diff --git a/docs/superpowers/plans/2026-06-13-bincraft-r-minor-enhancements.md b/docs/superpowers/plans/2026-06-13-bincraft-r-minor-enhancements.md deleted file mode 100644 index b52735a..0000000 --- a/docs/superpowers/plans/2026-06-13-bincraft-r-minor-enhancements.md +++ /dev/null @@ -1,470 +0,0 @@ -# bincraft R-minor Enhancements Implementation Plan - -> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking. - -**Goal:** Teach bincraft to (a) build/serve per-R-minor package indexes and (b) drive `process_cran_updates()` from the ABI classifier so only risky packages are built per R minor. - -**Architecture:** Two additive, low-risk changes to the bincraft R package. `upload_package_index()` gains an `r_minor` argument so a per-minor slot (`…/contrib//`) gets its own `PACKAGES*`. `process_cran_updates()` gains `r_minor_detection`/`r_minor_sensitive_only` and classifies each candidate via `needs_per_minor_recompile()` (already in the package), passing a concrete `is_r_minor_sensitive` logical to the unchanged `build_binary_package()`. - -**Tech Stack:** R package, `testthat` (3e) + `mockery` for tests, `roxygen2` for docs, `s3fs`/`cranlike` for the index. Repo: `https://codefloe.com/rpkgs/bincraft` (this plan is executed in a clone of that repo, NOT in build-cran-binaries). - -**Pre-req:** PR #49 (ABI classifier) is already merged on `main`; `abi_classify()`, `needs_per_minor_recompile()`, `abi_risky_linking_deps()` are exported. - ---- - -### Task 1: `package_index_remote_dir()` pure helper - -**Files:** -- Modify: `R/package_index.R` (top of file, before `add_to_package_index`) -- Test: `tests/testthat/test-package_index.R` (new) - -- [ ] **Step 1: Write the failing test** - -```r -# tests/testthat/test-package_index.R -test_that("package_index_remote_dir builds the generic slot when r_minor is NULL", { - expect_identical( - package_index_remote_dir("bucket", "amd64", "alpine323"), - file.path("bucket", "amd64", "alpine323", "latest", "src", "contrib") - ) -}) - -test_that("package_index_remote_dir appends the minor slot when r_minor is set", { - expect_identical( - package_index_remote_dir("bucket", "amd64", "alpine323", r_minor = "4.4"), - file.path("bucket", "amd64", "alpine323", "latest", "src", "contrib", "4.4") - ) -}) -``` - -- [ ] **Step 2: Run test to verify it fails** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_file("tests/testthat/test-package_index.R")'` -Expected: FAIL — `could not find function "package_index_remote_dir"`. - -- [ ] **Step 3: Add the helper** - -```r -# R/package_index.R — add near the top, above add_to_package_index() -#' Build the S3 remote contrib dir for a package index -#' -#' @param r_minor Optional `"major.minor"` string (e.g. `"4.4"`). When non-NULL -#' the path points at the per-minor slot. -#' @keywords internal -package_index_remote_dir <- function(s3_bucket, arch, codename, r_minor = NULL) { - base <- file.path(s3_bucket, arch, codename, "latest", "src", "contrib") - if (is.null(r_minor)) { - base - } else { - file.path(base, r_minor) - } -} -``` - -- [ ] **Step 4: Run test to verify it passes** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_file("tests/testthat/test-package_index.R")'` -Expected: PASS (2/2). - -- [ ] **Step 5: Commit** - -```bash -git add R/package_index.R tests/testthat/test-package_index.R -git commit -m "feat(index): add package_index_remote_dir helper for per-minor slots" -``` - ---- - -### Task 2: per-minor support in `upload_package_index()` - -**Files:** -- Modify: `R/package_index.R` (`upload_package_index`, signature + the `remote_bin_dir` block at lines ~117-124; `add_to_package_index` for consistency) - -- [ ] **Step 1: Add `r_minor` to the signature and use the helper** - -In `upload_package_index()`, add `r_minor = NULL` to the argument list (after `arch = NULL`). Replace the inline `remote_bin_dir <- file.path(s3_bucket, arch, codename, "latest", "src", "contrib")` block with: - -```r - remote_bin_dir <- package_index_remote_dir(s3_bucket, arch, codename, r_minor) -``` - -Do the same replacement in `add_to_package_index()` (it has the identical inline construction); add `r_minor = NULL` to its signature too. - -- [ ] **Step 2: Add the roxygen param** - -Above `upload_package_index` and `add_to_package_index`, add: - -```r -#' @param r_minor Optional `"major.minor"` string. When set, the index is -#' written/read under the per-minor slot `…/contrib//` instead of the -#' generic `…/contrib/` slot. -``` - -- [ ] **Step 3: Regenerate docs** - -Run: `R -q -e 'devtools::document()'` -Expected: updated `man/upload_package_index.Rd`, `man/add_to_package_index.Rd`, no errors. - -- [ ] **Step 4: Verify package still loads and existing tests pass** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_dir("tests/testthat")'` -Expected: PASS — no regressions; the new path test from Task 1 still green. - -- [ ] **Step 5: Commit** - -```bash -git add R/package_index.R man/ -git commit -m "feat(index): upload/update PACKAGES for a per-minor slot via r_minor" -``` - ---- - -### Task 3: `classify_r_minor_sensitive()` internal helper - -**Files:** -- Modify: `R/process_cran_updates.R` (add helper near the top) -- Test: `tests/testthat/test-process_cran_updates.R` (new) - -- [ ] **Step 1: Write the failing test** - -```r -# tests/testthat/test-process_cran_updates.R -test_that("classify_r_minor_sensitive returns TRUE for a risky package", { - skip_if_not_installed("mockery") - mockery::stub(classify_r_minor_sensitive, "clone_repository", function(pkg, tag, url, dest) { - dir.create(dest, recursive = TRUE, showWarnings = FALSE) - writeLines( - c("Package: dummy", "Version: 1.0", "NeedsCompilation: yes", "LinkingTo: