Author	SHA1	Message	Date
pat-s	98371fb9c5	fix(patches): replace the RcppParallel system-TBB patch with a link-order fix (#145) ... ## 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 The workaround it implemented is obsolete too. 6.x bundles **oneTBB 2022** and builds it with cmake, which works on musl and with g++ 8-15, so the 5.x reason for linking a system TBB is gone.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: #145	2026-07-31 06:41:46 +00:00
pat-s	8d0c4b7ccd	fix(patches): widen RcppParallel system-tbb scope to the whole redhat family (#139) ... 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: #139	2026-07-28 06:57:08 +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	3cc323d99e	fix(patches): widen RcppParallel system-tbb scope to all oneTBB-2021 platforms (#137) ... ## 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: #137	2026-07-20 20:59:47 +00:00
pat-s	6df945d147	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: #135	2026-07-20 09:56:21 +00:00
pat-s	b4b7d53a83	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 <pkg>`) -- 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: #134	2026-07-18 08:37:04 +00:00
pat-s	6c03f278ec	feat(local): aggregate blocked-on-dependency reporting by dependency (#131) ... ## 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: #131	2026-07-16 21:24:03 +00:00
pat-s	118a92889f	fix(local): make the trial-build gate detect non-throwing build failures (#130) ... ## 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: #130	2026-07-16 08:24:03 +00:00
pat-s	f9d399fac0	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: #128	2026-07-16 08:23:54 +00:00
pat-s	ff9f5f5177	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: #126	2026-07-15 15:43:02 +00:00
pat-s	1bca6004fd	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: #125	2026-07-15 14:50:19 +00:00
pat-s	4bca17e4ac	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: #124	2026-07-15 08:28:15 +00:00
pat-s	21a2fe9e6c	feat(local): report unclassified and dependency-blocked failures for discovery (#122) ... ## Why Issue #120 (the auto-proposed-patches issue) only lists **auto-proposable** fixes -- currently just the TBB signatures. So a reasonable read of it was "TBB is our only build failure", when in fact three whole categories are simply not shown there: - **Unclassified failures** -- anything that doesn't match a seeded signature is routed to human triage and never appears (we've only seeded TBB and libuv signatures). - **Dependency-blocked failures** -- the ~800 RcppParallel dependents (post #121) are still failing; they only show as a log line. - Human-only signatures (libuv). These blind spots are exactly where the *next* signatures should come from, so they deserve the same visibility as the proposals. ## What Extend the feedback-loop tracker to surface the classifier's blind spots: - **`unclassified_summary()`** -- groups every unknown-signature failure by normalised fingerprint, ranked by build count, capped with an explicit `dropped_groups` count (no silent truncation), each with example packages + platforms. These are the candidates for new `build_signatures()` rules. - **`blocked_summary()`** -- lists each dependency (e.g. RcppParallel) and how many dependents wait on it. - `proposal-tracking.R` prints both sections, and a new **`--open-issue`** mode posts/updates a *"Unclassified build failures (needs signatures) (#115)"* Forgejo issue. - The weekly crow pipeline now runs the tracker with `--open-issue`, so it maintains a second tracking issue alongside the proposals one. Read-only on the DB; the only writes are the two issues. ## Verification - New tests cover `unclassified_summary` (ranking + both caps) and `blocked_summary`. - Tracker smoke with a stubbed DB (proposable + blocked + unclassified mix) prints the hit rate, `Blocked on a dependency: RcppParallel: 2 dependent(s)`, and `Unclassified failures ... [2 builds | 2 pkgs] ld: undefined reference ...`. - Full suite: 95 tests pass; all pre-commit hooks pass (air, prettier, markdownlint, yamllint, validate-patches). Reviewed-on: #122	2026-07-15 07:46:29 +00:00
