-rebuild-missing.yaml | 306 +++++++++++++++--- .crow/weekly-rebuild-reindex.yaml | 193 +++++++++++ local/rebuild-missing-helpers.R | 87 +++++ local/rebuild-missing.R | 194 +++++++++++ local/tests/test-rebuild-missing.R | 94 ++++++ .../2026-08-12-shard-weekly-rebuild-design.md | 167 ++++++++++ 6 files changed, 1005 insertions(+), 36 deletions(-) create mode 100644 .crow/weekly-rebuild-reindex.yaml create mode 100644 local/rebuild-missing-helpers.R create mode 100644 local/rebuild-missing.R create mode 100644 local/tests/test-rebuild-missing.R create mode 100644 specs/2026-08-12-shard-weekly-rebuild-design.md diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index c86fe5a..5afb3c3 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -1,12 +1,21 @@ # Consolidated weekly-rebuild-missing pipeline (all platforms, both arches). -# One matrix row per OS/arch replaces the former per-platform files. +# Three matrix rows per OS/arch, one per shard of that slot's rebuild list. # Routing is preserved 1:1: # - cron: each existing `weekly-rebuild-missing--` cron fires only -# its matching matrix row (via the per-row `cron:` name filter). +# its matching matrix rows (via the per-row `cron:` name filter), +# which is now all three shards of that slot. # - manual: `weekly_rebuild_missing` dropdown, default "all" (matches the # previous bare manual trigger that ran every os/arch); pick a # single - to run just one. # Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64). +# +# The shard picks up its own slice and re-derives what is still outstanding +# from the bucket, so a restart resumes rather than replaying; see +# local/rebuild-missing.R. +# +# Re-indexing and the CDN purge deliberately do NOT live here. Three shards +# writing one slot's PACKAGES concurrently would race, so they moved to +# .crow/weekly-rebuild-reindex.yaml, which depends on this pipeline. variables: # Gates this pipeline. A manual pipeline creation instantiates every file in # .crow/, and a declared default is applied even when the run never passed @@ -53,74 +62,326 @@ matrix: ARCH: amd64 R_VERSION: 4.5.3 IMG: alpine:3.22 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: alpine-322 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.22 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: alpine-322 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.22 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: alpine-322 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.22 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: alpine-322 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.22 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: alpine-322 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.22 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: alpine-323 ARCH: amd64 R_VERSION: 4.5.3 IMG: alpine:3.23 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: alpine-323 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: alpine-323 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: alpine-323 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.23 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: alpine-323 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: alpine-323 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: alpine-324 ARCH: amd64 R_VERSION: 4.5.3 IMG: alpine:3.24 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: alpine-324 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: alpine-324 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: alpine-324 ARCH: arm64 R_VERSION: 4.5.3 IMG: alpine:3.24 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: alpine-324 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: alpine-324 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: redhat-8 ARCH: amd64 R_VERSION: 4.4.3 IMG: redhat:8 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: redhat-8 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:8 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: redhat-8 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:8 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: redhat-8 ARCH: arm64 R_VERSION: 4.4.3 IMG: redhat:8 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: redhat-8 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:8 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: redhat-8 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:8 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: redhat-9 ARCH: amd64 R_VERSION: 4.4.3 IMG: redhat:9 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: redhat-9 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:9 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: redhat-9 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:9 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: redhat-9 ARCH: arm64 R_VERSION: 4.4.3 IMG: redhat:9 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: redhat-9 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:9 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: redhat-9 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:9 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: redhat-10 ARCH: amd64 R_VERSION: 4.5.3 IMG: redhat:10 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: redhat-10 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: redhat:10 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: redhat-10 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: redhat:10 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: redhat-10 ARCH: arm64 R_VERSION: 4.5.3 IMG: redhat:10 + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: redhat-10 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: redhat:10 + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: redhat-10 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: redhat:10 + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: ubuntu-2204 ARCH: amd64 R_VERSION: 4.4.3 IMG: ubuntu:jammy + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2204 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2204 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: ubuntu-2204 ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:jammy + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2204 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2204 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: ubuntu-2404 ARCH: amd64 R_VERSION: 4.4.3 IMG: ubuntu:noble + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2404 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2404 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: ubuntu-2404 ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:noble + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2404 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2404 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: ubuntu-2604 ARCH: amd64 R_VERSION: 4.4.3 IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 3 - OS: ubuntu-2604 ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 3 steps: - name: 'Rebuild missing binaries' @@ -153,6 +414,12 @@ steps: PLATFORM: ${OS} ARCH: ${ARCH} NCPUS: 2 + SPLIT_INTO: ${SPLIT_INTO} + SPLIT_INDEX: ${SPLIT_INDEX} + # Wall clock after which the shard stops cleanly instead of having to be + # killed. A kill matches neither `success` nor `failure`, so it would skip + # the dependent re-index and leave rebuilt binaries behind a stale edge. + REBUILD_BUDGET_HOURS: 20 commands: - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages @@ -162,18 +429,7 @@ steps: - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")' - - $XVFB $XVFB_ARGS -- /opt/R/$R_VERSION/bin/R -q -e "sink(stdout(), type = 'message'); options(crayon.enabled = TRUE, Ncpus = $NCPUS, future.globals.onReference = NULL); pkgs <- readLines('/tmp/rebuild_pkgs.txt'); if (length(pkgs) == 0) { cat('Nothing to rebuild\n'); q('no') }; excluded <- jsonlite::fromJSON('local/excluded-packages.json')[['package']]; pkgs <- setdiff(pkgs, excluded); cat(sprintf('Rebuilding %d packages\n', length(pkgs))); n <- length(pkgs); for (i in seq_along(pkgs)) { x <- pkgs[i]; cat(sprintf('[%d/%d] %s\n', i, n, x)); tryCatch(bincraft::build_binary_package(x, tag_limit = 1L, patches = 'local/patches', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE), error = function(e) cat(sprintf('ERROR building %s - %s\n', x, conditionMessage(e)))) }" 2>&1 - # A rebuild replaces objects in place, so the slot's index still advertises - # the old MD5 and, for anything that had been served from source, no Built - # stamp. Re-index here rather than waiting for the next process-updates - # run, or the rebuilt binaries stay invisible to clients until then. - # The codename is detected from the image's /etc/os-release. - - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))' - - | - for RBIN in /opt/R/[0-9]*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - /opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true - done + - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1 backend_options: docker: resources: @@ -183,25 +439,3 @@ steps: limits: memory: 18Gi cpu: 3000m - - - name: Purge CDN cache - image: reg.devxy.io/docker.io/library/alpine:3.24 - environment: - OTEL_R_TRACES_EXPORTER: none - OTEL_R_LOGS_EXPORTER: none - OTEL_R_METRICS_EXPORTER: none - BUNNYNET_API_KEY: - from_secret: BUNNYNET_API_KEY - REPO_RO_TOKEN: - from_secret: REPO_RO_TOKEN - # All hostnames on the zone share this id, so one purge covers - # cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com. - BUNNY_PULLZONE: '3857050' - commands: - - apk add --no-cache -q bash curl git - - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE" - # A rebuild that died part-way still replaced objects, and those are exactly - # the ones a stale edge would keep hiding, so purge either way. - when: - - status: [success, failure] diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml new file mode 100644 index 0000000..224596b --- /dev/null +++ b/.crow/weekly-rebuild-reindex.yaml @@ -0,0 +1,193 @@ +# Re-index and purge after weekly-rebuild-missing. +# +# weekly-rebuild-missing runs three shards per slot. Each of them replaces +# objects in place, so the slot's index still advertises the old MD5 and, for +# anything that had been served from source, no Built stamp. Re-indexing from +# inside a shard would mean three concurrent `upload_package_index()` calls on +# one prefix: `cranlike::update_PACKAGES()` lists the live bucket, so an early +# lister that uploads last publishes an index missing its siblings' work. +# +# So it happens exactly once per slot, here, after every shard has finished. +# `runs_on: [success, failure]` keeps that true when a shard fails; only an +# explicit cancel skips it, and this pipeline can then be triggered on its own. + +variables: + # Mirrors the gate on weekly-rebuild-missing so a manual run re-indexes + # exactly the slots it rebuilt. A manual pipeline creation instantiates every + # file in .crow/, so the default must match no matrix row. + weekly_rebuild_missing: + description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." + options: + - none + - all + - alpine-322-amd64 + - alpine-322-arm64 + - alpine-323-amd64 + - alpine-323-arm64 + - alpine-324-amd64 + - alpine-324-arm64 + - redhat-8-amd64 + - redhat-8-arm64 + - redhat-9-amd64 + - redhat-9-arm64 + - redhat-10-amd64 + - redhat-10-arm64 + - ubuntu-2204-amd64 + - ubuntu-2204-arm64 + - ubuntu-2404-amd64 + - ubuntu-2404-arm64 + - ubuntu-2604-amd64 + - ubuntu-2604-arm64 + default: none + +when: + - event: cron + cron: weekly-rebuild-missing-${OS}-${ARCH} + - event: manual + evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"' + +depends_on: + - weekly-rebuild-missing + +runs_on: [success, failure] + +skip_clone: true + +labels: + group: rpkgs-${ARCH} + +matrix: + include: + - OS: alpine-322 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.22 + - OS: alpine-322 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.22 + - OS: alpine-323 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + - OS: alpine-323 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.23 + - OS: alpine-324 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: alpine-324 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: alpine:3.24 + - OS: redhat-8 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:8 + - OS: redhat-8 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:8 + - OS: redhat-9 