Rcpp"), - file.path(dest, "DESCRIPTION") - ) - dir.create(file.path(dest, "src")) - writeLines("// Rcpp glue", file.path(dest, "src", "x.cpp")) - }) - expect_true(classify_r_minor_sensitive("dummy", "1.0", "https://github.com/cran")) -}) - -test_that("classify_r_minor_sensitive returns FALSE for a pure-r package", { - skip_if_not_installed("mockery") - mockery::stub(classify_r_minor_sensitive, "clone_repository", function(pkg, tag, url, dest) { - dir.create(dest, recursive = TRUE, showWarnings = FALSE) - writeLines(c("Package: dummy", "Version: 1.0", "NeedsCompilation: no"), - file.path(dest, "DESCRIPTION")) - }) - expect_false(classify_r_minor_sensitive("dummy", "1.0", "https://github.com/cran")) -}) - -test_that("classify_r_minor_sensitive fails safe to TRUE on clone error", { - skip_if_not_installed("mockery") - mockery::stub(classify_r_minor_sensitive, "clone_repository", function(...) stop("boom")) - expect_true(classify_r_minor_sensitive("dummy", "1.0", "https://github.com/cran")) -}) -``` - -- [ ] **Step 2: Run test to verify it fails** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_file("tests/testthat/test-process_cran_updates.R")'` -Expected: FAIL — `could not find function "classify_r_minor_sensitive"`. - -- [ ] **Step 3: Add the helper** - -```r -# R/process_cran_updates.R — add above process_cran_updates() -#' Classify a single CRAN package for R-minor sensitivity -#' -#' Clones the package source to a temp dir and runs -#' [needs_per_minor_recompile()]. Fails safe to `TRUE` (build per minor) if the -#' clone or classification errors, so a possibly-ABI-fragile binary is never -#' served from the cross-minor generic slot by mistake. -#' @keywords internal -classify_r_minor_sensitive <- function( - package_name, - tag, - source_org_url = "https://github.com/cran", - local_clone_dir = tempdir() -) { - dest <- file.path( - local_clone_dir, - sprintf("classify_%s_%s", package_name, tag) - ) - on.exit(unlink(dest, recursive = TRUE, force = TRUE), add = TRUE) - tryCatch( - { - clone_repository(package_name, tag, source_org_url, dest) - isTRUE(as.logical(needs_per_minor_recompile(dest))) - }, - error = function(e) { - log_warn(sprintf( - "{.fun classify_r_minor_sensitive}: failed for {.pkg %s} {.field %s}: %s. Treating as r-minor-sensitive.", # nolint - package_name, - tag, - conditionMessage(e) - )) - TRUE - } - ) -} -``` - -- [ ] **Step 4: Run test to verify it passes** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_file("tests/testthat/test-process_cran_updates.R")'` -Expected: PASS (3/3). - -- [ ] **Step 5: Commit** - -```bash -git add R/process_cran_updates.R tests/testthat/test-process_cran_updates.R -git commit -m "feat(updates): add classify_r_minor_sensitive helper" -``` - ---- - -### Task 4: wire classifier detection into `process_cran_updates()` - -**Files:** -- Modify: `R/process_cran_updates.R` (`process_cran_updates` signature + the build loop at lines ~262-289) -- Modify: `tests/testthat/test-process_cran_updates.R` (add routing tests) - -- [ ] **Step 1: Write the failing tests** - -```r -# append to tests/testthat/test-process_cran_updates.R -test_that("classifier mode passes per-package is_r_minor_sensitive to build", { - skip_if_not_installed("mockery") - recorded <- list() - mockery::stub(process_cran_updates, "get_updated_cran_packages", - function(...) data.frame(name = c("riskypkg", "purepkg"), - version = c("1.0", "2.0"), stringsAsFactors = FALSE)) - mockery::stub(process_cran_updates, "get_new_cran_packages", - function(...) data.frame(name = character(), version = character())) - mockery::stub(process_cran_updates, "tools::CRAN_package_db", - function(...) data.frame(Package = character(), OS_type = character())) - mockery::stub(process_cran_updates, "classify_r_minor_sensitive", - function(name, tag, ...) name == "riskypkg") - mockery::stub(process_cran_updates, "build_binary_package", - function(name, tag, ..., is_r_minor_sensitive) { - recorded[[name]] <<- is_r_minor_sensitive - invisible(TRUE) - }) - - process_cran_updates( - platform = "alpine-323", process_removed = FALSE, - r_minor_detection = "classifier", - s3_endpoint = "x", s3_region = "x", s3_bucket = "x" - ) - - expect_true(recorded[["riskypkg"]]) - expect_false(recorded[["purepkg"]]) -}) - -test_that("r_minor_sensitive_only drops non-risky candidates", { - skip_if_not_installed("mockery") - built <- character() - mockery::stub(process_cran_updates, "get_updated_cran_packages", - function(...) data.frame(name = c("riskypkg", "purepkg"), - version = c("1.0", "2.0"), stringsAsFactors = FALSE)) - mockery::stub(process_cran_updates, "get_new_cran_packages", - function(...) data.frame(name = character(), version = character())) - mockery::stub(process_cran_updates, "tools::CRAN_package_db", - function(...) data.frame(Package = character(), OS_type = character())) - mockery::stub(process_cran_updates, "classify_r_minor_sensitive", - function(name, tag, ...) name == "riskypkg") - mockery::stub(process_cran_updates, "build_binary_package", - function(name, tag, ..., is_r_minor_sensitive) { built <<- c(built, name); invisible(TRUE) }) - - process_cran_updates( - platform = "alpine-323", process_removed = FALSE, - r_minor_detection = "classifier", r_minor_sensitive_only = TRUE, - s3_endpoint = "x", s3_region = "x", s3_bucket = "x" - ) - - expect_identical(built, "riskypkg") -}) -``` - -- [ ] **Step 2: Run tests to verify they fail** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_file("tests/testthat/test-process_cran_updates.R")'` -Expected: FAIL — `unused argument (r_minor_detection = ...)