pat-s	9bc4973159	fix(local): stop proposing per-dependent patches for dependency-cascade failures (#121) ... ## Problem The scheduled `--open-issue` run (issue #120) posted **800+** proposed entries, all `rcppparallel-bundled-tbb` on `ubuntu-2604`, each pre-filling `RcppParallel/disable-tbb.patch` for an unrelated package (`ACEsimFit`, `AovBay`, `AdaptGauss`, ...). Root cause: those packages fail on ubuntu-2604 only because their **RcppParallel dependency** does not build there. bincraft records RcppParallel's TBB error text against each dependent, so every one of them matches the `rcppparallel-bundled-tbb` signature. Proposing a RcppParallel source patch for `ACEsimFit` is not just noise -- it is **broken**: the diff targets RcppParallel's `Makevars.in`, so it cannot apply to a dependent's source. ## Fix Add an optional `applies_to` field that pins a package-specific fix to the package it targets: - A signature whose fix is a curated per-package source patch (`rcppparallel-bundled-tbb` -> `RcppParallel`) is only ever proposed **for that package**. - Other packages matching the signature are downstream failures, reported as **"blocked on `<dependency>`"** and never proposed a bogus entry. Fix the dependency once and the whole cascade clears. Generic levers (the `tbb-stddef-removed` makevars fix) are unaffected -- they carry no `applies_to`, so they still apply to any matching package. ## Changes - gate proposal generation in `build_triage_report()` on `applies_to`; add a `blocked_on` field to group records - surface blocked groups in both `failing-builds-report.R` and `propose-patches.R` instead of the misleading "already registered" note - document `applies_to` in the signature-table header ## Verification - New tests: RcppParallel dependents are blocked (no `proposed_entries`, `blocked_on = "RcppParallel"`), while RcppParallel *itself* is still proposed when it is the failing package. - Reproduced the avalanche end-to-end with a stubbed DB: 5 dependents now report "Blocked on RcppParallel: 5 package(s) fail because RcppParallel does not build" and **zero** candidates are emitted; a genuine `tbb-stddef` proposal in the same run is unaffected. - Full suite: 84 tests pass; all pre-commit hooks pass. Refs #120. Note: the underlying build problem (RcppParallel failing on ubuntu-2604 despite its registry entry) is real and separate -- this PR stops the classifier from spamming broken per-dependent proposals about it. Reviewed-on: #121	2026-07-14 18:40:41 +00:00
pat-s	f1dd661213	fix(local): route multi-signature packages to human triage in the proposer (#119) ... ## Problem A live `propose-patches.R --open-issue` run aborted with: ``` Patch registry validation FAILED: - ambiguous duplicate entries: hmmTMB|ubuntu-2604|*, imt|ubuntu-2604|*, refundBayes|ubuntu-2604|* Error: Candidate registry failed validation; not writing or proposing. ``` Root cause: a package whose failing builds match **more than one** auto-proposable signature (e.g. some logs hit `tbb-stddef-removed`, others `rcppparallel-bundled-tbb`) landed in two separate signature groups, so the proposer emitted two candidate entries with the same `package|platforms|versions` key. The validator's ambiguous-duplicate check then failed the whole candidate set, aborting the run — so even the unambiguous candidates (e.g. `vacalibration`) never got proposed. ## Fix Add a pure, tested `dedupe_candidates()` that: - keeps a package's candidate only when it maps to a **single** signature (collapsing an accidental repeat under the same signature), and - routes a package that maps to **multiple** signatures (conflicting fix tiers -- makevars vs source patch) to **human triage** instead of guessing between them. The proposer prints the skipped ambiguous packages and proceeds with the clean candidates, so one ambiguous package no longer blocks the rest. This matches the issue #115 guardrail: don't auto-pick when the fix is ambiguous. ## Verification - New unit tests in `test-proposal-tracking-lib.R` cover the single-signature, multi-signature (conflict), duplicate-under-one-signature, and empty cases. - Reproduced the original failure end-to-end with a stubbed DB (`hmmTMB` ambiguous + `vacalibration` clean): `hmmTMB` is now listed under "Ambiguous -> human triage", `vacalibration` is proposed, and the candidate registry validates (`Patch registry OK`). - Full suite: 78 tests pass; all pre-commit hooks pass. Reviewed-on: #119	2026-07-14 17:11:54 +00:00