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: redhat:9 + - OS: redhat-9 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: redhat:9 + - OS: redhat-10 + ARCH: amd64 + R_VERSION: 4.5.3 + IMG: redhat:10 + - OS: redhat-10 + ARCH: arm64 + R_VERSION: 4.5.3 + IMG: redhat:10 + - OS: ubuntu-2204 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + - OS: ubuntu-2204 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:jammy + - OS: ubuntu-2404 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + - OS: ubuntu-2404 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:noble + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + +steps: + - name: 'Re-index the slot' + image: reg.devxy.io/rpkgs/build-env-${IMG} + pull: true + environment: + OTEL_R_TRACES_EXPORTER: none + OTEL_R_LOGS_EXPORTER: none + OTEL_R_METRICS_EXPORTER: none + RED_HAT_DEV_PW: + from_secret: RED_HAT_DEV_PW + B2_S3_ACCESS_KEY: + from_secret: B2_S3_ACCESS_KEY + B2_S3_SECRET_KEY: + from_secret: B2_S3_SECRET_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + GIT_USER: pat-s + R_LIBS_USER: /mnt/cache/R-pkgs + R_VERSION: ${R_VERSION} + PLATFORM: ${OS} + ARCH: ${ARCH} + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - mkdir -p /mnt/cache/R-pkgs + - rm -rf /mnt/cache/R-pkgs/00LOCK-* + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + # The codename is detected from the image's /etc/os-release. + - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))' + - | + for RBIN in /opt/R/[0-9]*/bin/R; do + RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) + /opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true + done + + - name: Purge CDN cache + image: reg.devxy.io/docker.io/library/alpine:3.24 + environment: + OTEL_R_TRACES_EXPORTER: none + OTEL_R_LOGS_EXPORTER: none + OTEL_R_METRICS_EXPORTER: none + BUNNYNET_API_KEY: + from_secret: BUNNYNET_API_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + # All hostnames on the zone share this id, so one purge covers + # cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com. + BUNNY_PULLZONE: '3857050' + commands: + - apk add --no-cache -q bash curl git + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE" + # Runs on every row rather than on one designated slot: a cron fires only + # its own slot's row, so gating on a named slot would leave every other + # slot unpurged. A manual "all" run therefore purges the zone 18 times, + # which is a cheap API call and rare. + # + # Run it even when the re-index above failed: the objects were still + # replaced, and a stale edge is exactly what keeps them hidden. + when: + - status: [success, failure] diff --git a/local/rebuild-missing-helpers.R b/local/rebuild-missing-helpers.R new file mode 100644 index 0000000..16a588e --- /dev/null +++ b/local/rebuild-missing-helpers.R @@ -0,0 +1,87 @@ +# Pure helpers for local/rebuild-missing.R, kept separate so local/tests can +# source them without executing a rebuild. + +# Interleaved slice of the rebuild list. +# +# The list is alphabetical and build cost clusters by name (Rcpp*, Bioc*, +# rstan*), so contiguous thirds would be badly unbalanced. Interleaving also +# makes each shard's progress counter representative of the slot as a whole. +shard_slice <- function(pkgs, split_into, split_index) { + split_into <- as.integer(split_into) + split_index <- as.integer(split_index) + if (is.na(split_into) || is.na(split_index)) { + stop("shard_slice(): split_into and split_index must be integers") + } + if (split_into < 1L || split_index < 1L || split_index > split_into) { + stop(sprintf( + "shard_slice(): need 1 <= split_index <= split_into, got %s of %s", + split_index, + split_into + )) + } + # seq() errors on a descending range, which is what an empty list or a shard + # index past the end would produce. + if (length(pkgs) < split_index) { + return(pkgs[0L]) + } + pkgs[seq.int(split_index, length(pkgs), by = split_into)] +} + +# Packages that still need building, decided from the bucket rather than from +# remembered progress. +# +# This is bincraft's `check_s3_root_package()` evaluated in bulk: an object +# whose ETag equals CRAN's published MD5sum is byte-identical to CRAN's source, +# so the build that was supposed to replace it has not happened yet. +# +# `etag_by_file` named by `_.tar.gz`, values are unquoted ETags +# `cran_version` named by package +# `cran_md5` named by `_` +# +# Unknown always means "already a binary", never "rebuild it", so an unreadable +# CRAN index or a multipart ETag can never mass-schedule work. +outstanding_packages <- function(pkgs, etag_by_file, cran_version, cran_md5) { + if (length(pkgs) == 0L) { + return(pkgs) + } + + # An empty table indexes to zero length rather than to NA, which would + # recycle the whole result away and silently report "nothing to build". + lookup <- function(table, key) { + if (length(table) == 0L) { + return(rep(NA_character_, length(key))) + } + unname(as.character(table[key])) + } + + version <- lookup(cran_version, pkgs) + file <- sprintf("%s_%s.tar.gz", pkgs, version) + etag <- lookup(etag_by_file, file) + md5 <- lookup(cran_md5, paste(pkgs, version, sep = "_")) + + # No CRAN version means the package cannot be resolved to a tarball at all; + # leave it in and let bincraft report why. + unresolved <- is.na(version) + # No object at the key: never built, so it is outstanding by definition. + absent <- !unresolved & is.na(etag) + # A multipart upload carries a compound ETag rather than an MD5. + unknown <- !is.na(etag) & grepl("-", etag, fixed = TRUE) + + is_source <- !unresolved & + !is.na(etag) & + !unknown & + !is.na(md5) & + etag == md5 + + pkgs[unresolved | absent | is_source] +} + +parse_rebuild_args <- function(args) { + pos <- args[!startsWith(args, "--")] + budget <- as.numeric(pos[3L]) + list( + split_into = as.integer(pos[1L]), + split_index = as.integer(pos[2L]), + budget_hours = if (is.na(budget)) 20 else budget + ) +} diff --git a/local/rebuild-missing.R b/local/rebuild-missing.R new file mode 100644 index 0000000..369024e --- /dev/null +++ b/local/rebuild-missing.R @@ -0,0 +1,194 @@ +### Rebuild one shard of a slot's missing-binary list. +# +# Usage: Rscript local/rebuild-missing.R [budget_hours] +# +# The list itself comes from local/fetch-rebuild-packages-from-issue.R, which +# writes $REBUILD_PKG_LIST (default /tmp/rebuild_pkgs.txt). +# +# Two properties matter here and are the reason this is a script rather than an +# `R -q -e` argument in the pipeline: +# +# * it is restartable. The outstanding set is re-derived from the bucket on +# every start, so a shard that died resumes where it stopped without any +# progress file, and without replaying thousands of per-package HEADs. +# * it terminates. A wall-clock budget stops the loop cleanly instead of the +# run having to be killed, which is what previously skipped the re-index and +# CDN purge and left rebuilt binaries hidden behind stale edge copies. + +options(error = function() { + cat("ERROR:", geterrmessage(), "\n", file = stdout()) + traceback(2) + q(status = 1) +}) + +library(bincraft, quietly = TRUE) + +source(file.path("local", "rebuild-missing-helpers.R")) + +args <- parse_rebuild_args(commandArgs(trailingOnly = TRUE)) +if (is.na(args$split_into) || is.na(args$split_index)) { + stop("usage: rebuild-missing.R [budget_hours]") +} + +list_file <- Sys.getenv("REBUILD_PKG_LIST", "/tmp/rebuild_pkgs.txt") +pkgs <- if (file.exists(list_file)) readLines(list_file) else character(0) +pkgs <- pkgs[nzchar(pkgs)] +if (length(pkgs) == 0L) { + cat("Nothing to rebuild\n") + q("no") +} + +excluded <- jsonlite::fromJSON("local/excluded-packages.json")[["package"]] +pkgs <- setdiff(pkgs, excluded) + +mine <- shard_slice(pkgs, args$split_into, args$split_index) +cat(sprintf( + "Shard %s/%s: %s of %s listed packages\n", + args$split_index, + args$split_into, + length(mine), + length(pkgs) +)) + +### Resume: ask the bucket what is still outstanding + +codename <- bincraft::set_codename(NULL) +local_machine <- Sys.info()[["machine"]] +arch <- if (grepl("arm64|aarch64", local_machine)) "arm64" else "amd64" +slot_dir <- sprintf( + "devxy-rpkgs-binaries/%s/%s/latest/src/contrib", + arch, + codename +) + +s3fs::s3_file_system( + aws_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + aws_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), + endpoint = "https://s3.eu-central-003.backblazeb2.com", + region_name = "eu-central-003", + refresh = TRUE +) + +# One paginated listing instead of a HEAD per package. Not recursed: the +# rebuild passes no `is_r_minor_sensitive`, so it only ever targets the flat +# path, and the resume filter matches that scope deliberately. +info <- tryCatch(s3fs::s3_dir_info(slot_dir), error = function(e) NULL) +etag_by_file <- if (is.null(info) || nrow(info) == 0L) { + cat(sprintf( + "WARNING: could not list %s; building the whole shard\n", + slot_dir + )) + stats::setNames(character(), character()) +} else { + stats::setNames( + gsub('^"|"$', "", as.character(info$etag)), + basename(as.character(info$uri)) + ) +} + +cran <- tryCatch( + { + con <- gzcon(url( + "https://cloud.r-project.org/src/contrib/PACKAGES.gz", + open = "rb" + )) + on.exit(close(con), add = TRUE) + read.dcf(con, fields = c("Package", "Version", "MD5sum")) + }, + error = function(e) { + cat(sprintf( + "WARNING: could not read CRAN's index (%s)\n", + conditionMessage(e) + )) + NULL + } +) +cran_version <- stats::setNames(character(), character()) +cran_md5 <- stats::setNames(character(), character()) +if (!is.null(cran)) { + cran_version <- stats::setNames( + as.character(cran[, "Version"]), + as.character(cran[, "Package"]) + ) + keep <- !is.na(cran[, "MD5sum"]) + cran_md5 <- stats::setNames( + as.character(cran[keep, "MD5sum"]), + paste(cran[keep, "Package"], cran[keep, "Version"], sep = "_") + ) +} + +before <- length(mine) +mine <- outstanding_packages(mine, etag_by_file, cran_version, cran_md5) +cat(sprintf( + "Resume: %s of %s already carry a binary; %s outstanding\n", + before - length(mine), + before, + length(mine) +)) + +if (length(mine) == 0L) { + cat("Nothing outstanding for this shard\n") + q("no") +} + +### Build + +options( + crayon.enabled = TRUE, + Ncpus = as.integer(Sys.getenv("NCPUS", "2")), + future.globals.onReference = NULL +) + +started <- Sys.time() +n <- length(mine) +completed <- 0L +for (i in seq_along(mine)) { + elapsed <- as.numeric(difftime(Sys.time(), started, units = "hours")) + if (elapsed > args$budget_hours) { + cat(sprintf( + "Budget of %sh reached after %d/%d packages; stopping cleanly. The next run resumes from the bucket.\n", + args$budget_hours, + completed, + n + )) + break + } + + x <- mine[i] + cat(sprintf("[%d/%d] %s\n", i, n, x)) + tryCatch( + bincraft::build_binary_package( + x, + tag_limit = 1L, + patches = "local/patches", + s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", + s3_region = "eu-central-003", + s3_bucket = "devxy-rpkgs-binaries", + s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), + s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), + metadata_db_host = "r-binaries.devxy.io", + metadata_db_name = "build_metadata", + metadata_db_table = "single_builds", + metadata_db_user = "rpkgs", + metadata_db_password = Sys.getenv("PGPASS"), + metadata_db_sslmode = "require", + metadata_db_port = 15432, + archive = TRUE, + upload = TRUE, + store_build_metadata = TRUE + ), + error = function(e) { + cat(sprintf("ERROR building %s - %s\n", x, conditionMessage(e))) + } + ) + completed <- completed + 1L +} + +cat(sprintf( + "Shard %s/%s finished: %d/%d packages processed in %.1fh\n", + args$split_index, + args$split_into, + completed, + n, + as.numeric(difftime(Sys.time(), started, units = "hours")) +)) diff --git a/local/tests/test-rebuild-missing.R b/local/tests/test-rebuild-missing.R new file mode 100644 index 0000000..a5e70b9 --- /dev/null +++ b/local/tests/test-rebuild-missing.R @@ -0,0 +1,94 @@ +source(file.path("..", "rebuild-missing-helpers.R")) + +test_that("shard_slice partitions the list without gaps or overlap", { + pkgs <- letters[1:10] + parts <- lapply(1:3, function(i) shard_slice(pkgs, 3, i)) + + expect_identical(parts[[1]], c("a", "d", "g", "j")) + expect_identical(parts[[2]], c("b", "e", "h")) + expect_identical(parts[[3]], c("c", "f", "i")) + + expect_identical(sort(unlist(parts)), sort(pkgs)) + expect_identical(anyDuplicated(unlist(parts)), 0L) +}) + +test_that("shard_slice is deterministic and survives short