`. - -- [ ] **Step 3: Add the parameters** - -In the `process_cran_updates()` signature, after `filter_r_minor_sensitive = FALSE,` add: - -```r - r_minor_detection = c("none", "issue", "classifier"), - r_minor_sensitive_only = FALSE, -``` - -Immediately after the three `stop()` validation lines at the top of the body, add: - -```r - r_minor_detection <- match.arg(r_minor_detection) - # back-compat: the old boolean maps onto the issue-list path - if (isTRUE(filter_r_minor_sensitive) && r_minor_detection == "none") { - r_minor_detection <- "issue" - } -``` - -- [ ] **Step 4: Replace the issue-filter gate** - -The existing block reads `if (filter_r_minor_sensitive) { all_pkgs <- get_r_minor_sensitive_packages(...) }`. Change its condition to: - -```r - if (r_minor_detection == "issue") { - all_pkgs <- get_r_minor_sensitive_packages( - r_minor_packages_forge_type, - r_minor_packages_issue_url, - interval, - updated_packages = updated_pkgs, - new_packages = new_pkgs - ) - } -``` - -Also change the two later `if (filter_r_minor_sensitive)` log branches to `if (r_minor_detection != "none")`. - -- [ ] **Step 5: Replace the build loop** - -Replace the `purrr::walk2(all_pkgs$name, all_pkgs$version, ~ { build_binary_package(... is_r_minor_sensitive = filter_r_minor_sensitive ...) })` block with: - -```r - if (nrow(all_pkgs) > 0L) { - sensitive <- switch( - r_minor_detection, - classifier = vapply( - seq_len(nrow(all_pkgs)), - function(i) { - classify_r_minor_sensitive( - all_pkgs$name[i], - all_pkgs$version[i], - local_clone_dir = local_clone_dir - ) - }, - logical(1L) - ), - issue = rep(TRUE, nrow(all_pkgs)), - none = rep(FALSE, nrow(all_pkgs)) - ) - - if (isTRUE(r_minor_sensitive_only)) { - all_pkgs <- all_pkgs[sensitive, , drop = FALSE] - sensitive <- sensitive[sensitive] - } - - purrr::pwalk( - list(all_pkgs$name, all_pkgs$version, sensitive), - function(.name, .version, .sensitive) { - build_binary_package( - .name, - .version, - platform = platform, - upload = upload, - archive = archive, - force = force, - store_build_metadata = store_build_metadata, - s3_endpoint = s3_endpoint, - s3_bucket = s3_bucket, - s3_region = s3_region, - s3_access_key_id = s3_access_key_id, - s3_secret_access_key = s3_secret_access_key, - is_r_minor_sensitive = .sensitive, - metadata_db_type = metadata_db_type, - metadata_db_host = metadata_db_host, - metadata_db_name = metadata_db_name, - metadata_db_table = metadata_db_table, - metadata_db_port = metadata_db_port, - metadata_db_user = metadata_db_user, - metadata_db_password = metadata_db_password, - metadata_db_sslmode = metadata_db_sslmode - ) - } - ) - } else { - log_info("No packages to process after filtering Windows-only packages") - } -``` - -- [ ] **Step 6: Run tests to verify they pass** - -Run: `R -q -e 'devtools::load_all("."); testthat::test_file("tests/testthat/test-process_cran_updates.R")'` -Expected: PASS (5/5 — 3 from Task 3 + 2 new). - -- [ ] **Step 7: Commit** - -```bash -git add R/process_cran_updates.R tests/testthat/test-process_cran_updates.R -git commit -m "feat(updates): classifier-driven per-package r-minor routing + sensitive-only pass" -``` - ---- - -### Task 5: docs, roxygen params, version bump, NEWS - -**Files:** -- Create: `man-roxygen/param-r_minor_detection.R`, `man-roxygen/param-r_minor_sensitive_only.R` -- Modify: `R/process_cran_updates.R` (roxygen `@template` lines), `DESCRIPTION`, `NEWS.md` - -- [ ] **Step 1: Add the man templates** - -```r -# man-roxygen/param-r_minor_detection.R -#' @param r_minor_detection How to decide which packages are R-minor-sensitive. -#' `"none"` (default) builds everything into the generic slot. `"issue"` uses -#' the curated tracking issue (the legacy `filter_r_minor_sensitive` path). -#' `"classifier"` classifies each candidate via [needs_per_minor_recompile()] -#' and routes only `risky` packages to the per-minor slot. -``` - -```r -# man-roxygen/param-r_minor_sensitive_only.R -#' @param r_minor_sensitive_only When `TRUE`, only R-minor-sensitive packages are -#' built (used for the additional per-minor passes under non-primary R versions). -``` - -- [ ] **Step 2: Reference the templates** - -In the roxygen block above `process_cran_updates`, add: - -```r -#' @template param-r_minor_detection -#' @template param-r_minor_sensitive_only -``` - -- [ ] **Step 3: Bump version and NEWS** - -In `DESCRIPTION` set `Version: 4.2.0`. Add to the top of `NEWS.md`: - -```markdown -# bincraft 4.2.0 - -* `process_cran_updates()` gains `r_minor_detection` (`"none"`/`"issue"`/`"classifier"`) - and `r_minor_sensitive_only`, classifying each candidate via the ABI classifier and - routing only `risky` packages to per-minor slots. -* `upload_package_index()` / `add_to_package_index()` gain an `r_minor` argument to - write/serve a per-minor `PACKAGES*` index under `…/contrib//`. -``` - -- [ ] **Step 4: Regenerate docs and run full check** - -Run: `R -q -e 'devtools::document()'` -Run: `R -q -e 'devtools::test()'` -Expected: docs regenerate clean; all tests PASS. - -- [ ] **Step 5: Commit, push, open PR** - -```bash -git add DESCRIPTION NEWS.md man-roxygen/ man/ R/process_cran_updates.R -git commit -m "docs(release): bincraft 4.2.0 — per-minor index + classifier-driven updates" -git push -u origin -fj -H codefloe.com pr create --base main --head --body "" "feat: per-minor index + classifier-driven r-minor builds (4.2.0)" -``` - ---- - -## Self-Review - -- **Spec coverage:** §"Required bincraft enhancements" item 1 (process_cran_updates) → Tasks 3-5; item 2 (upload_package_index per-minor) → Tasks 1-2. `build_binary_package` unchanged per the spec — no task, correct. -- **Type consistency:** helper named `package_index_remote_dir` (Tasks 1-2), `classify_r_minor_sensitive` (Tasks 3-4) consistently; params `r_minor_detection`/`r_minor_sensitive_only`/`r_minor` consistent across signature, tests, and docs. -- **Placeholders:** none — every code/edit step shows the actual