pat-s	af481f5129	ci(crow): add weekly patch-proposal + feedback-loop pipeline (#118) ... Adds the scheduled pipeline for the failure-triage proposer/tracker landed in #117 (issue #115, steps 3 + 4). ## `.crow/weekly-patch-proposals.yaml` A single (non-matrix) job -- the classifier groups over all of `single_builds`, so unlike the per-platform `weekly-audit-missing` it runs once globally. Weekly it: 1. `propose-patches.R --open-issue` -- posts/updates a Forgejo tracking issue with the auto-proposable registry entries (human reviews, trial-builds, opens the PR; nothing merges). 2. `proposal-tracking.R` -- logs the feedback-loop metrics (signature hit rate, proposed-vs-merged, retirement candidates). Low blast radius: clones read-only (`REPO_RO_TOKEN`); the only write is the tracking issue via `FORGEJO_TOKEN`. It builds nothing (no B2 keys, no bincraft). Triggers: `cron: weekly-patch-proposals` (register the cron in the crow UI) or manual with `task=weekly-patch-proposals`, matching the `archive-missed-packages` convention. Documented under "Scheduled run" in `local/patches/README.md`. `yamllint` and the other pre-commit hooks pass. Reviewed-on: #118	2026-07-14 15:17:16 +00:00
pat-s	1c297c01bf	feat(local): auto-propose registry patches and track the feedback loop (#117) ... Implements steps 3 + 4 of #115, building on the classifier merged in #116. Now that bincraft **v4.4.3** applies registry `patch`/`makevars`/`configure_args` to the *target* package build (previously deps-only), a trial patched build is a meaningful acceptance gate, so the "propose" half is viable. ## Step 3 — propose, do not apply - **`local/propose-patches.R`** — for each classified, safe fix affecting a package with no current registry entry, emits a pre-filled `registry.json` entry and validates the candidate set against a *temporary* merged registry (the real one is never touched unless asked). - default: print candidates + validation, **take no action** - `--write`: append entries to `registry.json` + the proposals ledger (you commit + open the PR) - `--open-issue`: post/update a Forgejo tracking issue (reuses the weekly-audit `httr2` + `FORGEJO_TOKEN` pattern) - **`local/trial-build-patch.R`** — isolated bincraft build of one package with the registry applied (no upload/archive/metadata; `patchhash` keeps it out of the real cache). Exit 0/1, so it gates a CI step or manual pre-merge check. The human gate stays: nothing merges. Acceptance = `validate-patches.R` passes (checked automatically) **and** the trial build succeeds. Novel source diffs and unknown signatures are never proposed (they carry `auto = FALSE`). ## Step 4 — feedback loop - **`local/proposal-tracking.R`** (read-only) — signature hit rate (builds/pkgs/addressed/open per signature), proposed-vs-merged (a proposal counts merged once its package is in the registry), and retirement candidates (registry entries whose package no longer fails, i.e. likely fixed upstream). - **`local/proposal-tracking-lib.R`** — the pure metric/ledger helpers. ## Supporting changes - Refactored the classify helpers to expose a pure `build_triage_report()` + a list-returning entry builder; `failing-builds-report.R` now renders from the shared function (no behaviour change). - `validate-patches.R` gains optional `PATCH_DIR`/`REGISTRY_FILE` overrides (backward-compatible) so a candidate registry can be validated in isolation. - Documented the propose/trial-build/tracking workflow in `local/patches/README.md`. ## Verification - 71 unit tests pass (incl. new `test-proposal-tracking-lib.R`) under the Dockerized R 4.5.3 build env. - All pre-commit hooks pass (`air-format`, `validate-patches`, prettier, etc.). - Smoke-tested all three entrypoints end-to-end with a stubbed DB: dry-run, `--write` (produces a registry that passes the canonical validator + a valid ledger, then reverted), and the tracker. Closes #115 Reviewed-on: #117	2026-07-14 15:03:24 +00:00