lists", { + expect_identical( + shard_slice(letters[1:10], 3, 2), + shard_slice(letters[1:10], 3, 2) + ) + expect_identical(shard_slice(character(0), 3, 1), character(0)) + # more shards than packages: the tail shards get nothing rather than erroring + expect_identical(shard_slice(c("a"), 3, 1), "a") + expect_identical(shard_slice(c("a"), 3, 2), character(0)) +}) + +test_that("shard_slice rejects an out-of-range index", { + expect_error(shard_slice(letters, 3, 4), "split_index") + expect_error(shard_slice(letters, 3, 0), "split_index") +}) + +test_that("outstanding_packages keeps source fallbacks and drops real binaries", { + cran_version <- c(httr = "1.4.8", R6 = "2.6.1", curl = "7.1.0") + cran_md5 <- c( + httr_1.4.8 = "8756015b94a9cff6f410ca4de8557f12", + R6_2.6.1 = "f01b1787f12797c29194d63c9afd5d70", + curl_7.1.0 = "8af2ccbf5d85dc18866f45f1f26f348d" + ) + etag <- c( + # byte-identical to CRAN: the build never happened + "httr_1.4.8.tar.gz" = "8756015b94a9cff6f410ca4de8557f12", + # a real binary was published + "R6_2.6.1.tar.gz" = "9d6087ee9adda3f0a3b8067cfc652c05" + # curl has no object at all + ) + + out <- outstanding_packages( + c("httr", "R6", "curl"), + etag, + cran_version, + cran_md5 + ) + expect_identical(out, c("httr", "curl")) +}) + +test_that("outstanding_packages treats unknowns as already built", { + cran_version <- c(a = "1.0", b = "1.0") + cran_md5 <- c(a_1.0 = "aaaa") + + # a multipart ETag carries no MD5, and `b` is missing from CRAN's index: + # neither may schedule a rebuild + etag <- c("a_1.0.tar.gz" = "abc-3", "b_1.0.tar.gz" = "bbbb") + + expect_identical( + outstanding_packages(c("a", "b"), etag, cran_version, cran_md5), + character(0) + ) +}) + +test_that("outstanding_packages keeps a package CRAN has no version for", { + out <- outstanding_packages( + "ghost", + c(), + c(other = "1.0"), + c(other_1.0 = "aaaa") + ) + expect_identical(out, "ghost") +}) + +test_that("outstanding_packages handles an empty list", { + expect_identical( + outstanding_packages(character(0), c(), c(), c()), + character(0) + ) +}) + +test_that("parse_rebuild_args defaults the budget", { + a <- parse_rebuild_args(c("3", "2")) + expect_identical(a$split_into, 3L) + expect_identical(a$split_index, 2L) + expect_identical(a$budget_hours, 20) + + b <- parse_rebuild_args(c("3", "2", "1.5")) + expect_identical(b$budget_hours, 1.5) +}) diff --git a/specs/2026-08-12-shard-weekly-rebuild-design.md b/specs/2026-08-12-shard-weekly-rebuild-design.md new file mode 100644 index 0000000..f4ccbaa --- /dev/null +++ b/specs/2026-08-12-shard-weekly-rebuild-design.md @@ -0,0 +1,167 @@ +# Design: Sharding and resuming the weekly rebuild + +Date: 2026-08-12 +Status: Approved (pending spec review) + +## Problem + +`weekly-rebuild-missing` runs one job per `-` and walks that slot's rebuild list serially in a single `R -q -e` invocation (`.crow/weekly-rebuild-missing.yaml:165`). +Until 2026-08-09 that was cheap, because every source fallback was skipped as "already built" and the list was effectively empty. +Since bincraft #105/#106/#107 and build-cran-binaries #159 the gate works, and the lists are now large. + +Share of records whose object is byte-identical to CRAN's source, measured against `cran.r-project.org` MD5s on 2026-08-12: + +| slot | records | source-served | share | +| ------------------ | ------: | ------------: | -----------: | +| `amd64/resolute` | 24 212 | 15 023 | 62.1% | +| `arm64/resolute` | 24 291 | 13 670 | 56.3% | +| `arm64/alpine324` | 24 328 | 9 514 | 39.2% | +| `amd64/alpine324` | 24 343 | 8 917 | 36.7% | +| `arm64/rhel10` | 24 695 | 5 384 | 21.9% | +| `amd64/rhel10` | 24 881 | 4 712 | 19.2% | +| 12 remaining slots | ~24 700 | 850 to 2 130 | 3.5% to 8.7% | + +A single serial job cannot absorb that. +Pipeline 10910 (`weekly_rebuild_missing:alpine-324-amd64`) started on 2026-08-09, ran for roughly two days, reached `[8692/23885] cholera`, and was killed there. + +Two distinct failures follow from that shape. + +**No parallelism.** The work is embarrassingly parallel across packages, but one job does all of it. + +**No resumability, and no clean stopping point.** The loop has no terminating condition other than exhausting the list, so the only way to stop it is a kill. +A restarted run re-reads the same list and walks it from the first entry. +It skips completed packages via `check_s3_root_package()`, but that costs a CRAN version resolution and an S3 `HEAD` per package, thousands of times, before it reaches new work. +Worse, a kill is not a pipeline failure: the `Purge CDN cache` step is guarded by `when: status: [success, failure]` (`.crow/weekly-rebuild-missing.yaml:206-207`), and on 10910 it produced no output at all. +So the ~4 600 binaries that run did publish stayed hidden behind stale edge copies. + +## Goal + +Turn each slot's rebuild into bounded, parallel, restartable units, without introducing state that can disagree with the bucket. + +## Design + +### 1. Shard the matrix three ways + +Each of the 18 `OS`/`ARCH` rows in `.crow/weekly-rebuild-missing.yaml` gains `SPLIT_INTO: 3` and `SPLIT_INDEX: 1|2|3`, giving 54 rows. +This mirrors `.crow/build-all-versions.yaml:57-98`, which already shards its matrix four ways per arch. + +Routing needs no change. +The cron filter `cron: weekly-rebuild-missing-${OS}-${ARCH}` and the manual `evaluate: weekly_rebuild_missing == "${OS}-${ARCH}"` both match all three shards of a slot. +Placement stays on the `rpkgs-${ARCH}` group label, so shards queue against available capacity rather than oversubscribing it. + +### 2. Extract the loop into `local/rebuild-missing.R` + +The build is currently a single ~1 500-character `R -q -e` argument. +Shard arithmetic and resume logic do not belong in a YAML string, and none of it is testable there. +The loop moves to `local/rebuild-missing.R`, invoked as `Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX`, mirroring `local/build-all.R`. +Its body is unchanged in substance: read `/tmp/rebuild_pkgs.txt`, subtract `local/excluded-packages.json`, loop with `tryCatch` around `bincraft::build_binary_package()`. + +The slice is **interleaved**, not contiguous: + +```r +# the list is alphabetical and build cost clusters by name (Rcpp*, Bioc*, +# rstan*), so contiguous thirds would be badly unbalanced +mine <- pkgs[seq(split_index, length(pkgs), by = split_into)] +``` + +`local/build-all.R:64` uses contiguous chunks via `cut()`. +That is fine there because its list is every CRAN package and version, so the chunks average out. +Here the list is a filtered backlog in which expensive families sit adjacent, so interleaving is the better default. +Interleaving also makes each shard's `[i/n]` progress representative of the slot as a whole. + +### 3. Resume by re-deriving state from the bucket + +Before the loop, the shard performs one `s3fs::s3_dir_info()` on `devxy-rpkgs-binaries///latest/src/contrib` and reads the `etag` column. +It fetches CRAN's `PACKAGES` once for the latest version and published `MD5sum` of every package. +A package is still outstanding if and only if the object at `_.tar.gz` has an ETag equal to CRAN's `MD5sum` for that version, which is the definition `check_s3_root_package()` already applies one package at a time. + +```r +# one paginated listing instead of ~2900 sequential HEAD requests per shard +info <- s3fs::s3_dir_info(slot_dir) +etag <- setNames(gsub('^"|"$', "", info$etag), basename(info$uri)) + +key <- sprintf("%s_%s.tar.gz", mine, cran_version[mine]) +# keep a package when no object exists yet, or when the object is still +# byte-identical to CRAN's source; drop it once a real binary is published +mine <- mine[is.na(etag[key]) | etag[key] == cran_md5[key]] +``` + +This is the whole resume mechanism. +There is no progress file, no volume, and no database cursor. +A restarted shard recomputes ground truth and continues where it stopped, and it is correct even when a sibling shard, a `process-updates` cron, or a manual `just rebuild` completed something in the meantime. + +Three properties make this the right source of truth: + +- **It is what the build itself checks.** Any other store can disagree with the bucket; this one cannot. +- **It is agent-independent.** `.crow/weekly-rebuild-missing.yaml` mounts no `volumes:`, unlike `.crow/build-all-versions.yaml:132-133`, so `/mnt/cache` is per-job and cannot carry progress anyway. +- **It costs one listing.** `cranlike`'s `s3` fork already does exactly this call against this bucket at ~24 000 objects, so the approach is proven at the required scale. + +It must read ETags rather than the slot index's `Built` field, which is how `local/packages-to-build.R:104-130` answers the same question. +Under this design the index is not rewritten until the dependent re-index pipeline runs (section 5), so mid-run it cannot reflect the current run's progress. + +Packages that genuinely fail to build re-publish their CRAN source, so they stay outstanding and would be retried on every restart. +That is already handled upstream: `bincraft::filter_packages_with_errors()` (`R/build_binaries.R:1018`, `:1143`) drops anything with `error_occurred = TRUE`, and `store_build_metadata = TRUE` is passed on every call. +No additional poison-pill filter is needed here. + +Only the flat `src/contrib` path is considered. +The rebuild call passes no `is_r_minor_sensitive`, so it defaults to `FALSE` and only ever targets the flat path; the resume filter matches that scope deliberately. + +### 4. Give each shard a wall-clock budget + +`local/rebuild-missing.R` takes a budget, defaulting to 20 hours, and breaks out of the loop once it is exceeded: + +```r +# exit cleanly rather than being killed, so the dependent re-index still runs +if (difftime(Sys.time(), started, units = "hours") > budget_hours) { + cat(sprintf("Budget of %sh reached after %d/%d packages; stopping cleanly\n", budget_hours, i, n)) + break +} +``` + +It exits 0 and reports how much of the slice it covered. +Every run then has a terminating condition, the re-index and purge always fire, and the remainder is picked up by the next run with no bookkeeping, because section 3 recomputes the outstanding set from scratch. + +### 5. Move the re-index and purge into `.crow/weekly-rebuild-reindex.yaml` + +Three shards per slot means three concurrent `upload_package_index()` calls on the same S3 prefix. +`cranlike::update_PACKAGES()` lists the live bucket, so an early lister that uploads last publishes an index missing its siblings' work. +The re-index steps (`.crow/weekly-rebuild-missing.yaml:171-176`) and the purge step (`:187-207`) therefore leave that file entirely. + +The new file carries: + +```yaml +depends_on: + - weekly-rebuild-missing +runs_on: [success, failure] +``` + +`runs_on: [success, failure]` validates as a workflow-level key under `crow lint`, so a failing shard no longer withholds the re-index. +The file uses the same 18-row matrix and the same `when:` gating as `weekly-rebuild-missing`, so it only re-indexes slots that actually ran. +Each row re-indexes the flat slot and every per-minor slot. +`scripts/purge_cdn_zone.sh` runs once on a single row, because all hostnames share pull zone `3857050` and 18 identical zone purges would be waste. + +## Failure behaviour + +| case | today | after | +| -------------------------- | ----------------------------------- | ----------------------------------------------------- | +| one package errors | `tryCatch` logs, loop continues | unchanged | +| a shard fails outright | purge runs, re-index does not | re-index and purge run via `runs_on` | +| a shard exceeds its budget | cannot happen, runs until killed | exits 0, re-index and purge run | +| a shard is killed | nothing runs | still nothing; trigger the re-index pipeline alone | +| a shard restarts | re-walks the list, HEAD per package | one listing, resumes at the first outstanding package | + +The known cost of `depends_on` being file-level rather than row-level: on the weekly cron no slot is re-indexed until the slowest of all 54 jobs finishes. +The 20-hour budget bounds that at roughly one day. + +## Out of scope + +- `build-all-versions` still cannot rebuild source fallbacks, because `local/build-all.R:113-122` drops every version with any `single_builds` row for the platform and arch, which is precisely the source-fallback set. That is a separate change. +- Bunny Perma-Cache eviction. `scripts/purge_cdn_zone.sh` purges the regular edge cache only; see the note