code; ``/`` in the final push step are deliberate operator inputs. -- **Release dependency:** the pipeline plan pins bincraft `4.2.0`, matching the bump here. diff --git a/docs/superpowers/plans/2026-06-13-pipeline-r-minor-builds.md b/docs/superpowers/plans/2026-06-13-pipeline-r-minor-builds.md deleted file mode 100644 index 6123278..0000000 --- a/docs/superpowers/plans/2026-06-13-pipeline-r-minor-builds.md +++ /dev/null @@ -1,471 +0,0 @@ -# Pipeline R-minor Builds Implementation Plan - -> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking. - -**Goal:** Make the full (`build-all-versions-*`) and iterative (`process-updates-*`) pipelines build R-minor-sensitive packages once per installed R minor, and everything else once into the generic slot. - -**Architecture:** A precompute step classifies packages (cheap CRAN-metadata rules + source download only for the ambiguous compiled subset) and emits a sensitivity flag. Build scripts pass a concrete `is_r_minor_sensitive` per package on the primary-R pass and re-run a sensitive-only pass under each additional `/opt/R/*` minor. Per-minor `PACKAGES` indexes are uploaded for each touched slot. - -**Tech Stack:** R scripts under `local/`, crow/woodpecker CI YAML under `.crow/`, bincraft `>= 4.2.0` (see `2026-06-13-bincraft-r-minor-enhancements.md`). - -**HARD DEPENDENCY:** bincraft `4.2.0` (the companion plan) must be merged and released first — Tasks 4-6 call `r_minor_detection`/`upload_package_index(r_minor=)` which only exist there. Tasks 1-3 (this repo's R scripts) can be written and unit-tested before the release. - ---- - -### Task 1: pure metadata classifier helper - -**Files:** -- Create: `local/r-minor-helpers.R` -- Test: `local/tests/test-r-minor-helpers.R` - -- [ ] **Step 1: Write the failing test** - -```r -# local/tests/test-r-minor-helpers.R -source(file.path("local", "r-minor-helpers.R")) - -test_that("pure-r (NeedsCompilation != yes) is not sensitive", { - expect_identical(classify_from_metadata("no", NA, c("Rcpp")), "not-sensitive") - expect_identical(classify_from_metadata("", "Rcpp", c("Rcpp")), "not-sensitive") -}) - -test_that("LinkingTo a risky dep is sensitive (version constraints stripped)", { - expect_identical(classify_from_metadata("yes", "Rcpp (>= 1.0)", c("Rcpp")), "sensitive") - expect_identical(classify_from_metadata("yes", "R6,\n cpp11", c("Rcpp", "cpp11")), "sensitive") -}) - -test_that("compiled but no risky LinkingTo is ambiguous (needs source)", { - expect_identical(classify_from_metadata("yes", "R6", c("Rcpp", "cpp11")), "ambiguous") - expect_identical(classify_from_metadata("yes", NA, c("Rcpp")), "ambiguous") -}) -``` - -- [ ] **Step 2: Run test to verify it fails** - -Run: `R -q -e 'library(testthat); testthat::test_file("local/tests/test-r-minor-helpers.R")'` -Expected: FAIL — `cannot open file 'local/r-minor-helpers.R'` / function not found. - -- [ ] **Step 3: Write the helper** - -```r -# local/r-minor-helpers.R -# Metadata-only ABI triage so the full build avoids downloading every source. -# Mirrors bincraft::abi_classify rules 1-2; "ambiguous" packages still need a -# source grep via bincraft::needs_per_minor_recompile(). - -classify_from_metadata <- function(needs_compilation, linking_to, risky_deps) { - nc <- if (length(needs_compilation) == 0L || is.na(needs_compilation)) { - "" - } else { - tolower(trimws(needs_compilation)) - } - if (!identical(nc, "yes")) { - return("not-sensitive") - } - lt <- if (length(linking_to) == 0L || is.na(linking_to)) "" else linking_to - linked <- trimws(unlist(strsplit(lt, "[,\n]"))) - linked <- sub("\\s*\\(.*\\)$", "", linked) # strip "(>= x)" constraints - linked <- linked[nzchar(linked)] - if (any(linked %in% risky_deps)) { - return("sensitive") - } - "ambiguous" -} -``` - -- [ ] **Step 4: Run test to verify it passes** - -Run: `R -q -e 'library(testthat); testthat::test_file("local/tests/test-r-minor-helpers.R")'` -Expected: PASS (3/3). - -- [ ] **Step 5: Commit** - -```bash -git add local/r-minor-helpers.R local/tests/test-r-minor-helpers.R -git commit -m "feat(local): metadata-only ABI triage helper" -``` - ---- - -### Task 2: add `r_minor_sensitive` to `packages-to-build.R` - -**Files:** -- Modify: `local/packages-to-build.R` (after `pkgs` is finalized, ~line 142) - -- [ ] **Step 1: Append the classification block** - -At the end of `local/packages-to-build.R` (after `setorder(pkgs, Package, Version)`), add: - -```r -### R-minor sensitivity (classify once per package, applied to all versions) -source(file.path("local", "r-minor-helpers.R")) -risky_deps <- bincraft::abi_risky_linking_deps() - -release_meta <- data.table( - Package = cran_release$Package, - NeedsCompilation = cran_release$NeedsCompilation, - LinkingTo = cran_release$LinkingTo -) - -meta <- release_meta[Package %in% unique(pkgs$Package)] -meta[, triage := mapply( - classify_from_metadata, - NeedsCompilation, - LinkingTo, - MoreArgs = list(risky_deps = risky_deps) -)] - -# Only the "ambiguous" compiled packages need a source grep. -ambiguous <- meta[triage == "ambiguous", Package] -sensitive_ambiguous <- character() -if (length(ambiguous) > 0L) { - tmp_src <- file.path(tempdir(), "abi_src") - dir.create(tmp_src, showWarnings = FALSE, recursive = TRUE) - sens <- vapply(ambiguous, function(pkg) { - out <- tryCatch({ - dl <- utils::download.packages( - pkg, destdir = tmp_src, - repos = "https://cloud.r-project.org", quiet = TRUE - ) - isTRUE(as.logical(bincraft::needs_per_minor_recompile(dl[1L, 2L]))) - }, error = function(e) TRUE) # fail safe: treat as sensitive - out - }, logical(1L)) - sensitive_ambiguous <- ambiguous[sens] -} - -sensitive_pkgs <- unique(c(meta[triage == "sensitive", Package], sensitive_ambiguous)) -pkgs[, r_minor_sensitive := Package %in% sensitive_pkgs] -sprintf("R-minor-sensitive packages: %s of %s", length(sensitive_pkgs), uniqueN(pkgs$Package)) -``` - -- [ ] **Step 2: Verify the script parses and the column is added (offline smoke)** - -Run: -```bash -R -q -e ' - library(data.table) - source("local/r-minor-helpers.R") - pkgs <- data.table(Package = c("A","B"), Version = c("1","1")) - cran_release <- data.frame(Package = c("A","B"), - NeedsCompilation = c("no","yes"), LinkingTo = c(NA,"Rcpp"), - stringsAsFactors = FALSE) - risky_deps <- c("Rcpp") - release_meta <- as.data.table(cran_release) - meta <- release_meta[Package %in% unique(pkgs$Package)] - meta[, triage := mapply(classify_from_metadata, NeedsCompilation, LinkingTo, - MoreArgs = list(risky_deps = risky_deps))] - sensitive_pkgs <- meta[triage == "sensitive", Package] - pkgs[, r_minor_sensitive := Package %in% sensitive_pkgs] - stopifnot(identical(pkgs$r_minor_sensitive, c(FALSE, TRUE))) - cat("OK\n")' -``` -Expected: prints `OK` (B classified sensitive via LinkingTo, A not). - -- [ ] **Step 3: Persist the sensitive subset in install-deps** - -In `.crow/build-all-versions-install-deps-amd64.yaml` and `...-arm64.yaml`, change the precompute command (line ~38) from saving only `pkgs_to_build.rds` to also saving the subset: - -```yaml - - /opt/R/$R_VERSION/bin/R -q -e "source('local/packages-to-build.R'); saveRDS(pkgs, '/mnt/cache/packages/pkgs_to_build.rds'); saveRDS(pkgs[r_minor_sensitive == TRUE], '/mnt/cache/packages/r_minor_sensitive_pkgs.rds'); sprintf('Precomputed %s package versions (%s r-minor-sensitive)', nrow(pkgs), nrow(pkgs[r_minor_sensitive == TRUE]))" -``` - -- [ ] **Step 4: Commit** - -```bash -git add local/packages-to-build.R .crow/build-all-versions-install-deps-amd64.yaml .crow/build-all-versions-install-deps-arm64.yaml -git commit -m "feat(full): classify r-minor sensitivity in install-deps precompute" -``` - ---- - -### Task 3: per-package flag + `--sensitive-only` in `build-all.R` - -**Files:** -- Modify: `local/build-all.R` -- Test: `local/tests/test-build-all-args.R` (new — covers the arg/flag parsing seam only) - -- [ ] **Step 1: Write the failing test for the arg parser** - -```r -# local/tests/test-build-all-args.R -source(file.path("local", "r-minor-helpers.R")) - -test_that("parse_build_args splits flags from positionals", { - a <- parse_build_args(c("--sensitive-only", "4", "2", "8")) - expect_true(a$sensitive_only) - expect_identical(a$split_into, 4L) - expect_identical(a$split_index, 2L) - expect_identical(a$ncpus, 8L) - - b <- parse_build_args(c("4", "2", "8")) - expect_false(b$sensitive_only) - expect_identical(b$split_into, 4L) -}) -``` - -- [ ] **Step 2: Add `parse_build_args` to the helpers and run the test** - -Append to `local/r-minor-helpers.R`: - -```r -parse_build_args <- function(args) { - sensitive_only <- "--sensitive-only" %in% args - pos <- args[!startsWith(args, "--")] - list( - sensitive_only = sensitive_only, - split_into = as.integer(pos[1L]), - split_index = as.integer(pos[2L]), - ncpus = as.integer(pos[3L]) - ) -} -``` - -Run: `R -q -e 'library(testthat); testthat::test_file("local/tests/test-build-all-args.R")'` -Expected: PASS (1/1, 5 expectations). - -- [ ] **Step 3: Rewire `build-all.R` to use the parser, the flag, and the per-row sensitivity** - -Replace the arg-parsing header and the `mapply` build loop of `local/build-all.R`. New top: - -```r -sink(stdout(), type = "message") -options(crayon.enabled = TRUE, future.globals.onReference = NULL) -source(file.path("local", "r-minor-helpers.R")) - -args <- commandArgs(trailingOnly = TRUE) -parsed <- parse_build_args(args) -split_into <- parsed$split_into -split_index <- parsed$split_index -ncpus <- parsed$ncpus -sensitive_only <- parsed$sensitive_only -options(Ncpus = ncpus) - -library(bincraft, quietly = TRUE) -library(future) -plan("sequential") - -pkgs <- if (sensitive_only) { - readRDS("/mnt/cache/packages/r_minor_sensitive_pkgs.rds") -} else { - readRDS("/mnt/cache/packages/pkgs_to_build.rds") -} -# Back-compat: tolerate an older RDS without the column (treat all as non-sensitive) -if (is.null(pkgs$r_minor_sensitive)) pkgs$r_minor_sensitive <- FALSE -sprintf("Total# of remaining package versions: %s (sensitive_only=%s)", nrow(pkgs), sensitive_only) -``` - -Keep the existing chunk-split, exclude-list, and `s3_cache` lines unchanged. Then replace the `mapply(...)` call with: - -```r -n <- nrow(chunk) -mapply(function(pkg, ver, sens, i) { - cat(sprintf("[%d/%d] %s_%s (r_minor_sensitive=%s)\n", i, n, pkg, ver, sens)) - bincraft::build_binary_package( - pkg, - tag = ver, - is_r_minor_sensitive = isTRUE(sens), - s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", - s3_region = "eu-central-003", - s3_bucket = "devxy-rpkgs-binaries", - s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), - s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"), - s3_package_cache = s3_cache, - metadata_db_host = "r-binaries.devxy.io", - metadata_db_name = "build_metadata", - metadata_db_table = "single_builds", - metadata_db_user = "rpkgs", - metadata_db_password = Sys.getenv("PGPASS"), - metadata_db_sslmode = "require", - metadata_db_port = 15432, - archive = TRUE, - upload = TRUE, - store_build_metadata = TRUE - ) -}, chunk$Package, chunk$Version, chunk$r_minor_sensitive, seq_len(n)) -``` - -Note: in `--sensitive-only` mode every row already has `r_minor_sensitive == TRUE`, so the same loop builds them into per-minor slots; no special-casing needed. - -- [ ] **Step 4: Verify the script parses** - -Run: `R -q -e 'invisible(parse(file="local/build-all.R")); cat("parsed OK\n")'` -Expected: `parsed OK`. - -- [ ] **Step 5: Commit** - -```bash -git add local/build-all.R local/r-minor-helpers.R local/tests/test-build-all-args.R -git commit -m "feat(full): per-package r-minor flag and --sensitive-only mode in build-all.R" -``` - ---- - -### Task 4: multi-R loop + per-minor index in `build-all-versions-*.yaml` - -> Depends on bincraft 4.2.0 (`upload_package_index(r_minor=)`). - -**Files:** -- Modify: `.crow/build-all-versions-amd64.yaml`, `.crow/build-all-versions-arm64.yaml` - -- [ ] **Step 1: Add the sensitive-only multi-R pass after the primary build** - -In each file's `commands:` (after the existing `Rscript local/build-all.R $SPLIT_INTO $SPLIT_INDEX $NCPUS` line and before the `process_unarchived_pkgs` line), insert this multiline command: - -```yaml - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive pass under R $RV ===" - R_VERSION="$RV" $XVFB $XVFB_ARGS -n $SPLIT_INDEX -- "$RBIN" Rscript local/build-all.R --sensitive-only $SPLIT_INTO $SPLIT_INDEX $NCPUS 2>&1 || true - done -``` - -(`$XVFB`/`$XVFB_ARGS` are already defined on the preceding line in this workflow.) Note the primary pass still runs `build-all.R` without `--sensitive-only`, building everything and routing sensitive packages into the primary minor slot. - -- [ ] **Step 2: Add a per-minor index upload step** - -Append a new step after the build step (mirroring the existing CDN/index pattern). Add to `commands` of a new `Upload per-minor indexes` step (or extend the existing index handling) the following, which uploads the generic index plus one per discovered minor: - -```yaml - - | - CODENAME=$(/opt/R/$R_VERSION/bin/Rscript -e "cat(bincraft::set_codename(NULL))") - # generic slot - /opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'))" - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - /opt/R/$R_VERSION/bin/R -q -e "bincraft::upload_package_index(codename = '$CODENAME', r_minor = '$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 -``` - -- [ ] **Step 3: Validate YAML** - -Run: `R -q -e 'invisible(lapply(c(".crow/build-all-versions-amd64.yaml",".crow/build-all-versions-arm64.yaml"), yaml::yaml.load_file)); cat("yaml OK\n")'` -Expected: `yaml OK`. - -- [ ] **Step 4: Commit** - -```bash -git add .crow/build-all-versions-amd64.yaml .crow/build-all-versions-arm64.yaml -git commit -m "feat(full): sensitive-only multi-R passes and per-minor index upload" -``` - ---- - -### Task 5: classifier + multi-R in all `process-updates-*.yaml` - -> Depends on bincraft 4.2.0 (`r_minor_detection`, `upload_package_index(r_minor=)`). - -**Files (14):** every `.crow/process-updates--.yaml`: -`alpine-322`, `alpine-323`, `redhat-8`, `redhat-9`, `redhat-10`, `ubuntu-2204`, `ubuntu-2404` × `amd64`, `arm64`. - -The transform is identical in shape; only the already-present `platform=`, `R_VERSION`, `ARCH`, and the index `codename=` differ per file (leave those as-is). - -- [ ] **Step 1: Edit the `process_cran_updates` call (primary pass)** - -In each file, inside the single long `bincraft::process_cran_updates(...)` argument list, add `r_minor_detection = 'classifier', ` immediately before `s3_endpoint = ...`. Leave all other args unchanged. - -- [ ] **Step 2: Add the sensitive-only multi-R pass** - -Immediately after the `process_cran_updates(...)` command line, insert (preserve the per-file `''` string and `$INTERVAL`): - -```yaml - - | - PRIMARY_MINOR=$(echo "$R_VERSION" | cut -d. -f1-2) - for RBIN in /opt/R/*/bin/R; do - RV=$(basename "$(dirname "$(dirname "$RBIN")")") - RMINOR=$(echo "$RV" | cut -d. -f1-2) - [ "$RMINOR" = "$PRIMARY_MINOR" ] && continue - echo "=== R-minor-sensitive update pass under R $RV ===" - xvfb-run "$RBIN" -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = NULL); bincraft::process_cran_updates(interval = $INTERVAL, platform = '', process_updated = TRUE, process_new = FALSE, process_removed = FALSE, r_minor_detection = 'classifier', r_minor_sensitive_only = TRUE, s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_table = 'single_builds', metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'require', metadata_db_port = 15432, archive = TRUE, upload = TRUE, store_build_metadata = TRUE)" || true - done -``` - -Replace `` with that file's existing platform string (e.g. `alpine-323`, `redhat-9`, `ubuntu-2404`). `process_removed = FALSE` on the extra passes (removals are handled once by the primary pass). - -- [ ] **Step 3: Add per-minor index upload** - -After the existing `upload_package_index(codename = "", ...)` line in each file, append (reusing the file's existing `codename`): - -```yaml - - | - for RBIN in /opt/R/*/bin/R; do - RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2) - /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(codename = "", 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 -``` - -Replace `` with the file's existing codename value (e.g. `alpine323`, `rhel9`, `ubuntu2404`). - -- [ ] **Step 4: Verify every file changed and parses** - -Run: -```bash -R -q -e 'fs <- Sys.glob(".crow/process-updates-*.yaml"); invisible(lapply(fs, yaml::yaml.load_file)); cat(length(fs), "files parse OK\n")' -grep -L "r_minor_detection = 'classifier'" .crow/process-updates-*.yaml -``` -Expected: `14 files parse OK`, and the `grep -L` prints **nothing** (every file contains the classifier arg). - -- [ ] **Step 5: Commit** - -```bash -git add .crow/process-updates-*.yaml -git commit -m "feat(updates): classifier-driven r-minor builds + per-minor index across platforms" -``` - ---- - -### Task 6: pin bincraft 4.2.0, remove the standalone workflow - -**Files:** -- Modify: all workflows pinning bincraft (`grep -rln "bincraft.git@v" .crow/`), and `.crow/build-all-versions-install-deps-*.yaml` (which installs from `main`) -- Delete: `.crow/build-r-minor-sensitive-packages.yaml` - -- [ ] **Step 1: Bump the pin** - -Run to find pins: `grep -rn "bincraft" .crow/ | grep -E "@v4\.1\.1|bincraft.git"`. In every `process-updates-*` file, change `bincraft.git@v4.1.1` (and the `packageVersion("bincraft") != "4.1.1"` guard) to `4.2.0`. - -- [ ] **Step 2: Remove the superseded workflow** - -```bash -git rm .crow/build-r-minor-sensitive-packages.yaml -``` - -- [ ] **Step 3: Verify no stale references** - -Run: `grep -rn "build-r-minor-sensitive\|@v4.1.1\|!