pat-s	f11ba7172f	feat(local): classify failing binary builds and pre-fill registry suggestions (#116) ... Implements steps 1 + 2 of #115: turn recorded build failures into triaged patch suggestions instead of hand-scraping Crow logs. ## What this adds A **read-only** reporting pipeline over the `single_builds` metadata table. It never writes to the DB or the registry. - `local/failing-builds-classify.R` — pure, DB-free helpers: - `normalise_error()` strips temp paths, version numbers, hex addresses, and the package name so the same root cause collapses to one fingerprint. - `fingerprint_error()` extracts the salient error line and normalises it. - `classify_error()` matches against a seed signature set; unmatched errors are never guessed at. - `propose_registry_entry()` renders a schema-valid `registry.json` entry. - `local/failing-builds-report.R` — entrypoint: queries `single_builds WHERE error_occurred = TRUE AND removed = FALSE`, groups by root cause (signature when classified, fingerprint otherwise), classifies each group, and prints a triaged report. Flags: `--platform`, `--arch`, `--min`, `--json`; `PLATFORM`/`ARCH` env fallbacks. - `local/tests/test-failing-builds-classify.R` — unit tests for the helpers. - `local/patches/README.md` — documents the workflow. ## Seed signatures Each rule carries a fix tier, confidence, and an auto/human-only flag: | Signature | Fix | Disposition | | --- | --- | --- | | `tbb/tbb_stddef.h: No such file` | makevars `-DTBB_INTERFACE_NEW` | auto-proposable | | RcppParallel bundled TBB (musl / new g++) | curated `disable-tbb.patch` | auto-proposable | | system `libuv.so` link leak | force vendored/static lib | **human triage** (novel source diff) | | unmatched | none | **human triage** | ## Guardrails honored - No autonomous novel source diffs: only known env/makevars levers and already-curated package patches are auto-proposable; anything needing a brand-new diff, and any unknown signature, is routed to human triage. - No DB or registry writes; no change to the public `src/contrib` index. - Reuses `single_builds.error_text`; no new failure-capture pipeline. ## Verification - All helper unit tests pass under the Dockerized R 4.5.3 build env. - Pre-commit hooks pass (`air-format`, `validate-patches`, prettier, etc.). - Smoke-tested the full report path with a stubbed DB; generated proposals pass the real `local/validate-patches.R`. Steps 3 (auto-open PRs) and 4 (feedback loop) are intentionally deferred, per the issue's suggestion to validate the signature set first. Closes #115 Reviewed-on: #116	2026-07-14 14:45:25 +00:00
pat-s	04059f20e3	fix(patches): add rstan entry to skip removed tbb_stddef.h (#114) ... ## Motivation `rstan` fails to compile when it is pulled in as a transitive dependency (e.g. of `ctsem`), aborting the dependency install: ``` /mnt/cache/R-pkgs/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: tbb/tbb_stddef.h: No such file or directory 9 | #include <tbb/tbb_stddef.h> ``` StanHeaders' `init_threadpool_tbb.hpp` unconditionally includes the legacy `<tbb/tbb_stddef.h>` to detect the TBB version, but that header was removed in oneTBB 2021+, which is the TBB that StanHeaders now bundles. ## Fix Add an `rstan` entry to `local/patches/registry.json` that pre-defines `TBB_INTERFACE_NEW` via `CPPFLAGS`. The header's own guard skips the removed include when that macro is already defined and selects the modern `tbb/global_control.h` + `tbb/task_arena.h` path that the bundled oneTBB actually provides: ```cpp #ifndef TBB_INTERFACE_NEW #include <tbb/tbb_stddef.h> // removed in oneTBB 2021+ #if TBB_VERSION_MAJOR >= 2020 #define TBB_INTERFACE_NEW #endif #endif #ifdef TBB_INTERFACE_NEW #include <tbb/global_control.h> // taken when we pre-define the macro #include <tbb/task_arena.h> ``` This is a makevars-tier override (no source diff), applied through bincraft's `R_MAKEVARS_USER`, so `CPPFLAGS` stays additive and does not clobber rstan's own `PKG_CPPFLAGS`. `-I/usr/local/include` is kept because the override replaces the default `CPPFLAGS`. ## Files changed - `local/patches/registry.json`: add the `rstan` entry (`versions: "*"`, `platforms: ["*"]`, `makevars.CPPFLAGS = "-DTBB_INTERFACE_NEW -I/usr/local/include"`). ## Behaviour change When bincraft resolves `rstan` (direct or transitive) it builds a patched binary with `TBB_INTERFACE_NEW` defined, so `rstan` (and dependents such as `ctsem`) compile against the bundled oneTBB. The scope is `["*"]` because the failure is bound to StanHeaders' bundled TBB version, not the OS or toolchain. Reviewed-on: #114	2026-07-14 13:52:17 +00:00