in `CLAUDE.md` and issue history. +- The audit that produces the rebuild list is unchanged. + +## Verification + +- `crow lint .crow/` passes for both pipeline files. +- `local/rebuild-missing.R` gets unit coverage in `local/tests/` for the two pure pieces: the interleaved slice (disjoint, covering, deterministic) and the outstanding-set filter (source-served ETag kept, binary ETag dropped, absent object kept). +- A single-slot manual run of `alpine-324-amd64` shard 1 confirms the listing shortcut against the live bucket, and that the reported outstanding count is close to the 8 917 measured above divided by three. +- Restarting that shard mid-run confirms it resumes rather than replaying, by comparing the outstanding count it reports on the second start. From aa4c95457f0ce7f79adea6705d54b098a10c50dd Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 13 Aug 2026 13:38:28 +0000 Subject: [PATCH 42/53] fix(rebuild): harden split workflow setup (#164) ## Motivation Weekly rebuild shards can all hit a transient CRAN DNS/index outage at once, and the dependent CDN purge always fails because it tries to clone over the checkout preserved from the re-index step. ## Changes - Retry `uvr add` resolution up to four times with bounded backoff. - Reuse the existing Crow workspace checkout in the CDN purge step. - Remove the purge step's unused Git package and repository token. ## Validation - `crow lint .crow/` - `shellcheck local/uvr-install.sh scripts/purge_cdn_zone.sh` - `git diff --check` Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/164 --- .crow/weekly-rebuild-reindex.yaml | 6 ++---- local/uvr-install.sh | 17 ++++++++++++++--- 2 files changed, 16 insertions(+), 7 deletions(-) diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml index 224596b..a67875d 100644 --- a/.crow/weekly-rebuild-reindex.yaml +++ b/.crow/weekly-rebuild-reindex.yaml @@ -173,14 +173,12 @@ steps: OTEL_R_METRICS_EXPORTER: none BUNNYNET_API_KEY: from_secret: BUNNYNET_API_KEY - REPO_RO_TOKEN: - from_secret: REPO_RO_TOKEN # All hostnames on the zone share this id, so one purge covers # cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com. BUNNY_PULLZONE: '3857050' commands: - - apk add --no-cache -q bash curl git - - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - apk add --no-cache -q bash curl + # Crow carries the checkout from the re-index step into this step. - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE" # Runs on every row rather than on one designated slot: a cron fires only # its own slot's row, so gating on a named slot would leave every other diff --git a/local/uvr-install.sh b/local/uvr-install.sh index 1e25e47..3966e85 100755 --- a/local/uvr-install.sh +++ b/local/uvr-install.sh @@ -84,9 +84,20 @@ 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. -"$uvr_bin" add --no-install "$@" +# --no-install resolves and locks only; retry because concurrent shards can +# expose short-lived DNS or CRAN-index failures and uvr rolls the manifest back +# cleanly after an unsuccessful resolution. +add_attempt=1 +while ! "$uvr_bin" add --no-install "$@"; do + if [ "$add_attempt" -ge 4 ]; then + echo "error: uvr add failed after ${add_attempt} attempts" >&2 + exit 1 + fi + add_delay=$((add_attempt * 10)) + echo "warning: uvr add attempt ${add_attempt} failed; retrying in ${add_delay}s" >&2 + sleep "$add_delay" + add_attempt=$((add_attempt + 1)) +done # TEMPORARY (drop once the images ship a uvr above v0.4.5): the sync below runs # `apt-get install` for every resolved system dependency without refreshing the From a1c1f5e78f2e22db0497fd749067661f063f35ff Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 13 Aug 2026 14:08:10 +0000 Subject: [PATCH 43/53] fix(cdn): align repository routing across pull zones (#165) ## Motivation `cran.rpkgs.com` and `cran.allianceswisspass.devxy.io` serve the same B2 repository through separate Bunny pull zones, but only the first zone was managed and purged after weekly reindexing. This allowed the Alliance endpoint to retain stale repository metadata and left locked `renv` restores unable to retrieve versions whose binary archive object was absent. ## Changes - Adopt the Alliance SwissPass pull zone `3265648` into OpenTofu and configure it with the shared B2 origin and middleware script. - Purge both Bunny pull zones after the weekly rebuild reindex. - Preserve the requested public hostname in middleware redirects. - Redirect missing archived binaries to the corresponding CRAN source package, checking whether the version is archived or still current. - Cover the existing archived-binary passthrough behavior in the edge routing matrix. ## Verification - `prek run -a` - `just edge-test` - `crow lint .crow/` - `tofu validate` - `bash -n scripts/purge_cdn_zone.sh` ## Deployment Run `tofu apply` to adopt pull zone `3265648`, publish the middleware release, and align both pull zones. After the apply, rerun the Alliance SwissPass CI restore that requested `cli 3.6.5` and `AzureStor 3.7.1`. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/165 --- .crow/weekly-rebuild-reindex.yaml | 8 ++--- cdn.tf | 56 +++++++++++++++++++++++++++++-- edge/rpkgs-router.test.ts | 7 ++++ edge/rpkgs-router.ts | 35 +++++++++++++++---- scripts/purge_cdn_zone.sh | 39 +++++++++++---------- 5 files changed, 115 insertions(+), 30 deletions(-) diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml index a67875d..bb00332 100644 --- a/.crow/weekly-rebuild-reindex.yaml +++ b/.crow/weekly-rebuild-reindex.yaml @@ -173,13 +173,13 @@ steps: OTEL_R_METRICS_EXPORTER: none BUNNYNET_API_KEY: from_secret: BUNNYNET_API_KEY - # All hostnames on the zone share this id, so one purge covers - # cran.devxy.io, cran.allianceswisspass.devxy.io and cran.rpkgs.com. - BUNNY_PULLZONE: '3857050' + # cran.rpkgs.com and cran.allianceswisspass.devxy.io are on separate + # Bunny pull zones, so both must be purged after the shared origin changes. + BUNNY_PULLZONES: '3857050 3265648' commands: - apk add --no-cache -q bash curl # Crow carries the checkout from the re-index step into this step. - - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" "$BUNNY_PULLZONE" + - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" $BUNNY_PULLZONES # Runs on every row rather than on one designated slot: a cron fires only # its own slot's row, so gating on a named slot would leave every other # slot unpurged. A manual "all" run therefore purges the zone 18 times, diff --git a/cdn.tf b/cdn.tf index 5e8899d..01191a5 100644 --- a/cdn.tf +++ b/cdn.tf @@ -32,7 +32,7 @@ # cache_stale = ["offline", "updating"] # use_background_update = true - # block_ips = var.cdn_block_ips +# block_ips = var.cdn_block_ips # # 50 TB # limit_bandwidth = 50000000000000 @@ -82,7 +82,7 @@ resource "bunnynet_pullzone" "cran_rpkgs_com" { cache_expiration_time = 31919000 websockets_enabled = false - errorpage_whitelabel = true + errorpage_whitelabel = true origin { type = "OriginUrl" @@ -147,6 +147,58 @@ resource "bunnynet_pullzone_hostname" "cran_rpkgs_com" { tls_enabled = true } +# Alliance SwissPass historically used a separate, manually configured pull +# zone. Adopt it so both public repositories use the same B2 origin, middleware +# release and cache behavior. +import { + to = bunnynet_pullzone.cran_allianceswisspass + id = "3265648" +} + +resource "bunnynet_pullzone" "cran_allianceswisspass" { + name = "cran-allianceswisspass" + + cache_errors = false + cache_expiration_time = 31919000 + websockets_enabled = false + errorpage_whitelabel = true + + origin { + type = "OriginUrl" + url = "https://devxy-rpkgs-binaries.s3.eu-central-003.backblazeb2.com" + middleware_script = bunnynet_compute_script.rpkgs_router.id + } + + routing { + filters = [ + "scripting", + ] + } + + s3_auth_enabled = true + s3_auth_key = var.B2_S3_ACCESS_KEY + s3_auth_secret = var.B2_S3_SECRET_KEY + s3_auth_region = "eu-central-003" + + cache_enabled = true + request_coalescing_enabled = true + block_post_requests = true + cache_vary_headers = ["User-Agent"] + + limit_requests = 5000 + limit_connections = 1000 + + safehop_enabled = true + add_canonical_header = true + cache_stale = ["offline", "updating"] + block_ips = var.cdn_block_ips + + # 50 TB + limit_bandwidth = 50000000000000 + + block_root_path = true +} + # resource "bunnynet_storage_zone" "devxy-r-binaries" { # name = "devxy-r-binaries-storage" # region = "DE" diff --git a/edge/rpkgs-router.test.ts b/edge/rpkgs-router.test.ts index 553185d..9493f8a 100644 --- a/edge/rpkgs-router.test.ts +++ b/edge/rpkgs-router.test.ts @@ -117,6 +117,13 @@ Deno.test('rpkgs-router', async (t) => { assertEquals(res.status, 200); }); + await t.step('serves an archived binary when it exists', async () => { + const path = `${SLOT}/Archive/xml2/xml2_1.5.2.tar.gz`; + const res = await probe(path, UA_R45_MUSL); + assertEquals(res.status, 200); + assertEquals(res.location, null); + }); + await t.step('does not redirect a path already under a minor', async () => { const res = await probe(`${SLOT}/4.5/PACKAGES.gz`, UA_R45_MUSL); assertEquals(res.location, null); diff --git a/edge/rpkgs-router.ts b/edge/rpkgs-router.ts index 9cd410b..9278d4a 100644 --- a/edge/rpkgs-router.ts +++ b/edge/rpkgs-router.ts @@ -27,6 +27,7 @@ import * as BunnySDK from 'https://esm.sh/@bunny.net/edgescript-sdk@0.12'; const PUBLIC_CDN_ORIGIN = 'https://cran.rpkgs.com'; const CRAN_ORIGIN = 'https://cran.r-project.org'; +const PUBLIC_CDN_HOSTS = new Set(['cran.rpkgs.com', 'cran.allianceswisspass.devxy.io']); /** Slots ("/", comma separated) whose per-minor index is a union. */ const UNION_SLOTS = new Set( @@ -47,6 +48,10 @@ const INDEX_FILE_REGEX = /^PACKAGES(\.gz|\.rds)?$/; const SRC_CONTRIB_REGEX = /^\/src\/contrib\/(.+)$/; +/** A binary archive URL whose upstream source counterpart CRAN can serve. */ +const ARCHIVE_TARBALL_REGEX = + /^\/(?:amd64|arm64)\/[a-z0-9._-]+\/latest\/src\/contrib\/Archive\/([^/]+)\/([^/]+\.tar\.gz)$/; + const MACOS_BIN_REGEX = /^\/bin\/macosx\/(big-sur-arm64|big-sur-x86_64|monterey-arm64|monterey-x86_64)\/contrib\/([0-9.]+)\/(.+)$/; @@ -85,6 +90,10 @@ function redirectTo(location: string, status = 302): Response { }); } +function publicCdnOrigin(url: URL): string { + return PUBLIC_CDN_HOSTS.has(url.hostname) ? url.origin : PUBLIC_CDN_ORIGIN; +} + function extractRMinor(userAgent: string): string | null { for (const regex of R_MINOR_REGEXES) { const match = userAgent.match(regex); @@ -181,15 +190,14 @@ BunnySDK.net.http const url = new URL(ctx.request.url); const path = normalizePathname(url.pathname); const userAgent = ctx.request.headers.get('User-Agent') || ''; + const publicOrigin = publicCdnOrigin(url); // macOS clients are served from CRAN's own binary tree. const srcContrib = path.match(SRC_CONTRIB_REGEX); if (srcContrib && /darwin/.test(userAgent)) { const mac = parseMacUserAgent(userAgent); if (mac) { - return Promise.resolve( - redirectTo(`${PUBLIC_CDN_ORIGIN}/bin/macosx/${mac.os}/contrib/${mac.rver}/${srcContrib[1]}`), - ); + return Promise.resolve(redirectTo(`${publicOrigin}/bin/macosx/${mac.os}/contrib/${mac.rver}/${srcContrib[1]}`)); } } @@ -213,7 +221,7 @@ BunnySDK.net.http if (target === path) { return Promise.resolve(ctx.request); } - return Promise.resolve(redirectTo(`${PUBLIC_CDN_ORIGIN}${target}`)); + return Promise.resolve(redirectTo(`${publicOrigin}${target}`)); } // The bare `https://cran.rpkgs.com` form, resolved from the User-Agent. @@ -224,12 +232,27 @@ BunnySDK.net.http } const rest = srcContrib ? srcContrib[1] : ''; - return Promise.resolve(redirectTo(`${PUBLIC_CDN_ORIGIN}${contribPath(slot, rest, userAgent)}`)); + return Promise.resolve(redirectTo(`${publicOrigin}${contribPath(slot, rest, userAgent)}`)); } return Promise.resolve(ctx.request); }) - .onOriginResponse((ctx) => { + .onOriginResponse(async (ctx) => { + const path = normalizePathname(new URL(ctx.request.url).pathname); + const archive = path.match(ARCHIVE_TARBALL_REGEX); + + // Binary archives can be incomplete when an older build never succeeded. + // Preserve renv/remotes version restores by falling back to CRAN's source + // package only for an absent archived tarball. A requested version can be + // either archived upstream or still current, so probe the archive first. + // Other 404s remain visible. + if (ctx.response.status === 404 && archive) { + const archiveUrl = `${CRAN_ORIGIN}/src/contrib/Archive/${archive[1]}/${archive[2]}`; + const archiveResponse = await fetch(archiveUrl, { method: 'HEAD' }); + const