= \"4.1.1\"" .crow/` -Expected: no matches. - -- [ ] **Step 4: Commit** - -```bash -git add .crow/ -git commit -m "chore: pin bincraft 4.2.0 and drop superseded standalone r-minor workflow" -``` - ---- - -### Task 7: integration smoke test (manual, gated on bincraft 4.2.0 release) - -- [ ] **Step 1: Run one iterative platform manually** via crow against a short interval and confirm: a known risky package (e.g. one LinkingTo Rcpp) lands under `…/contrib//` for each installed minor, and a pure-r package lands only in the generic slot. - -- [ ] **Step 2: Confirm a client install resolves the per-minor slot.** From an R `4.4` and an R `4.5` container: -```r -install.packages("", repos = "https://cran.devxy.io/") -library() # must load without "undefined symbol" -``` -Expected: loads under both minors. If the per-minor `PACKAGES` is missing, revisit bincraft Task 2. - -- [ ] **Step 3: Spot-check the full build** on one platform with a small `SPLIT_INTO`, verifying the sensitive-only extra passes ran and produced per-minor artifacts. - ---- - -## Self-Review - -- **Spec coverage:** install-deps precompute → Tasks 1-2; `build-all.R` per-row flag + `--sensitive-only` → Task 3; full-build multi-R loop + per-minor index → Task 4; iterative classifier + multi-R + per-minor index → Task 5; remove standalone workflow + version pin → Task 6; per-minor index client-serviceability risk → Task 7 verification. -- **Type/name consistency:** `classify_from_metadata` and `parse_build_args` live in `local/r-minor-helpers.R` and are used in Tasks 2-3; the RDS column is `r_minor_sensitive` everywhere; the subset file is `/mnt/cache/packages/r_minor_sensitive_pkgs.rds` in install-deps (Task 2) and `build-all.R` (Task 3). -- **Placeholders:** ``/`` in Task 5 are explicit per-file substitutions (the values already exist in each file), not unfilled blanks. No "TBD"/"handle errors" placeholders. -- **Dependency ordering:** Tasks 1-3 are pure R-script work, unit-testable now; Tasks 4-6 are gated on bincraft 4.2.0; Task 7 is post-release verification. diff --git a/docs/superpowers/specs/2026-06-13-r-minor-sensitive-builds-design.md b/docs/superpowers/specs/2026-06-13-r-minor-sensitive-builds-design.md deleted file mode 100644 index 248a1a7..0000000 --- a/docs/superpowers/specs/2026-06-13-r-minor-sensitive-builds-design.md +++ /dev/null @@ -1,155 +0,0 @@ -# R-minor-sensitive binary builds — design - -## Problem - -CRAN binaries are currently built once, under a single R minor version, and served from a -single generic slot (`…/latest/src/contrib/`). -That is wrong for the minority of packages whose compiled code reaches into volatile R -internals: a binary built under R 4.5 will fail to load under R 4.4 with an -`undefined symbol` error. - -bincraft v4.1.0+ can now detect these packages automatically via the ABI classifier -(`abi_classify()` / `needs_per_minor_recompile()`, added in bincraft PR #49, -). -The exec-env images now ship multiple R minor versions under `/opt/R/`. -This design uses both to build R-minor-specific binaries for the sensitive packages only, -in both the iterative (`process-updates-*`) and full (`build-all-versions-*`) pipelines. - -## Background: how bincraft already behaves - -- `abi_classify(path)` returns a tier: `pure-r` (~78.6%), `safe-compiled` (~7.7%), or - `risky` (~13.6%). `needs_per_minor_recompile(path)` is the boolean wrapper - (`TRUE` iff `risky`). Both need the package source (DESCRIPTION + `src/`). -- `build_binary_package(…, is_r_minor_sensitive = TRUE)` uploads the artifact into a - per-minor slot `…/latest/src/contrib//` and records `r_version` in the - build metadata. With `FALSE` it uses the generic slot. The minor is derived from the - **running interpreter** (`R.version`), so producing a 4.4 binary requires running - `/opt/R/4.4.x/bin/R`. -- `process_cran_updates()` orchestrates the iterative flow with a single - `is_r_minor_sensitive` bool for the whole run and no per-package classification or - R-version loop. -- `upload_package_index()` writes/uploads `PACKAGES*` for the **generic slot only**; it - has no per-minor support. The current standalone r-minor workflow never builds a - per-minor index, so per-minor slots are effectively unservable today. - -## Core model - -Collapse the three tiers to one boolean per package: - -``` -r_minor_sensitive := (abi_classify(pkg)$tier == "risky") -``` - -| group | tiers | built under | slot | -| ------------------------------ | ---------------------- | -------------------- | ---------------------------- | -| non-sensitive (~86%) | pure-r, safe-compiled | primary R only | generic `contrib/` | -| sensitive (~14%) | risky | every installed minor| per-minor `contrib//` | - -- **Primary R** = the existing `R_VERSION` env var in each workflow. Its pass builds the - non-sensitive packages (generic slot) *and* the sensitive packages for its own minor slot. -- **Extra minors** = every other R version discovered by scanning `/opt/R/` at runtime. - Each runs a **sensitive-only** pass. An image with a single R version degrades cleanly - to just the primary pass. -- The loop over minors always lives at the shell/script layer (one `/opt/R//bin/R` - invocation per minor), never inside a single `build_binary_package()` call. - -Classification granularity: classify **once per package** (its release