pat-s	a4b274f281	fix(ci): bound pkgcache _metadata growth to stop macmini disk-fill (#110) ... ## Problem The arm64 `build-all` pipeline fills the macmini (gaia) host disk despite an 8h prune. Root cause is not images or job volumes: it is the persistent dep-cache volume, specifically `pkgcache/R/pkgcache/_metadata`, which grew to ~165 GB. `{pkgcache}` mints a new content hash for the "patched" binaries repo on every PACKAGES change, so each per-package build writes a fresh ~70 MB `pkgs-<hash>.rds` (+ `patched-<hash>/`) that is never evicted (2407 snapshots observed). When the disk hits 100% OrbStack stops and the on-host prune can no longer connect to the daemon, so it never self-heals. ## Change (Workstream A of the disk-fill fix) - Add `trim_pkgcache_metadata()` to `local/r-minor-helpers.R`: keeps the newest `keep` (default 20) `patched-*`/`pkgs-*.rds` entries under `_metadata`, deleting only entries older than `min_age_secs` (default 600s) so it never races the up-to-4 concurrent split-jobs sharing the volume. Preserves `pkg/` downloads and the stable CRAN/BioC/INLA repo dirs. No-op when `R_PKG_CACHE_DIR` is empty (amd64) or `_metadata` is absent (first run). - Call it every 25 packages inside the build loop in `local/build-all.R`. - Add a defensive start-of-run cleanup of `_metadata/patched-*` + `pkgs-*.rds` to the two workflows that mount the persistent volume (`build-all-versions.yaml`, `build-all-versions-install-deps.yaml`). Only these paths are touched; `process-updates.yaml`/`weekly-rebuild-missing.yaml` (no persistent volume) are unchanged. Follow-ups (separate workstreams): on-host self-healing prune watcher + OrbStack disk cap (ansible), and Prometheus/Grafana alerting (k8s-talos). Upstream: bincraft patched-repo hash churn is the true source fix. New unit tests (6) for the helper; full suite 24/24 green. Reviewed-on: #110	2026-07-13 09:31:29 +00:00
pat-s	ffc2319558	fix(build-all): exclude previously-errored versions in prefilter (#113) ... ## Motivation Build jobs were cycling through hundreds of packages that were only ever printed as `Skipping … due to previous build error recorded in metadata DB`, wasting wall-clock on per-package preparation before dropping each one. ## Cause The prefilter query in `local/build-all.R` selected only successfully-built versions (`error_occurred = FALSE`) into `built`, so line 112 removed only those from the chunk. Every previously-errored version stayed in the work list and was walked one-by-one, each hitting the internal skip in `build_binary_package()`. This also explains the misleading `Skipped 0 already-built package versions` line for alphabetical chunks whose leading packages only have error records. ## Changes - `local/build-all.R`: drop the `AND error_occurred = FALSE` clause so `built` holds every version already attempted (built or errored) for this platform/arch; the existing filter then removes all of them up front. - Rename the log line to `already-attempted` so the reported count reflects successes and errors. - Update the surrounding comment to explain why errored versions are excluded. ## Behaviour change Previously-errored versions are now dropped before the build loop instead of being iterated and individually skipped. No package that would otherwise build is affected, `build_binary_package()` already skipped these internally. Retrying errored versions is out of scope and would need a separate opt-in flag on both the prefilter and the in-loop skip. Reviewed-on: #113	2026-07-13 09:28:45 +00:00