sourceUrl = archiveResponse.ok ? archiveUrl : `${CRAN_ORIGIN}/src/contrib/${archive[2]}`; + return redirectTo(sourceUrl); + } + ctx.response.headers.append('X-Via', 'MyMiddleware'); return Promise.resolve(ctx.response); }); diff --git a/scripts/purge_cdn_zone.sh b/scripts/purge_cdn_zone.sh index 391a814..4853245 100755 --- a/scripts/purge_cdn_zone.sh +++ b/scripts/purge_cdn_zone.sh @@ -18,35 +18,38 @@ # objects were replaced. The cost is a cold cache for everything else, which is # why this is not used by the daily update path. # -# All hostnames on the zone (cran.devxy.io, cran.allianceswisspass.devxy.io, -# cran.rpkgs.com) share pull zone 3857050, so one purge covers all of them. +# The public hostnames currently use separate pull zones, so callers must pass +# every zone that serves the repository. # # Usage: -# purge_cdn_zone.sh +# purge_cdn_zone.sh [...] # set -euo pipefail if (($# < 2)); then - echo "usage: $0 " >&2 + echo "usage: $0 [...]" >&2 exit 2 fi api_key="$1" -zone_id="$2" +shift -echo "Purging BunnyCDN pull zone ${zone_id}" +for zone_id in "$@"; do + echo "Purging BunnyCDN pull zone ${zone_id}" -status=$( - curl -sS -o /tmp/purge_zone_response.txt -w '%{http_code}' -X POST \ - -H "AccessKey: ${api_key}" \ - -H "Content-Length: 0" \ - "https://api.bunny.net/pullzone/${zone_id}/purgeCache" -) + response_file="/tmp/purge_zone_response_${zone_id}.txt" + status=$( + curl -sS -o "${response_file}" -w '%{http_code}' -X POST \ + -H "AccessKey: ${api_key}" \ + -H "Content-Length: 0" \ + "https://api.bunny.net/pullzone/${zone_id}/purgeCache" + ) -if [[ "${status}" != "200" && "${status}" != "204" ]]; then - echo "Purge of pull zone ${zone_id} failed with HTTP ${status}:" >&2 - cat /tmp/purge_zone_response.txt >&2 - exit 1 -fi + if [[ "${status}" != "200" && "${status}" != "204" ]]; then + echo "Purge of pull zone ${zone_id} failed with HTTP ${status}:" >&2 + cat "${response_file}" >&2 + exit 1 + fi -echo "Purged pull zone ${zone_id} (HTTP ${status})" + echo "Purged pull zone ${zone_id} (HTTP ${status})" +done From 9bded261eecba451d4d544fbde68a68cd1180873 Mon Sep 17 00:00:00 2001 From: pat-s Date: Thu, 13 Aug 2026 14:13:04 +0000 Subject: [PATCH 44/53] fix(cdn): restore Alliance pull-zone hostname (#166) ## Motivation Applying #165 recreated the Alliance SwissPass pull zone without its custom hostname because the hostname association was not represented in OpenTofu. The recreated zone also received a new numeric ID, making the weekly purge configuration stale. ## Changes - Manage `cran.allianceswisspass.devxy.io` as a pull-zone hostname with TLS and forced HTTPS. - Resolve the Alliance pull-zone ID from its hostname before purging instead of persisting a replaceable numeric ID. - Install `jq` in the purge step for the Bunny API lookup. ## Verification - Targeted `prek` hooks pass. - `tofu validate` passes. - `crow lint .crow/` passes. - `just edge-test` passes all 14 routing steps. - `bash -n scripts/purge_cdn_zone.sh` passes. ## Deployment Run `tofu apply` to restore the Alliance hostname on the recreated pull zone. Reviewed-on: https://git.devxy.io/devxy/build-cran-binaries/pulls/166 --- .crow/weekly-rebuild-reindex.yaml | 4 ++-- cdn.tf | 7 ++++++ scripts/purge_cdn_zone.sh | 40 +++++++++++++++++++++++++++---- 3 files changed, 45 insertions(+), 6 deletions(-) diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml index bb00332..250b225 100644 --- a/.crow/weekly-rebuild-reindex.yaml +++ b/.crow/weekly-rebuild-reindex.yaml @@ -175,9 +175,9 @@ steps: from_secret: BUNNYNET_API_KEY # cran.rpkgs.com and cran.allianceswisspass.devxy.io are on separate # Bunny pull zones, so both must be purged after the shared origin changes. - BUNNY_PULLZONES: '3857050 3265648' + BUNNY_PULLZONES: '3857050 cran.allianceswisspass.devxy.io' commands: - - apk add --no-cache -q bash curl + - apk add --no-cache -q bash curl jq # Crow carries the checkout from the re-index step into this step. - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" $BUNNY_PULLZONES # Runs on every row rather than on one designated slot: a cron fires only diff --git a/cdn.tf b/cdn.tf index 01191a5..96877b2 100644 --- a/cdn.tf +++ b/cdn.tf @@ -199,6 +199,13 @@ resource "bunnynet_pullzone" "cran_allianceswisspass" { block_root_path = true } +resource "bunnynet_pullzone_hostname" "cran_allianceswisspass" { + pullzone = bunnynet_pullzone.cran_allianceswisspass.id + name = "cran.allianceswisspass.devxy.io" + force_ssl = true + tls_enabled = true +} + # resource "bunnynet_storage_zone" "devxy-r-binaries" { # name = "devxy-r-binaries-storage" # region = "DE" diff --git a/scripts/purge_cdn_zone.sh b/scripts/purge_cdn_zone.sh index 4853245..648dfc3 100755 --- a/scripts/purge_cdn_zone.sh +++ b/scripts/purge_cdn_zone.sh @@ -19,22 +19,54 @@ # why this is not used by the daily update path. # # The public hostnames currently use separate pull zones, so callers must pass -# every zone that serves the repository. +# every zone that serves the repository. A zone can be identified by its +# numeric ID or by one of its hostnames; hostname lookup avoids persisting IDs +# that change when a zone is recreated. # # Usage: -# purge_cdn_zone.sh [...] +# purge_cdn_zone.sh [...] # set -euo pipefail if (($# < 2)); then - echo "usage: $0 [...]" >&2 + echo "usage: $0 [...]" >&2 exit 2 fi api_key="$1" shift -for zone_id in "$@"; do +resolve_zone_id() { + local zone="$1" + local response_file + local zone_id + + if [[ "${zone}" =~ ^[0-9]+$ ]]; then + echo "${zone}" + return + fi + + response_file=$(mktemp) + curl -sS -o "${response_file}" \ + -H "AccessKey: ${api_key}" \ + "https://api.bunny.net/pullzone" + zone_id=$( + jq -r --arg hostname "${zone}" \ + '(.Items // .)[] | select(any(.Hostnames[]?; .Value == $hostname)) | .Id' \ + "${response_file}" + ) + rm -f "${response_file}" + + if [[ -z "${zone_id}" ]]; then + echo "Could not find BunnyCDN pull zone for hostname ${zone}" >&2 + exit 1 + fi + + echo "${zone_id}" +} + +for zone in "$@"; do + zone_id=$(resolve_zone_id "${zone}") echo "Purging BunnyCDN pull zone ${zone_id}" response_file="/tmp/purge_zone_response_${zone_id}.txt" From 706fd10d79206ed2784cd7f6bbac1a5e897e390b Mon Sep 17 00:00:00 2001 From: automation-bot Date: Fri, 14 Aug 2026 00:32:00 +0000 Subject: [PATCH 45/53] chore(deps): update terraform bunnynet to ~> 0.18 --- .terraform.lock.hcl | 72 ++++++++++++++++++++++----------------------- provider.tf | 2 +- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index aca8ce1..a21cf43 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -38,43 +38,43 @@ provider "registry.opentofu.org/hashicorp/http" { } provider "registry.terraform.io/bunnyway/bunnynet" { - version = "0.17.0" - constraints = "~> 0.17" + version = "0.18.0" + constraints = "~> 0.18" hashes = [ - "h1:+qDt35lVSK7acw6a1xHuPYrqmZEcHSmtd+6n1TxNuYw=", - "h1:1dCu2l4DhPBjizVAH/WwAjT1Xbo52K4PMvHoD5zUhuU=", - "h1:Dvn46Auwuel4jqrqZXs2D7kdujNhs17LEmqhuY0k4/4=", - "h1:M5eDL3m2uSEr1XATJW0foHzKl8pFhCtgKuOM24bJRwU=", - "h1:PddaC7nM/gY4x9i3xy6TxOs9MAu2/6g58Xs/gv4DRV8=", - "h1:QVIKiZluI+NQAKu8NpFBl3Nvyx+d81vW9btEUdIQREc=", - "h1:S6TnzXHsRoGYvC1vJBkDiVEc0spceksY4n6x5WN5iYw=", - "h1:VcxZDWqCWMSjcUsC1K4sB6uYEoeoou+BC0ePoJXmf3A=", - "h1:W0y/agBVqls1cJlFGFYMu2VnqoPXFzxVHPIYe3OqfYQ=", - "h1:XmNd5fP9a0O77ve5BMQP2vARExgIa7rYl6KvyUYXPSs=", - "h1:e0EFKrWSQwaa/kGhnha4DXk4T68Av8QxP84mRSdWC9M=", - "h1:eM+/lUiU0pNSgQKoqKPgE3xJrJ0MHIpKG+yhaGB/P0M=", - "h1:fPWWA4T0/y7GX+tCGN23l1jODhZ3uCdR/MKgZDXYpAE=", - "h1:g+r2GVi4gVC4DuQg3PL70gW9BDskgWUzCBIMXTUq63A=", - "h1:gaZ8eALDtVHqykVDHav8004gHiMGaYR/3KwET0FUgao=", - "h1:kbqW25eaiv4N/N/z+sxLdJZ15yh5cgnRD/q6RclPMLc=", - "h1:rGjxue3mXRyQQqpywTXC4zK//JAtf0Cz7RP+uPMMJjw=", - "zh:05943fef14c2028f4722bf078aa1889229e94302f7678cc6f63adb669d8ea612", - "zh:26a163930a92a7408f7bbd0130064b84df8a232b500d8c6c3989952986308539", - "zh:41305feaaade55391447521ec309f3c038b631ca542907ad95132fab71a7e116", - "zh:606919a930f0299948504adbdcd0f239a8af5c418f85741c48f8add370a3d038", - "zh:66963d5b445639511939fc508513fd31da3ee1d4ee1a565ee396c9532897a349", - "zh:6c981ec0c8545556395c43e2511861ab65ee9ecf2a960480e7889c3af0d23af3", - "zh:7334a1bdb726ce1f1bf0a3155f30f84f65206980c229c832ff5f0b0718c44e0b", - "zh:75f6c86bf74511e605423332d113711c76c8028361a32282fb3359d6c7ecae9e", - "zh:7aebb1a01cfe8be54903853202ae06eba14ad99c37d230ed93ce7d6633e05e9b", + "h1:+6VXZmSSeIchab8WY+UFZxaXu6poxZbiJenYwog+Z2M=", + "h1:Bz94gADR83NmrsZC50LheryVcS9erG6tF052hNPqz0U=", + "h1:FGkcn6ieyNPr56Riv75IsCa6okZ9ZHqqFd08Y4i5cPI=", + "h1:GqPjTKaOlhhNIxpPHWJpWdGkEtvUDtuOkjYbVIInfgU=", + "h1:NMDWYRisSFwepjfYsf4MrcyP7Ihjlty937l1BW1Cztg=", + "h1:OusNMAZdIIbxWwHXwH8tYzdbXZPRS8dW7cncSYcHfNI=", + "h1:OzgasS4oZCZjYAOrqGy7RpPNbTPX5wGaaw7TDnasSJM=", + "h1:RyK3DC7cM4T2I83OvnO+UXU+eCXLG5vDlYZ/bWKHq7g=", + "h1:U/JKg4BNWii2mK3bNsOWYMBTpkXqGsWb1ypSJvSKl9Y=", + "h1:UjSUm1AU2wZ8eyC3LDRwWatW9cKD/I0rk7MOeUDDkWc=", + "h1:a888ExTeqWKxaB2GBsDIRSm8jOOMLkPFcABrJxxA8qc=", + "h1:aShYLfSapfo1Ozy33zL5WfmYt5UF2m5EziespPOGNAk=", + "h1:bHdpp2ecmvDoezqg8TirE32SnuDb108/NZ4xBGvJy98=", + "h1:lLYZN5cetXgLPJjo+eR+kwodOYGsQetzV6bg5Ki58tk=", + "h1:szi71DaqI4yB6fI55hBbtVZg1GDWJVkO9+WF/1sZ+IE=", + "h1:vK4jZYZZhD6M4cRmX+171mxoJgb2FSNiBNAUhtm/TNs=", + "h1:yNnSUskn43648XU/YS0e9NUdoHImo7pFMIlBzujBoxY=", + "zh:0c3adf039df2fead1e36b8e7887d965223f03b6b5cdd921ec0c98beaa04fdec0", + "zh:12a3db29733e6619e216fac9aa774cbf67da2105f48c5c4dee8df046d69656fa", + "zh:1330b83c949165434e4d0db5e097a1741376cdb66c06c37b2a97ecea8e06b0f0", + "zh:186113259ab0f80ab9079f0a8a810e93ee097f6740100a0a444f805e8772c12e", + "zh:242fe10185da8a700b0e9a6a52e3d1f6592e8e189aaf5e9a79cf515ad5c7ff25", + "zh:28b005b0aa9485c492326fbb4287d3cb465f25a8d572b8c740e041e040d80aa2", + "zh:3b2cd0daa767dfff67dd39c98d1c82b25e70eb81df77c0d6dd762a0dedec16e1", + "zh:3f14b244740f6c6420d298846708e9f3853c8eda685d3a4d71fb0ffec021ad9c", + "zh:469bfd08deefd90e89c930e5e45bfd06a58a1eadb85dfbee9fc48ae296e8a8c9", + "zh:634d96b84b2e77d25baa074c357e831252c8b8114926ef72e1afb68a4bc9eb65", + "zh:6e837b9485e56f84b5e2bb396fa549b628b8e075257fa01bf8c796ce91d20e58", "zh:890df766e9b839623b1f0437355032a3c006226a6c200cd911e15ee1a9014e9f", - "zh:9041d0e20c9ceea532de6eebf5cb3a27dad0bb49d3f5b5154be2a08d68fbbf1f", - "zh:a6bbf65431a02be4df0ebb1cbe01185ad357ff6e33c01bd0558f59bed90c8f36", - "zh:c6d075a31096f080c388dfe46036f451c0cc114c3311a4f46ab8dbe1938a202f", - "zh:dd8703f7b55b8bc8e10f8718bea889781100b18e932b04898995b63178c3d36e", - "zh:dd92a5cd4e133a4000e7e5bc8cce876ae0ed803543cedd2f3d590661ba244d04", - "zh:e024fdf121bebc48c1e6debea344c6d4f174117f3ae605fca6e13b9705d92d22", - "zh:ee0e80c31b438e35fa1608f6a2f5824d2806db1e5e8b9f7a90986585c7bcb895", - "zh:fc2d4b705411b48f8c045981f9368a3ea2f74969dd6302008c31ff0bedd51f0a", + "zh:89e02979311e6727a50586b04cb343e9bbec74a6f4d1dba9352971e4334d64c9", + "zh:a6796143fe61ae52d236b7ea96bddbc6317851a0e2117eb2f55cd73c803b4b6f", + "zh:ad2542160e7b57ee8a016cddbf1d32663baf74fe30fcf24df64da75cb13128b0", + "zh:bfee81c153e8b50121fd58eedeeb84bfa64a3d17f23900e35143c4a86474cbd2", + "zh:eeba652697908712cd1ce2c7d2925f6e6bb2d18ea5d3e6ca185e88eeb80f3c80", + "zh:f0b5b8fd6942647c358440591d56a5cb82fda92f7866898654a66ec901174f1f", ] } diff --git a/provider.tf b/provider.tf index badbbc1..d4f2564 100644 --- a/provider.tf +++ b/provider.tf @@ -2,7 +2,7 @@ terraform { required_providers { bunnynet = { source = "registry.terraform.io/BunnyWay/bunnynet" - version = "~> 0.17" + version = "~> 0.18" } } } From 132d1d2d3cd37611db98733a57d8345a218e152b Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 14 Aug 2026 06:44:10 +0000 Subject: [PATCH 46/53] docs(ci): clarify parallel manual matrix runs --- .crow/process-updates.yaml | 6 +++--- .crow/weekly-audit-missing.yaml | 6 +++--- .crow/weekly-rebuild-missing.yaml | 8 ++++---- .crow/weekly-rebuild-reindex.yaml | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.crow/process-updates.yaml b/.crow/process-updates.yaml index 7600876..021d6cb 100644 --- a/.crow/process-updates.yaml +++ b/.crow/process-updates.yaml @@ -3,15 +3,15 @@ # Routing is preserved 1:1: # - cron: each existing `process-cran-updates--` cron fires only # its matching matrix row (via the per-row `cron:` name filter). -# - manual: pick a target from the `process_cran_updates` dropdown -# ("all" = every os/arch). +# - manual: pick a target from the `process_cran_updates` dropdown; +# "all" fans out every os/arch as parallel matrix workflows. # Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64). variables: # Gates this