version) and apply -the resulting flag to all archived versions of that package. Tier rarely changes across -recent versions; this avoids multiplying source downloads. - -## Full build — `build-all-versions-*` + `local/` - -### install-deps step (`local/packages-to-build.R`) - -After computing `pkgs_to_build`, add an `r_minor_sensitive` logical column: - -1. Pull `NeedsCompilation` and `LinkingTo` from `tools::CRAN_package_db()` (already loaded). -2. Resolve cheaply, no download: - - `NeedsCompilation != "yes"` → not sensitive (rule 1, pure-r). - - `LinkingTo` references any `bincraft::abi_risky_linking_deps()` entry → sensitive - (rule 2). -3. For the remaining compiled, non-LinkingTo-risky packages only: download the source and - call `bincraft::needs_per_minor_recompile()` (rules 3/4). -4. Join the per-package flag onto every `(Package, Version)` row. - -Outputs: -- `pkgs_to_build.rds` — now carries the `r_minor_sensitive` column. -- `r_minor_sensitive_pkgs.rds` — the sensitive subset, for the extra-minor passes. - -### build step (`local/build-all.R` + `.crow/build-all-versions-{amd64,arm64}.yaml`) - -- `build-all.R` gains an optional `--sensitive-only` mode (or an arg flag). In normal mode - it builds the full chunk, passing `is_r_minor_sensitive = ` per package. In - sensitive-only mode it reads `r_minor_sensitive_pkgs.rds`, intersects with its chunk, and - builds those with `is_r_minor_sensitive = TRUE`. -- The workflow step keeps the existing matrix split. After the primary `Rscript build-all.R` - invocation, a shell loop discovers non-primary `/opt/R/*` minors and runs - `Rscript build-all.R --sensitive-only ` under each. -- Index upload step: generic index as today, plus a per-minor index for each minor slot - that received artifacts (depends on the `upload_package_index()` enhancement below). - -## Iterative build — `process-updates-*` - -Driven by the bincraft enhancement below; the single build step becomes: - -1. Primary-R pass: - `process_cran_updates(…, r_minor_detection = "classifier")`. - Each updated/new package is classified; risky → primary minor slot, rest → generic slot. - Removed-package handling stays as-is. -2. Shell loop over non-primary `/opt/R/*` minors: - `process_cran_updates(…, r_minor_detection = "classifier", r_minor_sensitive_only = TRUE)`. - Builds only risky updates into their respective minor slots. -3. Index upload extended to cover each touched minor slot in addition to the generic slot. - -## Required bincraft enhancements (separate PR, coordinated release) - -`build_binary_package()` needs **no change** — it already accepts a concrete -`is_r_minor_sensitive` logical and routes the slot accordingly. Classification stays at -the orchestration layer (mirroring the full-build precompute), which keeps -`build_binary_package`'s pre-build S3 skip-check and source clone untouched. - -1. `process_cran_updates()`: - - Add `r_minor_detection = c("none", "issue", "classifier")` (default `"none"` to - preserve current behavior; `"issue"` is today's `filter_r_minor_sensitive` path). - - Add `r_minor_sensitive_only` (default `FALSE`). - - With `"classifier"`: for each candidate `(name, version)`, clone the source to a temp - dir and call `bincraft::needs_per_minor_recompile()`; pass the resulting concrete - logical as `is_r_minor_sensitive` to `build_binary_package()`. When - `r_minor_sensitive_only = TRUE`, drop non-risky candidates before building. - - Implemented via a small internal helper `classify_r_minor_sensitive(name, tag, - source_org_url, local_clone_dir)` returning a logical — the unit-testable seam. -2. `upload_package_index()`: - - Add an `r_minor = NULL` argument. When non-NULL (e.g. `"4.4"`), point the remote dir - at `…/contrib//` and write/upload `PACKAGES*` (and `Meta/archive.rds`) there, - mirroring the generic-slot logic. Extract the remote-dir construction into a pure - helper `package_index_remote_dir(s3_bucket, arch, codename, r_minor = NULL)` — the - unit-testable seam. - -These two are the only bincraft changes; detection itself (PR #49) is already merged. - -## Scope and cleanup - -- In scope: `.crow/process-updates-*` (iterative) and `.crow/build-all-versions-*` + - `local/build-all.R` + `local/packages-to-build.R` (full), across amd64 and arm64 and all - platforms (alpine, ubuntu, redhat). The per-platform workflow files share the same edit. -- Removed: `.crow/build-r-minor-sensitive-packages.yaml` — superseded by the integrated - flow (it was manual, alpine-3.21-only, and issue-list-driven). -- Out of scope (call out, do not change here): `weekly-rebuild-missing-*`, - `archive-missed-packages`, and the audit workflows. Revisit separately if per-minor - rebuilds are wanted there too. - -## Open risks / notes - -- **R-version discovery**: assumes `/opt/R//bin/R` layout and that the primary - `R_VERSION` is one of the installed versions. Parse minor as `major.minor` from each - discovered version; dedupe by minor (build once per minor even if two patch releases - coexist). -- **Per-minor index correctness**: clients resolving `bin//contrib//` require the - per-minor `PACKAGES` to exist; the `upload_package_index()` enhancement is a hard - dependency for the sensitive artifacts to be usable. Verify against a real client - install before declaring done. -- **Classification cost**: bounded by downloading sources only for the compiled, - non-LinkingTo-risky subset in install-deps. Worth measuring on a full run; if still too - heavy, consider caching classifications keyed by package+version in the metadata DB. -- **Double download**: install-deps classification downloads some sources that the build - step re-downloads. Acceptable for now; the metadata-DB cache above would also remove this.