pat-s	36d3bc8604	fix(patches): force fs to build vendored static libuv (#111) ... ## Problem The `fs` 2.1.0 binary links **system libuv** (`readelf -d fs.so` shows `NEEDED libuv.so.1`). fs's `configure` prefers system libuv whenever `pkg-config` resolves it, and our build images ship `libuv-devel` (installed as a pak build-time system requirement), so the resulting binary is dynamically linked against `libuv.so.1`. That binary fails to load on any consumer machine without runtime libuv: ```text unable to load shared object '.../fs/libs/fs.so': libuv.so.1: cannot open shared object file: No such file or directory ``` `install.packages()`/renv do **not** install `SystemRequirements` (only `pak` does, and only inside the build container), so most consumers hit this. Older fs 1.6.x always vendored libuv, so only the 2.x binaries regressed. Reproduced in a clean `reg.devxy.io/r/r-alma:4.5-9`. ## Fix Add `local/patches/fs/force-vendored-libuv.patch`, registered for all platforms. It short-circuits `configure` to `cp -f src/Makevars.vendor src/Makevars; exit 0` before the pkg-config detection, forcing the bundled static libuv build (`tools/libuv-v1.52.0.tar.gz`, built via cmake). An env/pkg-config override (`PKG_CONFIG_LIBDIR`) was tried first but the rebuilt binary still linked `libuv.so.1` (the registry `env` tier does not reach fs's configure step), so a source patch is used instead. ## Verification Built end-to-end inside the real `build-env-redhat:9` image (system libuv present): - patch fires (`Building static libuv (bincraft: forced vendored)`), - cmake compiles the vendored libuv, - resulting `fs.so` has **no `libuv.so.1`** in `NEEDED` (only libR, libstdc++, libm, libgcc_s, libc). `Rscript local/validate-patches.R` passes (2 entries). cmake confirmed present in the build-env images. ## Follow-up (not in this PR) - Rebuild `fs 2.1.0` on every affected platform (rhel8/9/10, ubuntu jammy/noble, alpine 3.22/3.23; amd64 + arm64) and purge the CDN binary paths. - CDN delivery gap: `purge_cdn_cache.sh` only purges `PACKAGES*`, never package binaries, so rebuilt binaries stay masked until their `.tar.gz` path is purged. Reviewed-on: #111	2026-07-07 18:12:36 +00:00
pat-s	1ad7a6bfe9	chore: resolve latest bincraft release dynamically (no hardcoded pins) (#107) ... ## Summary Stop hardcoding the bincraft version. Every `.crow` workflow and the build-one image pinned `@vX.Y.Z` (and a `packageVersion() != "X.Y.Z"` guard), so each bincraft release meant editing the version in ~8 places — and it was easy to miss one (the Dockerfile lagged at v4.2.1; v4.4.1 shipped without the empty-env fix because of exactly this churn). ## Change New `local/install-bincraft.R` resolves the **latest release tag dynamically**: - `git ls-remote --tags` on the public repo (no token), - keep `vX.Y.Z` tags, pick the highest version (filtered/sorted in R for portability, not via git `--sort`/refspec which behaved inconsistently under `system2()`), - `pak::pak("git::…@<latest>")` — idempotent on the git ref, so re-runs keep the package unless a newer tag exists. All call sites now invoke the helper instead of a pinned version: - `.crow/build-all-versions.yaml` (primary + per-minor pass) - `.crow/build-all-versions-install-deps.yaml` - `.crow/process-updates.yaml` (primary + per-minor pass) - `.crow/weekly-rebuild-missing.yaml` - `.crow/archive-missed-packages.yaml` - `docker/build-one.Dockerfile` (ships the helper into the image; `ensure_bincraft` sources it) ## Effect Tag a new bincraft release → the next CI run / `just rebuild` picks it up automatically. No more pin edits, and no more "forgot to bump the Dockerfile" drift. ## Verified - Resolver returns the current latest tag (`v4.4.2`) via `git ls-remote` + R-side version sort. - All five workflow YAMLs parse; helper R parses; air/editorconfig clean. Note: this tracks the latest **tag**, so cutting a release is still the deliberate gate — CI won't pick up un-tagged main. Reviewed-on: #107	2026-07-01 08:10:02 +00:00
pat-s	e59590e2d6	fix: RcppParallel disable-TBB source patch (env var was a no-op) (#106) ... ## Summary Fixes the RcppParallel patch, which was a **no-op** and left the build hanging. The previous registry entry set `env: { RCPP_PARALLEL_USE_TBB: "0" }`. But `RCPP_PARALLEL_USE_TBB` is a **compile-time `-D` flag** in RcppParallel's Makevars — it is never read from the environment. So the override did nothing: `USE_TBB=Linux` (hardcoded from `uname`) still triggered the **bundled Intel TBB build**, which hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604). The `Applying patch …` log only meant the env was set, not that it had any effect. ## Fix Replace the env entry with a **source