pipeline. A manual pipeline creation instantiates every file in # .crow/, and a declared default is applied even when the run never passed # this variable, so the default must be a value that matches no matrix row. process_cran_updates: - description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." + description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." options: - none - all diff --git a/.crow/weekly-audit-missing.yaml b/.crow/weekly-audit-missing.yaml index 3a9d98f..428aa04 100644 --- a/.crow/weekly-audit-missing.yaml +++ b/.crow/weekly-audit-missing.yaml @@ -3,15 +3,15 @@ # Routing is preserved 1:1: # - cron: each existing `weekly-audit-missing--` cron fires only # its matching matrix row (via the per-row `cron:` name filter). -# - manual: pick a target from the `weekly_audit_missing` dropdown -# ("all" = every os/arch). +# - manual: pick a target from the `weekly_audit_missing` dropdown; +# "all" fans out every os/arch as parallel matrix workflows. # Arch placement is via the group label (rpkgs-amd64, rpkgs-arm64). variables: # Gates this pipeline. A manual pipeline creation instantiates every file in # .crow/, and a declared default is applied even when the run never passed # this variable, so the default must be a value that matches no matrix row. weekly_audit_missing: - description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." + description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." options: - none - all diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index 5afb3c3..9639792 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -4,9 +4,9 @@ # - cron: each existing `weekly-rebuild-missing--` cron fires only # its matching matrix rows (via the per-row `cron:` name filter), # which is now all three shards of that slot. -# - manual: `weekly_rebuild_missing` dropdown, default "all" (matches the -# previous bare manual trigger that ran every os/arch); pick a -# single - to run just one. +# - manual: pick a target from the `weekly_rebuild_missing` dropdown; +# "all" fans out every os/arch and shard as parallel matrix +# workflows, while a single - runs its three shards. # Arch placement is handled by the group label (rpkgs-amd64, rpkgs-arm64). # # The shard picks up its own slice and re-derives what is still outstanding @@ -21,7 +21,7 @@ variables: # .crow/, and a declared default is applied even when the run never passed # this variable, so the default must be a value that matches no matrix row. weekly_rebuild_missing: - description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." + description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." options: - none - all diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml index 250b225..2e0f2a0 100644 --- a/.crow/weekly-rebuild-reindex.yaml +++ b/.crow/weekly-rebuild-reindex.yaml @@ -16,7 +16,7 @@ variables: # exactly the slots it rebuilt. A manual pipeline creation instantiates every # file in .crow/, so the default must match no matrix row. weekly_rebuild_missing: - description: "Manual run target: a specific -, 'all' for every os/arch, or 'none' to run nothing." + description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." options: - none - all From b75fd2f1c43cf0355e3e2eb9e51d73f16a1321eb Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 14 Aug 2026 06:56:41 +0000 Subject: [PATCH 47/53] fix(ci): split oversized weekly rebuild matrix --- .crow/weekly-rebuild-missing-ubuntu-2604.yaml | 140 ++++++++++++++++++ .crow/weekly-rebuild-missing.yaml | 41 +---- .crow/weekly-rebuild-reindex-ubuntu-2604.yaml | 110 ++++++++++++++ .crow/weekly-rebuild-reindex.yaml | 9 -- 4 files changed, 253 insertions(+), 47 deletions(-) create mode 100644 .crow/weekly-rebuild-missing-ubuntu-2604.yaml create mode 100644 .crow/weekly-rebuild-reindex-ubuntu-2604.yaml diff --git a/.crow/weekly-rebuild-missing-ubuntu-2604.yaml b/.crow/weekly-rebuild-missing-ubuntu-2604.yaml new file mode 100644 index 0000000..0082e0e --- /dev/null +++ b/.crow/weekly-rebuild-missing-ubuntu-2604.yaml @@ -0,0 +1,140 @@ +# ubuntu-2604 rows split from weekly-rebuild-missing.yaml. +# +# The complete rebuild matrix has 54 permutations, while Crow accepts at most +# 50 per workflow. Keeping these six rows in a companion workflow lets a manual +# "all" run fan out every slot and shard without exceeding that compiler limit. + +variables: + # This is the same gate as the main rebuild workflow. The safe default must + # match no row because every file in .crow/ is evaluated on a manual run. + weekly_rebuild_missing: + description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." + options: + - none + - all + - alpine-322-amd64 + - alpine-322-arm64 + - alpine-323-amd64 + - alpine-323-arm64 + - alpine-324-amd64 + - alpine-324-arm64 + - redhat-8-amd64 + - redhat-8-arm64 + - redhat-9-amd64 + - redhat-9-arm64 + - redhat-10-amd64 + - redhat-10-arm64 + - ubuntu-2204-amd64 + - ubuntu-2204-arm64 + - ubuntu-2404-amd64 + - ubuntu-2404-arm64 + - ubuntu-2604-amd64 + - ubuntu-2604-arm64 + default: none + +when: + - event: cron + cron: weekly-rebuild-missing-${OS}-${ARCH} + - event: manual + evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"' + +skip_clone: true + +labels: + group: rpkgs-${ARCH} + +matrix: + include: + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 3 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 3 + +steps: + - name: 'Rebuild missing binaries' + image: reg.devxy.io/rpkgs/build-env-${IMG} + pull: true + environment: + OTEL_R_TRACES_EXPORTER: none + OTEL_R_LOGS_EXPORTER: none + OTEL_R_METRICS_EXPORTER: none + RED_HAT_DEV_PW: + from_secret: RED_HAT_DEV_PW + B2_S3_ACCESS_KEY: + from_secret: B2_S3_ACCESS_KEY + B2_S3_SECRET_KEY: + from_secret: B2_S3_SECRET_KEY + PGPASS: + from_secret: PGPASS + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + GITHUB_PAT: + from_secret: GITHUB_PAT + FORGEJO_TOKEN: + from_secret: FORGEJO_TOKEN + GIT_USER: pat-s + UVR_CACHE_DIR: /mnt/cache/uvr/cache + UVR_PACKAGES_DIR: /mnt/cache/uvr/packages + R_LIBS_USER: /mnt/cache/R-pkgs + R_VERSION: ${R_VERSION} + CCACHE_DIR: /mnt/cache/ccache + PLATFORM: ${OS} + ARCH: ${ARCH} + NCPUS: 2 + SPLIT_INTO: ${SPLIT_INTO} + SPLIT_INDEX: ${SPLIT_INDEX} + # Wall clock after which the shard stops cleanly instead of having to be + # killed. A kill matches neither `success` nor `failure`, so it would skip + # the dependent re-index and leave rebuilt binaries behind a stale edge. + REBUILD_BUDGET_HOURS: 20 + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages + - rm -rf /mnt/cache/R-pkgs/00LOCK-* + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' + - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 + - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")' + - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1 + backend_options: + docker: + resources: + requests: + memory: 5Gi + cpu: 3000m + limits: + memory: 18Gi + cpu: 3000m diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index 9639792..aeb2f50 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -1,5 +1,7 @@ -# Consolidated weekly-rebuild-missing pipeline (all platforms, both arches). +# Main weekly-rebuild-missing workflow (all slots except ubuntu-2604). # Three matrix rows per OS/arch, one per shard of that slot's rebuild list. +# ubuntu-2604 lives in weekly-rebuild-missing-ubuntu-2604.yaml so a manual +# "all" run stays below Crow's 50-permutation matrix limit. # Routing is preserved 1:1: # - cron: each existing `weekly-rebuild-missing--` cron fires only # its matching matrix rows (via the per-row `cron:` name filter), @@ -346,43 +348,6 @@ matrix: IMG: ubuntu:noble SPLIT_INTO: 3 SPLIT_INDEX: 3 - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 1 - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 2 - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 3 - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 1 - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 2 - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 3 - steps: - name: 'Rebuild missing binaries' image: reg.devxy.io/rpkgs/build-env-${IMG} diff --git a/.crow/weekly-rebuild-reindex-ubuntu-2604.yaml b/.crow/weekly-rebuild-reindex-ubuntu-2604.yaml new file mode 100644 index 0000000..3ab086a --- /dev/null +++ b/.crow/weekly-rebuild-reindex-ubuntu-2604.yaml @@ -0,0 +1,110 @@ +# Re-index ubuntu-2604 after its split rebuild workflow finishes. + +variables: + # Mirrors the shared rebuild gate. The default must match no matrix row so + # unrelated manual runs do not rewrite package indexes. + weekly_rebuild_missing: + description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." + options: + - none + - all + - alpine-322-amd64 + - alpine-322-arm64 + - alpine-323-amd64 + - alpine-323-arm64 + - alpine-324-amd64 + - alpine-324-arm64 + - redhat-8-amd64 + - redhat-8-arm64 + - redhat-9-amd64 + - redhat-9-arm64 + - redhat-10-amd64 + - redhat-10-arm64 + - ubuntu-2204-amd64 + - ubuntu-2204-arm64 + - ubuntu-2404-amd64 + - ubuntu-2404-arm64 + - ubuntu-2604-amd64 + - ubuntu-2604-arm64 + default: none + +when: + - event: cron + cron: weekly-rebuild-missing-${OS}-${ARCH} + - event: manual + evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"' + +depends_on: + - weekly-rebuild-missing-ubuntu-2604 + +runs_on: [success, failure] + +skip_clone: true + +labels: + group: rpkgs-${ARCH} + +matrix: + include: + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + +steps: + - name: 'Re-index the slot' + image: reg.devxy.io/rpkgs/build-env-${IMG} + pull: true + environment: + OTEL_R_TRACES_EXPORTER: none + OTEL_R_LOGS_EXPORTER: none + OTEL_R_METRICS_EXPORTER: none + RED_HAT_DEV_PW: + from_secret: RED_HAT_DEV_PW + B2_S3_ACCESS_KEY: + from_secret: B2_S3_ACCESS_KEY + B2_S3_SECRET_KEY: + from_secret: B2_S3_SECRET_KEY + REPO_RO_TOKEN: + from_secret: REPO_RO_TOKEN + GIT_USER: pat-s + R_LIBS_USER: /mnt/cache/R-pkgs + R_VERSION: ${R_VERSION} + PLATFORM: ${OS} + ARCH: ${ARCH} + commands: + - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . + - mkdir -p /mnt/cache/R-pkgs + - rm -rf /mnt/cache/R-pkgs/00LOCK-* + - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + # The codename is detected from the image's /etc/os-release. + - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))' + - | + for RBIN in /opt/R/[0-9]*/bin/R; do + RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) + /opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true + done + + - name: Purge CDN cache + image: reg.devxy.io/docker.io/library/alpine:3.24 + environment: + OTEL_R_TRACES_EXPORTER: none + OTEL_R_LOGS_EXPORTER: none + OTEL_R_METRICS_EXPORTER: none + BUNNYNET_API_KEY: + from_secret: BUNNYNET_API_KEY + # cran.rpkgs.com and cran.allianceswisspass.devxy.io are on separate + # Bunny pull zones, so both must be purged after the shared origin changes. + BUNNY_PULLZONES: '3857050 cran.allianceswisspass.devxy.io' + commands: + - apk add --no-cache -q bash curl jq + # Crow carries the checkout from the re-index step into this step. + - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" $BUNNY_PULLZONES + # Run even when the re-index above failed: the objects were still replaced, + # and a stale edge is exactly what keeps them hidden. + when: + - status: [success, failure] diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml index 2e0f2a0..f38f6d5 100644 --- a/.crow/weekly-rebuild-reindex.yaml +++ b/.crow/weekly-rebuild-reindex.yaml @@ -122,15 +122,6 @@ matrix: ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:noble - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - steps: - name: 'Re-index the slot' image: reg.devxy.io/rpkgs/build-env-${IMG} From 50495f5c3bb6e3e97d9d42d639c5f9828b6207b6 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 14 Aug 2026 07:01:56 +0000 Subject: [PATCH 48/53] Revert "fix(ci): split oversized weekly rebuild matrix" This reverts commit b75fd2f1c43cf0355e3e2eb9e51d73f16a1321eb. --- .crow/weekly-rebuild-missing-ubuntu-2604.yaml | 140 ------------------ .crow/weekly-rebuild-missing.yaml | 41 ++++- .crow/weekly-rebuild-reindex-ubuntu-2604.yaml | 110 -------------- .crow/weekly-rebuild-reindex.yaml | 9 ++ 4 files changed, 47 insertions(+), 253 deletions(-) delete mode 100644 .crow/weekly-rebuild-missing-ubuntu-2604.yaml delete mode 100644 .crow/weekly-rebuild-reindex-ubuntu-2604.yaml diff --git a/.crow/weekly-rebuild-missing-ubuntu-2604.yaml b/.crow/weekly-rebuild-missing-ubuntu-2604.yaml deleted file mode 100644 index 0082e0e..0000000 --- a/.crow/weekly-rebuild-missing-ubuntu-2604.yaml +++ /dev/null @@ -1,140 +0,0 @@ -# ubuntu-2604 rows split from weekly-rebuild-missing.yaml. -# -# The complete rebuild matrix has 54 permutations, while Crow accepts at most -# 50 per workflow. Keeping these six rows in a companion workflow lets a manual -# "all" run fan out every slot and shard without exceeding that compiler limit. - -variables: - # This is the same gate as the main rebuild workflow. The safe default must - # match no row because every file in .crow/ is evaluated on a manual run. - weekly_rebuild_missing: - description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." - options: - - none - - all - - alpine-322-amd64 - - alpine-322-arm64 - - alpine-323-amd64 - - alpine-323-arm64 - - alpine-324-amd64 - - alpine-324-arm64 - - redhat-8-amd64 - - redhat-8-arm64 - - redhat-9-amd64 - - redhat-9-arm64 - - redhat-10-amd64 - - redhat-10-arm64 - - ubuntu-2204-amd64 - - ubuntu-2204-arm64 - - ubuntu-2404-amd64 - - ubuntu-2404-arm64 - - ubuntu-2604-amd64 - - ubuntu-2604-arm64 - default: none - -when: - - event: cron - cron: weekly-rebuild-missing-${OS}-${ARCH} - - event: manual - evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"' - -skip_clone: true - -labels: - group: rpkgs-${ARCH} - -matrix: - include: - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 1 - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 2 - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 3 - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 1 - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 2 - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - SPLIT_INTO: 3 - SPLIT_INDEX: 3 - -steps: - - name: 'Rebuild missing binaries' - image: reg.devxy.io/rpkgs/build-env-${IMG} - pull: true - environment: - OTEL_R_TRACES_EXPORTER: none - OTEL_R_LOGS_EXPORTER: none - OTEL_R_METRICS_EXPORTER: none - RED_HAT_DEV_PW: - from_secret: RED_HAT_DEV_PW - B2_S3_ACCESS_KEY: - from_secret: B2_S3_ACCESS_KEY - B2_S3_SECRET_KEY: - from_secret: B2_S3_SECRET_KEY - PGPASS: - from_secret: PGPASS - REPO_RO_TOKEN: - from_secret: REPO_RO_TOKEN - GITHUB_PAT: - from_secret: GITHUB_PAT - FORGEJO_TOKEN: - from_secret: FORGEJO_TOKEN - GIT_USER: pat-s - UVR_CACHE_DIR: /mnt/cache/uvr/cache - UVR_PACKAGES_DIR: /mnt/cache/uvr/packages - R_LIBS_USER: /mnt/cache/R-pkgs - R_VERSION: ${R_VERSION} - CCACHE_DIR: /mnt/cache/ccache - PLATFORM: ${OS} - ARCH: ${ARCH} - NCPUS: 2 - SPLIT_INTO: ${SPLIT_INTO} - SPLIT_INDEX: ${SPLIT_INDEX} - # Wall clock after which the shard stops cleanly instead of having to be - # killed. A kill matches neither `success` nor `failure`, so it would skip - # the dependent re-index and leave rebuilt binaries behind a stale edge. - REBUILD_BUDGET_HOURS: 20 - commands: - - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R - - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' - - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi - - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh httr2 - - /opt/R/$R_VERSION/bin/R -q -e 'source("local/fetch-rebuild-packages-from-issue.R")' - - $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- /opt/R/$R_VERSION/bin/Rscript local/rebuild-missing.R $SPLIT_INTO $SPLIT_INDEX $REBUILD_BUDGET_HOURS 2>&1 - backend_options: - docker: - resources: - requests: - memory: 5Gi - cpu: 3000m - limits: - memory: 18Gi - cpu: 3000m diff --git a/.crow/weekly-rebuild-missing.yaml b/.crow/weekly-rebuild-missing.yaml index aeb2f50..9639792 100644 --- a/.crow/weekly-rebuild-missing.yaml +++ b/.crow/weekly-rebuild-missing.yaml @@ -1,7 +1,5 @@ -# Main weekly-rebuild-missing workflow (all slots except ubuntu-2604). +# Consolidated weekly-rebuild-missing pipeline (all platforms, both arches). # Three matrix rows per OS/arch, one per shard of that slot's rebuild list. -# ubuntu-2604 lives in weekly-rebuild-missing-ubuntu-2604.yaml so a manual -# "all" run stays below Crow's 50-permutation matrix limit. # Routing is preserved 1:1: # - cron: each existing `weekly-rebuild-missing--` cron fires only # its matching matrix rows (via the per-row `cron:` name filter), @@ -348,6 +346,43 @@ matrix: IMG: ubuntu:noble SPLIT_INTO: 3 SPLIT_INDEX: 3 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 3 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 1 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 2 + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + SPLIT_INTO: 3 + SPLIT_INDEX: 3 + steps: - name: 'Rebuild missing binaries' image: reg.devxy.io/rpkgs/build-env-${IMG} diff --git a/.crow/weekly-rebuild-reindex-ubuntu-2604.yaml b/.crow/weekly-rebuild-reindex-ubuntu-2604.yaml deleted file mode 100644 index 3ab086a..0000000 --- a/.crow/weekly-rebuild-reindex-ubuntu-2604.yaml +++ /dev/null @@ -1,110 +0,0 @@ -# Re-index ubuntu-2604 after its split rebuild workflow finishes. - -variables: - # Mirrors the shared rebuild gate. The default must match no matrix row so - # unrelated manual runs do not rewrite package indexes. - weekly_rebuild_missing: - description: "Manual run target: a specific -, 'all' to run every os/arch in parallel, or 'none' to run nothing." - options: - - none - - all - - alpine-322-amd64 - - alpine-322-arm64 - - alpine-323-amd64 - - alpine-323-arm64 - - alpine-324-amd64 - - alpine-324-arm64 - - redhat-8-amd64 - - redhat-8-arm64 - - redhat-9-amd64 - - redhat-9-arm64 - - redhat-10-amd64 - - redhat-10-arm64 - - ubuntu-2204-amd64 - - ubuntu-2204-arm64 - - ubuntu-2404-amd64 - - ubuntu-2404-arm64 - - ubuntu-2604-amd64 - - ubuntu-2604-arm64 - default: none - -when: - - event: cron - cron: weekly-rebuild-missing-${OS}-${ARCH} - - event: manual - evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"' - -depends_on: - - weekly-rebuild-missing-ubuntu-2604 - -runs_on: [success, failure] - -skip_clone: true - -labels: - group: rpkgs-${ARCH} - -matrix: - include: - - OS: ubuntu-2604 - ARCH: amd64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - - OS: ubuntu-2604 - ARCH: arm64 - R_VERSION: 4.4.3 - IMG: ubuntu:resolute - -steps: - - name: 'Re-index the slot' - image: reg.devxy.io/rpkgs/build-env-${IMG} - pull: true - environment: - OTEL_R_TRACES_EXPORTER: none - OTEL_R_LOGS_EXPORTER: none - OTEL_R_METRICS_EXPORTER: none - RED_HAT_DEV_PW: - from_secret: RED_HAT_DEV_PW - B2_S3_ACCESS_KEY: - from_secret: B2_S3_ACCESS_KEY - B2_S3_SECRET_KEY: - from_secret: B2_S3_SECRET_KEY - REPO_RO_TOKEN: - from_secret: REPO_RO_TOKEN - GIT_USER: pat-s - R_LIBS_USER: /mnt/cache/R-pkgs - R_VERSION: ${R_VERSION} - PLATFORM: ${OS} - ARCH: ${ARCH} - commands: - - git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git . - - mkdir -p /mnt/cache/R-pkgs - - rm -rf /mnt/cache/R-pkgs/00LOCK-* - - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R - # The codename is detected from the image's /etc/os-release. - - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))' - - | - for RBIN in /opt/R/[0-9]*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - /opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" || true - done - - - name: Purge CDN cache - image: reg.devxy.io/docker.io/library/alpine:3.24 - environment: - OTEL_R_TRACES_EXPORTER: none - OTEL_R_LOGS_EXPORTER: none - OTEL_R_METRICS_EXPORTER: none - BUNNYNET_API_KEY: - from_secret: BUNNYNET_API_KEY - # cran.rpkgs.com and cran.allianceswisspass.devxy.io are on separate - # Bunny pull zones, so both must be purged after the shared origin changes. - BUNNY_PULLZONES: '3857050 cran.allianceswisspass.devxy.io' - commands: - - apk add --no-cache -q bash curl jq - # Crow carries the checkout from the re-index step into this step. - - bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" $BUNNY_PULLZONES - # Run even when the re-index above failed: the objects were still replaced, - # and a stale edge is exactly what keeps them hidden. - when: - - status: [success, failure] diff --git a/.crow/weekly-rebuild-reindex.yaml b/.crow/weekly-rebuild-reindex.yaml index f38f6d5..2e0f2a0 100644 --- a/.crow/weekly-rebuild-reindex.yaml +++ b/.crow/weekly-rebuild-reindex.yaml @@ -122,6 +122,15 @@ matrix: ARCH: arm64 R_VERSION: 4.4.3 IMG: ubuntu:noble + - OS: ubuntu-2604 + ARCH: amd64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + - OS: ubuntu-2604 + ARCH: arm64 + R_VERSION: 4.4.3 + IMG: ubuntu:resolute + steps: - name: 'Re-index the slot' image: reg.devxy.io/rpkgs/build-env-${IMG} From c7b4dca6e2209c1b56932f37843ef586497fe4e9 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Mon, 17 Aug 2026 00:31:56 +0000 Subject: [PATCH 49/53] chore(deps): lock file maintenance --- .terraform.lock.hcl | 62 ++++++++++++++++++++++----------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index a21cf43..ff935fa 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -2,38 +2,38 @@ # Manual edits may be lost in future updates. provider "registry.opentofu.org/hashicorp/http" { - version = "3.6.0" + version = "3.6.1" hashes = [ - "h1:0n4RBz9zNw6TTddh5+x7E8L2+qzPXNwKhK4uoZ/DUwE=", - "h1:22Ob7lpzMBSqdrCvoFN5EgmhGPHPBovV/9qo0c/Cd+A=", - "h1:2IRBvmWOYrq/ooaYYn2i86jZb7iIUvlg0KlmOMfDHoQ=", - "h1:5mucXikk4OcW3un3u94QnMx4AB4Wfih+sXeMd5QxSNk=", - "h1:5oU7Zm+2gAVGmxqtJ9E8uTudUkYy/DEn/y3IWphdv4k=", - "h1:5w0R4b1/VSzpqQF1tXXPr/qmaQLPVRXamOmPKWFcTk4=", - "h1:AEVeJr8xGmwad+JUUQ833C3x5d4W+W2szF5DfwxYppw=", - "h1:CPHJ+0zQbS/cX1m55Y90jIOgf1jV3ocUUnqsXAh+9Eg=", - "h1:JPewnGDOJudNer5+ghqwXoaJkfot3QRq9uiEYvo+JHU=", - "h1:QzbluV2vQLxsJYxjpziQCmPndIoJ/UGS4/UHH/GpwUM=", - "h1:TjUNbUdqweRBq/ycQ4ixpNkx5qaYwpXEOn9QCpqNZP8=", - "h1:XNbcODP60ajj21N/OO7af8bBg1ltIsYkq9egn7BYbiY=", - "h1:tgrbgmX7WYQz9G9ncgu7TkpVB+RlLjJA/Rvp9KPlZH8=", - "h1:vLxthX/ZWsOZ+aHKbAMqmNKqD0K5f4nJ8ppy0Ioyup0=", - "h1:wZOdGBAZkY8OKEPjKz82j1HloAKOmmvtjWyTxM+I110=", - "zh:0f719fa5426bc883e9fa6abf7f6498e48025edafbc29015e2f5c028f1cca3b9d", - "zh:1b4d7dafefd6c61764b2f9ed6943ceb9a200dee3590d18747e3a5f6b20ce85e0", - "zh:1d23a712984866d29f7b07028a4e99c783c71f1a5dddf08bc3d4e7da9d91a1fa", - "zh:257d23d58c3bb024b6bc8eb88736eaf912e934ad47c639d0c3c742bddda849a1", - "zh:479860e1a5468f5e04013b9364c9496d7ed0804bf9a1acd8e07558d57609993d", - "zh:4cb5e681bf599b411b27c4a2c4066a5fb2ed79aaa3a1a3cb5a30002fec062ce9", - "zh:4fb35c3f643dae9f3670d719397a415f815a0b95f8ed7bd8a72f27a94ba78092", - "zh:59ba40825ab38db5b4a0989a2db0df35cc15d8984f898176011ba352f27d77b7", - "zh:61fc1252eb88088638f4c69ea4e2171cde2e5089fa632ac1e943b13787348f73", - "zh:7c5d6dd5f7cbc460e95d368be35c29b4e0402069b8912dbd5d1cd7fa9acef216", - "zh:7f76d756240d4284642f359ad470226e5378670239aadc366ef54d9d914d4d2e", - "zh:8133ad0814098177e0d067c816ccf1bf48bbadacd18f6f2c808c90447505723b", - "zh:c93be06269bb728f1968f8c50506de56c887017ac1d6e4be1f925651d8437eb6", - "zh:ef47b78a10a82e6cf53344a6a85a94041c28286c10a70541c564d762f1cfede0", - "zh:f5796a53a74999135bd9087aff50fddda59129d09b2f9b1902ff8c0c1e047e48", + "h1:7fra+jbUXbG5wMaz5L6RKMBv6gIuenJcBiIww87GoXo=", + "h1:BzSV3Ie9XMXF7sZHKAS54CzV95v5GBZNhQ4nrprUgfQ=", + "h1:CkrbSKS+pNVgvP3bMe2WoYHaFCIWJUkCtlC5vyTAdLI=", + "h1:FboJEwgVIRmqUJkjEoSRpfavVCJotUTe1zzT+pBzcV0=", + "h1:GlXELDLSZrdV3Svx1jjEBAXiJFkkdF/Hgx1qrmRK5hE=", + "h1:VuXFI2IcnZ6t4sDqtvkuIzbPK1CJQa0CkaM0MBuOlSU=", + "h1:WmL2nFQbSzRiDsDiwUbZbBp/cxGQrXrZnB7A4LGSvJU=", + "h1:Zdj26awWJ+m8kMoAMhItsIDcDFg81PWgKKJrvNi3WOI=", + "h1:lHvYYIumeZ+KJgCrmhCLnRGzrvNMjSHBTdV24coyMEc=", + "h1:pAOYMwA6Zki3ujAbG20b49u1IYXdBz56pW1JHqKdX5U=", + "h1:qi9GUp2+g69C8zY6Z68u4fWPwcZlDTa/CtdhvPgWbMA=", + "h1:w5A3xJ2mowj2wgiE3oNfOI0lFJf5X9IgxOJ6SErMczA=", + "h1:xAO03iJyuNGSOqolIcXcofH8cocgUb6Cnzq6yivbWcI=", + "h1:xXigGPwW8MlrB6Br2ce+Bf35BbdzdPKa97T/q/xrrcA=", + "h1:yDYzQ2ncNE9q1288xAgflIPq98bOOYsAb9tq6vkbFzw=", + "zh:129d7d5944b31f40916b1ca86b31cef65a6b02fd36008809d13c561894bfedb9", + "zh:24631608288b0bcd35c1fc63dc5839572254d881c0589ebba036be52b2fc04d6", + "zh:5a0f100d7eb256463fe5a2aa1a7128391147b2c5fc895ff1b1ef54fc5b8f15ab", + "zh:6a8a1126ab9ca61be3b62ec184f6b2e7cbf01cde810acc548cee27d71277b09b", + "zh:6fffef54fd3aada85c074e34d41386aa09c79a308a4679132da31c7272733c6c", + "zh:899c992d2aa290ebe1304da0289c5104a630bca421cc6a88ce55bf0960aab1b4", + "zh:960fd6c2847859a843dd9dbfc95a0037a470aa744094d155a38a057175cf1502", + "zh:9b032b685a644634158ace5529e260dfc4447a280056f02858d205ea26753f69", + "zh:bba5477c97020c28ed12d4f5b36be2c1bf14d946d7e44b3690e5c23cd7ddf5e6", + "zh:c2ff6c33efef52441fa3485137972792031626dcabca2b1d8b6527d45f185279", + "zh:cd492b3dfd150de6bef8ad505293d3d53c6c907706f36d0e497b4fc027d8edb6", + "zh:d1f832bc33c42781454dc020c6937e7d0133155a5a9f64335309d64a34b36bb7", + "zh:d42e9cbebc77643556853b1ebbec14cefe70c57ee86cd3b8c71fbe7f523f07df", + "zh:d4c0466f578d7f990646bb0847e31ba3797f2100b6380ee1ca736887546c7621", + "zh:d9d81ecebfe6edabdd4c527f3f4debde3e052ff87c5ef4c67497ab3d7539e424", ] } From