Author	SHA1	Message	Date
pat-s	0703969088	fix(audit): count a source fallback as a missing binary (#157) ... ## 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: #157	2026-08-09 10:37:41 +00:00
pat-s	71f3f0c601	fix(audit): replace arch subsection in place instead of appending duplicates (#138) ... ## 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 `### <arch>` 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 (`^### <arch>( |$)`) 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: #138	2026-07-21 08:51:23 +00:00
pat-s	d558e27c11	feat: R-minor-sensitive binary builds (full + iterative) (#84) ... ## Summary Builds R-minor-sensitive CRAN packages once per installed R minor version (into per-minor S3 slots `…/contrib/<x.y>/`) and everything else once into the generic slot, driven by bincraft 4.2.0's ABI classifier. Both the full and iterative pipelines are covered. ## What's in here **Detection / precompute** - `local/r-minor-helpers.R` — pure `classify_from_metadata()` (NeedsCompilation / risky `LinkingTo`) + `parse_build_args()`, with unit tests. - `local/packages-to-build.R` — adds a per-package `r_minor_sensitive` flag: cheap CRAN-metadata rules first, source download + `bincraft::needs_per_minor_recompile()` only for the ambiguous compiled subset (fail-safe to sensitive). Classified once per package, applied to all versions. **Full build** - `local/build-all.R` — passes the per-row `is_r_minor_sensitive` flag; new `--sensitive-only` mode builds just the risky subset. - `.crow/build-all-versions-{amd64,arm64}.yaml` — install-deps persists the sensitive subset; build step runs a sensitive-only pass under each non-primary `/opt/R/*` minor; new step uploads the generic index plus a per-minor index for each minor. **Iterative build** - All 14 `.crow/process-updates-*.yaml` — primary pass uses `r_minor_detection = 'classifier'`; a sensitive-only multi-R pass builds risky updates under each other minor; per-minor index upload added. **Tooling / housekeeping** - Pins bincraft `v4.1.1` → `v4.2.0` across all workflows; removes the superseded standalone `build-r-minor-sensitive-packages.yaml`. - Adds prek/pre-commit hooks (prettier, markdownlint, editorconfig-checker, yamllint, air) and applies them repo-wide; excludes the verbatim GPL `LICENSE.md` and auxiliary shell scripts. - Design + implementation docs under `docs/superpowers/`. ## Requires before merge - A `v4.2.0` git tag must be pushed on the bincraft repo (codefloe.com/rpkgs/bincraft) — the workflow install steps pin `@v4.2.0`. The full-build install-deps clones `main`, so it is unaffected. Reviewed-on: #84	2026-06-14 08:04:40 +00:00
pat-s	84c59d1984	fix: audit workflows	2026-04-21 21:54:48 +02:00
pat-s	ffb8c42511	feat: add weekly missing binaries audit R script	2026-04-11 21:41:59 +02:00