Repository files (latest commit first)

Filename	Latest commit message	Latest commit date
pat-s 523424bd68 fix(abi): inspect flat objects of packages CRAN has removed (#212) ... ## Why The backfill decided which flat objects were worth inspecting by looking the package up in **CRAN's current index**: ```r compiled_names <- cran[NeedsCompilation == "yes", "Package"] keep <- flat_pkg %in% compiled_names ``` CRAN lists only what it currently ships. A package CRAN has **archived** is absent from that index, so it is never recognised as compiled and never inspected, and no verdict is ever recorded for it. `union_index_records()` meanwhile reads the slot's *own* `NeedsCompilation`, finds `yes`, and drops the record because the source classifier flags the package and no safe verdict exists to clear it. The repair cannot rescue it either: it works from recorded verdicts, and there is no row. The result is unrecoverable, and identical in shape to #132 but from a different cause: dropped from every per-minor index, on every re-index, forever. ## Evidence `mixedMem` and `vcpen` survived a backfill, two re-indexes and a repair while missing from all three rhel8 per-minor indexes on **both** architectures: ``` rhel8 amd64 4.5: missing=3 [mixedMem timbr vcpen] rhel8 arm64 4.5: missing=2 [mixedMem vcpen] ``` Neither appears anywhere in either repair log, because neither was ever in the unsafe set. Their per-minor objects are 404 at every minor. And in CRAN's index: ``` mixedMem CRAN version=ABSENT NeedsCompilation=ABSENT vcpen CRAN version=ABSENT NeedsCompilation=ABSENT ``` Both removed from CRAN. Their flat records in our own index say `NeedsCompilation: yes`. ## What changed `NeedsCompilation` now comes from the slot's own flat index, which describes exactly the objects being inspected rather than a different repository's opinion of them. - Fetched **from the bucket**, not over HTTPS. This runs inside R, so the edge would route the request to a per-minor index and the flat objects would not all be there. Same reason the object listing above it comes from S3 (#203). - Keyed on `<package>_<version>`, not the package name: a slot can carry several versions and only some of them compile. - Refuses to proceed on an empty read, so an unreadable index cannot silently mean "nothing is compiled" and skip the entire slot. ## Effect Re-running the backfill on a slot will now inspect these objects and record verdicts, after which the index writer keeps the safe ones and the repair can act on the unsafe ones. Already-recorded objects are still skipped, so re-running stays cheap. Reviewed-on: #212		2026-09-09 18:35:33 +00:00
..
patches	fix(patches): support RcppParallel 6.2.1	2026-08-30 14:26:37 +00:00
tests	feat(rebuild): shard the weekly rebuild and make each shard resumable (#163)	2026-08-12 08:30:29 +00:00
archive-missed-pkgs.R	feat: R-minor-sensitive binary builds (full + iterative) (#84)	2026-06-14 08:04:40 +00:00
backfill-abi-classification.R	feat(abi): backfill classifier verdicts for pre-per-minor packages (#199)	2026-09-04 10:34:49 +00:00
backfill-flat-safety.R	fix(abi): inspect flat objects of packages CRAN has removed (#212)	2026-09-09 18:35:33 +00:00
build-all.R	fix(build): strip the s3 scheme so per-minor objects reach their pass (#192)	2026-09-02 07:11:10 +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
list-unsafe-flat-objects.R	fix(abi): do not error on the nothing-to-repair path (#208)	2026-09-09 10:55:15 +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	fix(build): scope the errored-package filter to the snapshot's R minor (#194)	2026-09-03 13:37:04 +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
prune-stale-flat-binaries.R	fix(abi): prune the objects recorded broken, not every risky package (#211)	2026-09-09 15:01:21 +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
rebuild-missing-helpers.R	feat(rebuild): shard the weekly rebuild and make each shard resumable (#163)	2026-08-12 08:30:29 +00:00
rebuild-missing.R	feat(rebuild): shard the weekly rebuild and make each shard resumable (#163)	2026-08-12 08:30:29 +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	fix(rebuild): harden split workflow setup (#164)	2026-08-13 13:38:28 +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
verify-repo-routing.R	fix(ci): do not print a missing timing as "NAs" (#210)	2026-09-09 15:01:29 +00:00
weekly-missing-binaries-audit.R	fix(audit): count a source fallback as a missing binary (#157)	2026-08-09 10:37:41 +00:00