d1da0c6cb46447d9b295389e4cda211d014d10fb Mon Sep 17 00:00:00 2001 From: automation-bot Date: Sat, 22 Aug 2026 00:32:09 +0000 Subject: [PATCH 50/53] chore(deps): update terraform bunnynet to v0.18.1 --- .terraform.lock.hcl | 70 ++++++++++++++++++++++----------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index ff935fa..ef9e47d 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -38,43 +38,43 @@ provider "registry.opentofu.org/hashicorp/http" { } provider "registry.terraform.io/bunnyway/bunnynet" { - version = "0.18.0" + version = "0.18.1" constraints = "~> 0.18" hashes = [ - "h1:+6VXZmSSeIchab8WY+UFZxaXu6poxZbiJenYwog+Z2M=", - "h1:Bz94gADR83NmrsZC50LheryVcS9erG6tF052hNPqz0U=", - "h1:FGkcn6ieyNPr56Riv75IsCa6okZ9ZHqqFd08Y4i5cPI=", - "h1:GqPjTKaOlhhNIxpPHWJpWdGkEtvUDtuOkjYbVIInfgU=", - "h1:NMDWYRisSFwepjfYsf4MrcyP7Ihjlty937l1BW1Cztg=", - "h1:OusNMAZdIIbxWwHXwH8tYzdbXZPRS8dW7cncSYcHfNI=", - "h1:OzgasS4oZCZjYAOrqGy7RpPNbTPX5wGaaw7TDnasSJM=", - "h1:RyK3DC7cM4T2I83OvnO+UXU+eCXLG5vDlYZ/bWKHq7g=", - "h1:U/JKg4BNWii2mK3bNsOWYMBTpkXqGsWb1ypSJvSKl9Y=", - "h1:UjSUm1AU2wZ8eyC3LDRwWatW9cKD/I0rk7MOeUDDkWc=", - "h1:a888ExTeqWKxaB2GBsDIRSm8jOOMLkPFcABrJxxA8qc=", - "h1:aShYLfSapfo1Ozy33zL5WfmYt5UF2m5EziespPOGNAk=", - "h1:bHdpp2ecmvDoezqg8TirE32SnuDb108/NZ4xBGvJy98=", - "h1:lLYZN5cetXgLPJjo+eR+kwodOYGsQetzV6bg5Ki58tk=", - "h1:szi71DaqI4yB6fI55hBbtVZg1GDWJVkO9+WF/1sZ+IE=", - "h1:vK4jZYZZhD6M4cRmX+171mxoJgb2FSNiBNAUhtm/TNs=", - "h1:yNnSUskn43648XU/YS0e9NUdoHImo7pFMIlBzujBoxY=", - "zh:0c3adf039df2fead1e36b8e7887d965223f03b6b5cdd921ec0c98beaa04fdec0", - "zh:12a3db29733e6619e216fac9aa774cbf67da2105f48c5c4dee8df046d69656fa", - "zh:1330b83c949165434e4d0db5e097a1741376cdb66c06c37b2a97ecea8e06b0f0", - "zh:186113259ab0f80ab9079f0a8a810e93ee097f6740100a0a444f805e8772c12e", - "zh:242fe10185da8a700b0e9a6a52e3d1f6592e8e189aaf5e9a79cf515ad5c7ff25", - "zh:28b005b0aa9485c492326fbb4287d3cb465f25a8d572b8c740e041e040d80aa2", - "zh:3b2cd0daa767dfff67dd39c98d1c82b25e70eb81df77c0d6dd762a0dedec16e1", - "zh:3f14b244740f6c6420d298846708e9f3853c8eda685d3a4d71fb0ffec021ad9c", - "zh:469bfd08deefd90e89c930e5e45bfd06a58a1eadb85dfbee9fc48ae296e8a8c9", - "zh:634d96b84b2e77d25baa074c357e831252c8b8114926ef72e1afb68a4bc9eb65", - "zh:6e837b9485e56f84b5e2bb396fa549b628b8e075257fa01bf8c796ce91d20e58", + "h1:1nbjHMc5QBwiAfkriGGuO+wLkrgwKjbeAK70sNQRDa4=", + "h1:2AkMQZEckeGl8efzFzpGUqIR5o4rhOt4GSmOOMBX8wg=", + "h1:4D42uIgbm5jI0TQWRfVXJZoG6WOyO3Mi0ZgC8KZjPmc=", + "h1:79iaWeho9vn6p5oFHx7cXCzrX9k0R2yS9iF7rNchX7E=", + "h1:7GKjnlsRnA88qGIZ+V4HseEWB1YmuPXkyVen4DOxRBM=", + "h1:9ZpZHafhWNCDM91hE+GK6ikvy9THlU4/opQoC78B6TU=", + "h1:J4eKuqfDRI+e1PRGkt6MJ6UT+ym3pFxYKN+jIm105Es=", + "h1:LvrSDB8WWxh6NcR7X97oxJ9FrB/UVyWau9V+rdxBkxU=", + "h1:NO36kn/RhmKhWVcM0qRUcbZveSv2idT6LUwOREBqBc4=", + "h1:UPrn5yfuJwaEggnIbKqd9eyNCzO9DRJhA0279J1LYLM=", + "h1:b+tjNcFfxqwWGDgumzm4QImqJLyemGanHbZ+F2qw6vU=", + "h1:gppmt6Jbng9QH8ulpSujYeCHSlC5kWEkYoiYzgFISNQ=", + "h1:kZkf+9F8Be+Ztt10sLUWIxnwgfBCHpxi3V66F3+HV5s=", + "h1:mZvRXynxrx0/Q0txogt/5fTVhKmRWX3rWoqLiwLdamw=", + "h1:ogkHPOIbdDgdmfoa0LaPIyX8QTJvWik3andNAJoR6pk=", + "h1:pCkHlvcWgM5FkwEsrxzT9L7S7ZDNfyWagWM0KMXYFBE=", + "h1:rbKmEiaOKwrbrzEf9iihpwFCwvlVVkyxZUfFeVuX180=", + "zh:198f5aab9e8bbbb6fa96e41b7d33a997e72666dfc7369f08849ff12a0f91f7d4", + "zh:1f152ab9c51353422a79d4c4ee965112972b0d4b3246c62a8e6848422f4cac26", + "zh:4776e4fc6f38b1eb4a64c866e617cebdb0344af51c4685aa3e47356a5502707f", + "zh:66828334af0bdecbde3c5913b9c48371ea119569631f43094e28e03ab1b5fa4a", + "zh:800a94528ed366242fb83ba8d22ca1407bb02826ac8805a83a0ab04ab5efb582", + "zh:862f5e7db0f81d5e57292f0cd44b4f530eaa59510756991037d1ed6fbff91e05", "zh:890df766e9b839623b1f0437355032a3c006226a6c200cd911e15ee1a9014e9f", - "zh:89e02979311e6727a50586b04cb343e9bbec74a6f4d1dba9352971e4334d64c9", - "zh:a6796143fe61ae52d236b7ea96bddbc6317851a0e2117eb2f55cd73c803b4b6f", - "zh:ad2542160e7b57ee8a016cddbf1d32663baf74fe30fcf24df64da75cb13128b0", - "zh:bfee81c153e8b50121fd58eedeeb84bfa64a3d17f23900e35143c4a86474cbd2", - "zh:eeba652697908712cd1ce2c7d2925f6e6bb2d18ea5d3e6ca185e88eeb80f3c80", - "zh:f0b5b8fd6942647c358440591d56a5cb82fda92f7866898654a66ec901174f1f", + "zh:91f8b0f92b7dd1e131e391c170fcb329c795747553d5cc71296b8803496bc33c", + "zh:95446852691ebbbfcd4998f8941d29577d61b15ac320bc4590ae48f4542aee39", + "zh:9ccb3382c4fc20735c3ee016240afa82d6cf745b8ec458a9e5159d1a03e4cd20", + "zh:a11991312edc9fe2567ecedadb2e87de8b1a41e97a0d117d1a1c58eaa68ae645", + "zh:ab729171af18063c34f5a7d33b598b870e082f2e7ba8ee60ca77dc4dede84432", + "zh:c2b58950da56179b93a7d590d0cf3a488070b973826d788401a94914eaeae072", + "zh:d1b6a91581f1580fad12f11b9593461f566153b6760299ba592746716d595583", + "zh:dad0ce1ac0fc934ab18fe4a744b768d8f9969099488b25d6c18c782b40478bfe", + "zh:e2cb8dfebfa0a358d0b52e15b04cfd82407a4c578c39b6ac62ac919b23ef97a6", + "zh:fc648d9464bcb6b360eb4885791675c2437f0d1c0e1b1b8f34fbb6d93a880ea9", + "zh:fd8250944e3794b9440cdaf4ac06f7a1672744e4bcb2e8a33b94c2ddf32ab988", ] } From f4ab6f9dc55d2e33822abf5d48e6517a33bd46e9 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Wed, 26 Aug 2026 00:32:02 +0000 Subject: [PATCH 51/53] chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.11.2 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 82461cb..2bf38b9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -36,7 +36,7 @@ repos: hooks: - id: air-format - repo: https://github.com/editorconfig-checker/editorconfig-checker - rev: v3.11.1 + rev: v3.11.2 hooks: - id: editorconfig-checker exclude: ^local/patches/.*\.patch$ From d2333c6cbe599fc5e43c7534d55bb2120e104245 Mon Sep 17 00:00:00 2001 From: automation-bot Date: Thu, 27 Aug 2026 00:33:08 +0000 Subject: [PATCH 52/53] chore(deps): update terraform bunnynet to v0.18.2 --- .terraform.lock.hcl | 70 ++++++++++++++++++++++----------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/.terraform.lock.hcl b/.terraform.lock.hcl index ef9e47d..9591b83 100644 --- a/.terraform.lock.hcl +++ b/.terraform.lock.hcl @@ -38,43 +38,43 @@ provider "registry.opentofu.org/hashicorp/http" { } provider "registry.terraform.io/bunnyway/bunnynet" { - version = "0.18.1" + version = "0.18.2" constraints = "~> 0.18" hashes = [ - "h1:1nbjHMc5QBwiAfkriGGuO+wLkrgwKjbeAK70sNQRDa4=", - "h1:2AkMQZEckeGl8efzFzpGUqIR5o4rhOt4GSmOOMBX8wg=", - "h1:4D42uIgbm5jI0TQWRfVXJZoG6WOyO3Mi0ZgC8KZjPmc=", - "h1:79iaWeho9vn6p5oFHx7cXCzrX9k0R2yS9iF7rNchX7E=", - "h1:7GKjnlsRnA88qGIZ+V4HseEWB1YmuPXkyVen4DOxRBM=", - "h1:9ZpZHafhWNCDM91hE+GK6ikvy9THlU4/opQoC78B6TU=", - "h1:J4eKuqfDRI+e1PRGkt6MJ6UT+ym3pFxYKN+jIm105Es=", - "h1:LvrSDB8WWxh6NcR7X97oxJ9FrB/UVyWau9V+rdxBkxU=", - "h1:NO36kn/RhmKhWVcM0qRUcbZveSv2idT6LUwOREBqBc4=", - "h1:UPrn5yfuJwaEggnIbKqd9eyNCzO9DRJhA0279J1LYLM=", - "h1:b+tjNcFfxqwWGDgumzm4QImqJLyemGanHbZ+F2qw6vU=", - "h1:gppmt6Jbng9QH8ulpSujYeCHSlC5kWEkYoiYzgFISNQ=", - "h1:kZkf+9F8Be+Ztt10sLUWIxnwgfBCHpxi3V66F3+HV5s=", - "h1:mZvRXynxrx0/Q0txogt/5fTVhKmRWX3rWoqLiwLdamw=", - "h1:ogkHPOIbdDgdmfoa0LaPIyX8QTJvWik3andNAJoR6pk=", - "h1:pCkHlvcWgM5FkwEsrxzT9L7S7ZDNfyWagWM0KMXYFBE=", - "h1:rbKmEiaOKwrbrzEf9iihpwFCwvlVVkyxZUfFeVuX180=", - "zh:198f5aab9e8bbbb6fa96e41b7d33a997e72666dfc7369f08849ff12a0f91f7d4", - "zh:1f152ab9c51353422a79d4c4ee965112972b0d4b3246c62a8e6848422f4cac26", - "zh:4776e4fc6f38b1eb4a64c866e617cebdb0344af51c4685aa3e47356a5502707f", - "zh:66828334af0bdecbde3c5913b9c48371ea119569631f43094e28e03ab1b5fa4a", - "zh:800a94528ed366242fb83ba8d22ca1407bb02826ac8805a83a0ab04ab5efb582", - "zh:862f5e7db0f81d5e57292f0cd44b4f530eaa59510756991037d1ed6fbff91e05", + "h1:3rZl+Co3WMpwj8SciPaCNXoGA31aSoqp6iweLarr5m4=", + "h1:6d9cKLhz8QOZ4R5yVX1G0TsWL+K1Abtfbm3xngndxto=", + "h1:EBjjkfp5Gx7nXP1DVO+tLhsow6fEUvaIjsCEFRT2fY8=", + "h1:Nu2DoHGOv2YN7ag4kFGpfnPeRDh6bzWqY5anW+ETGpM=", + "h1:OnvZxg28m4/UJeEhHVLU4kM2MZ704sxRzYfLWlLxnhA=", + "h1:PiCse2/UcB7nkPxosveHsJN/jKdBC8AH6tKTxcHSYKw=", + "h1:QAahdtlDBUon7eMwNN0D2V6CxgasOXIi+9/UExik6Sg=", + "h1:Su5z0A7/UaSm/E7FJnFjpDVQaa1Ju5+fZ8Mirf8E+k8=", + "h1:UA3a78FJAPAGqCCvlIg9ekPltpVsrmEhwFLalWCFnew=", + "h1:XAlCTNHRtgUkNjdUItkiak6ajjT7wFJzJN8frXKD5Ms=", + "h1:ZgLBOPebYxH059z1cGHmjYO8CTf+tbWPb3VbO97S2YM=", + "h1:anR91C2F6NDJoQQQIy6KHChodnTaSKnApSWSGM4jSX0=", + "h1:gVmaNmIu4gEiITM+CAb66e+zncAqzNBYkniTZfvxZ5Y=", + "h1:pODlGrkPqHV4yhXiO7LLLu11HtcuxOAB2zUx3B8w1vI=", + "h1:qEYeHEKVRcc78q5xiRGJSY8DGQpLj40KafEXUxFfaQc=", + "h1:qdVz+O0lLHhyf5YX3ujmoVvAGlKqvi+YOPUzVTqpKzY=", + "h1:yTrPkdc9eQkxfPLBYydFf0fpcjarP5w0sdLPzekD9RQ=", + "zh:0fe3987c927d81196c97504470ce4d26c3ad0014f8ee3d0c1be422d08cfcf49c", + "zh:15c36dc69e058876921ac887213e1716217d159b7ee7f0f233e21fb35be85178", + "zh:29d58d7b76dcb142a06d4edd15b8500fe6c1afb7f7c056ada17e2d42bb999fbd", + "zh:33d313836c0e985186b3456c0946e062b27cacfcb08611d0a394f36db9ee1aef", + "zh:47e085e52e9b24ad85fa2988dbb8604256a970a6f53f7fa6aab04d8ae756a738", + "zh:4ba4f87571ca72fbc6c24ab71f2f7b5a086938262e2d8e5c0b39701ed52f8bbc", + "zh:4c6bae97b543c5b328e1ecbcf7c976351b4b381654e9d3e569270dcab3ba816c", "zh:890df766e9b839623b1f0437355032a3c006226a6c200cd911e15ee1a9014e9f", - "zh:91f8b0f92b7dd1e131e391c170fcb329c795747553d5cc71296b8803496bc33c", - "zh:95446852691ebbbfcd4998f8941d29577d61b15ac320bc4590ae48f4542aee39", - "zh:9ccb3382c4fc20735c3ee016240afa82d6cf745b8ec458a9e5159d1a03e4cd20", - "zh:a11991312edc9fe2567ecedadb2e87de8b1a41e97a0d117d1a1c58eaa68ae645", - "zh:ab729171af18063c34f5a7d33b598b870e082f2e7ba8ee60ca77dc4dede84432", - "zh:c2b58950da56179b93a7d590d0cf3a488070b973826d788401a94914eaeae072", - "zh:d1b6a91581f1580fad12f11b9593461f566153b6760299ba592746716d595583", - "zh:dad0ce1ac0fc934ab18fe4a744b768d8f9969099488b25d6c18c782b40478bfe", - "zh:e2cb8dfebfa0a358d0b52e15b04cfd82407a4c578c39b6ac62ac919b23ef97a6", - "zh:fc648d9464bcb6b360eb4885791675c2437f0d1c0e1b1b8f34fbb6d93a880ea9", - "zh:fd8250944e3794b9440cdaf4ac06f7a1672744e4bcb2e8a33b94c2ddf32ab988", + "zh:9ba7ab56537963db2449d217528a751469c9dc4e413dec3e3d63fd7daf3db4ef", + "zh:a3c48eda7e11b03b831f2a639797524bb335f155f0dff0e999cf3496994da8b3", + "zh:aab8f4814d55ef8c6c285d2496ae412437017d0fd1be70106f7b3a4a6e764feb", + "zh:b92b9beacf71ae894717c2036ceb68db52c9c43af4a01b8209eceae9f91a2c8e", + "zh:da389285938e22e1249e6a00cebf12a9f67334743f0b3f66399e6881028bda11", + "zh:dadcc33d06e6f64a17d1965478af5e8bbdc971e92ec9b14e384c5d43861d63f7", + "zh:e090c916e6da685125194af4f0a1fd772494a0c63f3f16ab3741782e17f4a8f9", + "zh:e5881e00fa970c08e66e8079b47d69b76def6e7ff3bdc35b68d7811e5ece55d1", + "zh:eeebb25a066a6287d545c91c0fc264acee5b28174d0979faeebdac3bd14f0fff", + "zh:f368195116c9ce0181aa7527c51ae5e7ab23d42fb966acf4eddca344621ae339", ] } From e9782bb529378d2b86e1bf87b1a32d49a1618ea8 Mon Sep 17 00:00:00 2001 From: pat-s Date: Fri, 28 Aug 2026 08:48:58 +0000 Subject: [PATCH 53/53] fix(ci): install RPostgres for metadata updates --- .crow/process-updates.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.crow/process-updates.yaml b/.crow/process-updates.yaml index 021d6cb..73bfff7 100644 --- a/.crow/process-updates.yaml +++ b/.crow/process-updates.yaml @@ -203,6 +203,7 @@ steps: - rm -rf /mnt/cache/R-pkgs/00LOCK-* /mnt/cache/R-pkgs/bincraft - mkdir -p /mnt/cache/uvr/cache /mnt/cache/uvr/packages /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages - /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R + - UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres - /opt/R/$R_VERSION/bin/R -q -e 'packageVersion("bincraft")' # rhel-10 ships xwfb-run (Xwayland) instead of xvfb-run; prefer it and start weston, else fall back to xvfb-run - XVFB=$(command -v xwfb-run 2>/dev/null || command -v xvfb-run); XVFB_ARGS=""; if command -v xwfb-run >/dev/null 2>&1; then dnf install -y -q weston 2>/dev/null; XVFB_ARGS="-c weston"; fi @@ -218,6 +219,7 @@ steps: LIB="/mnt/cache/R-pkgs-$RMINOR" mkdir -p "$LIB" R_LIBS_USER="$LIB" "$(dirname "$RBIN")/Rscript" local/install-bincraft.R || true + R_LIBS_USER="$LIB" UVR_R_BIN="$RBIN" local/uvr-install.sh RPostgres || true R_LIBS_USER="$LIB" $XVFB $XVFB_ARGS -- "$(dirname "$RBIN")/R" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '${OS}', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, patches = 'local/patches', r_minor_detection = 'classifier',r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true done - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "${OS_ID}", s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))'