Repository files (latest commit first)

Filename	Latest commit message	Latest commit date
pat-s 0da29ab3f6 fix(index): add a slot repair for a broken Built stamp and retire alpine 3.21 (#150) ... ## 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: #150		2026-08-07 09:15:04 +00:00
..
patches	fix(patches): force RcppParallel to use its bundled oneTBB (#146)	2026-07-31 09:48:41 +00:00
tests	refactor: migrate package installation from pak to uvr (#147)	2026-07-31 12:19:26 +00:00
archive-missed-pkgs.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
build-all.R	refactor: migrate package installation from pak to uvr (#147)	2026-07-31 12:19:26 +00:00
build-one.R	feat: patch registry + wiring for per-package patching (#103)	2026-06-30 08:50:19 +00:00
check-cdn-cache.sh	add alpine321 to scripts	2024-12-29 10:18:55 +01:00
check-NA.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
debug-packages-writing.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
dedupe-audit-issue.R	fix(audit): replace arch subsection in place instead of appending duplicates (#138)	2026-07-21 08:51:23 +00:00
detect-duplicates.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
excluded-packages.json	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
failing-builds-classify.R	feat(local): aggregate blocked-on-dependency reporting by dependency (#131)	2026-07-16 21:24:03 +00:00
failing-builds-report.R	feat(local): detect dependency-cascade failures generally, not just RcppParallel (#128)	2026-07-16 08:23:54 +00:00
fetch-rebuild-packages-from-issue.R	fix(audit): replace arch subsection in place instead of appending duplicates (#138)	2026-07-21 08:51:23 +00:00
find-R-api-packages.sh	chore(local): add S3 migration and CRAN-source helper scripts	2026-06-14 13:02:48 +02:00
install-bincraft.R	refactor: migrate package installation from pak to uvr (#147)	2026-07-31 12:19:26 +00:00
label-removed-cran-packages.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
last-processed-by-platform.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
migrate-s3-hetzner-to-backblaze.sh	chore(local): add S3 migration and CRAN-source helper scripts	2026-06-14 13:02:48 +02:00
missing-cran-packages-db.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
missing-cran-packages.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
missing-packages-in-index.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
packages-to-build.R	refactor: migrate package installation from pak to uvr (#147)	2026-07-31 12:19:26 +00:00
packages-without-any-binary.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
proposal-tracking-lib.R	feat(local): aggregate blocked-on-dependency reporting by dependency (#131)	2026-07-16 21:24:03 +00:00
proposal-tracking.R	feat(local): aggregate blocked-on-dependency reporting by dependency (#131)	2026-07-16 21:24:03 +00:00
propose-patches.R	feat(local): aggregate blocked-on-dependency reporting by dependency (#131)	2026-07-16 21:24:03 +00:00
query-pkgs-without-old-versions.R	chore(local): add S3 migration and CRAN-source helper scripts	2026-06-14 13:02:48 +02:00
r-minor-helpers.R	refactor: migrate package installation from pak to uvr (#147)	2026-07-31 12:19:26 +00:00
repair-built-stamp.R	fix(index): add a slot repair for a broken Built stamp and retire alpine 3.21 (#150)	2026-08-07 09:15:04 +00:00
test-package-loading.R	refactor: migrate package installation from pak to uvr (#147)	2026-07-31 12:19:26 +00:00
trial-build-patch.R	fix(local): make trial-build-patch.R detect non-throwing build failures (#134)	2026-07-18 08:37:04 +00:00
trial-build-registry.R	fix(local): make the trial-build gate detect non-throwing build failures (#130)	2026-07-16 08:24:03 +00:00
uvr-install.sh	chore(deps): update dependency nbafrank/uvr to v0.4.5	2026-08-04 02:32:01 +00:00
validate-patches.R	feat(local): auto-propose registry patches and track the feedback loop (#117)	2026-07-14 15:03:24 +00:00
weekly-missing-binaries-audit.R	fix(audit): replace arch subsection in place instead of appending duplicates (#138)	2026-07-21 08:51:23 +00:00