patch** (`local/patches/RcppParallel/disable-tbb.patch`) on `src/Makevars.in` that, on Linux: - leaves `USE_TBB` unset → the whole bundled-TBB build/link path is skipped (no hang), and - forces `PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=0` → the sources compile the **TinyThread** backend (needed because `RcppParallel.h` otherwise auto-defaults TBB on for glibc Linux). ## Verification In a Linux container, applying the patch and running `R CMD INSTALL RcppParallel`: ``` bundled_TBB_build=0 # bundled TBB build never runs * DONE (RcppParallel) # installs via TinyThread ``` ## Note bincraft's `apply_source_patch` shells out to `patch`. If a build-env image lacks the `patch` tool (common on Alpine), the patch will report "did not apply cleanly" and fall back to an unpatched (hanging) build. If that happens, the follow-up is to switch bincraft's patch application to `git apply` (git is always present) — happy to do that if needed. Reviewed-on: #106	2026-06-30 13:27:01 +00:00
pat-s	55a18fd87d	feat: patch registry + wiring for per-package patching (#103) ... ## Summary Adds the curated **patch registry** and wiring that drives bincraft's new package-patching mechanism (see bincraft PR `feat/package-patching`). Lets specific packages be patched (env/configure/Makevars overrides or source diffs) before pak installs them — including as transitive dependencies — so compiler-/OS-specific failures like RcppParallel's bundled TBB stop cascading. ## What's included - `local/patches/registry.json` — initial entry: RcppParallel with `RCPP_PARALLEL_USE_TBB=0` for alpine / ubuntu-2604, plus `local/patches/README.md` schema docs. - `local/validate-patches.R` — validates schema, referenced patch files, and ambiguous overlaps; clean failure + exit 1 (no stacktrace). - `.pre-commit-config.yaml` — a `validate-patches` hook (re-runs when the registry or the validator changes). - `local/build-one.R` / `local/build-all.R` — pass `patches = "local/patches"` to `bincraft::build_binary_package()`. - `specs/2026-06-30-package-patching-design.md` and `plans/2026-06-30-package-patching-implementation.md`. ## ⚠️ Merge ordering (blocker) This PR adds a `patches = ...` argument to `build_binary_package()` calls. The `.crow/*.yaml` workflows currently pin bincraft **v4.2.3**, which does not accept that argument — CI will error with `unused argument (patches=...)` until: 1. bincraft **v4.3.0** is released (PR `feat/package-patching`), and 2. the pin is bumped in `.crow/build-all-versions-install-deps.yaml`, `.crow/build-all-versions.yaml`, and `.crow/process-updates.yaml`. The `.crow` pin bump will be added to this PR once bincraft v4.3.0 is tagged. Do not merge before then. Reviewed-on: #103	2026-06-30 08:50:19 +00:00
pat-s	83c761b736	feat(ci): OS/OS_VERSION manual dropdowns + restore lost crow fix (#97) ... ## Summary Two changes: 1. **`OS`/`OS_VERSION` manual-run dropdowns** — give these form variables explicit `options:` lists (like `target_arch` and `R_VERSION`), so the manual-run form shows dropdowns instead of free-text, in both `build-all-versions.yaml` and `build-all-versions-install-deps.yaml`. Crow form variables are independent (no cascading), so the operator still has to pick a coherent `OS` + `OS_VERSION` combination (e.g. `redhat` + `9`, not `alpine` + `jammy`). 2. **Repairs `main`** — the crow fix from PR #96 (`bc2f6f1`) was lost when that PR was squashed (only the first commit was captured). As a result `main` currently carries the `OS: ${OS}` env vars that break Crow parsing (`unable to parse variable name`) and the unfixed `build-all.R`. This PR re-applies that fix: drop the env additions and derive `platform`/`arch` inside `build-all.R` from the container (bincraft codename → platform mapping + `Sys.info()` arch). ## Notes - `OS_VERSION` options are quoted strings so tags like `8`/`9`/`10` aren't parsed as integers. - Validated: both YAMLs parse, `build-all.R` parses. Reviewed-on: #97	2026-06-18 11:39:11 +00:00
pat-s	fa955c10bf	fix: recompute package snapshot when missing from cache (#95) ... ## Summary `build-all.R` reads three snapshot files from `/mnt/cache/packages/` that the `build-all-versions-install-deps` step precomputes: `pkgs_to_build.rds`, `r_minor_sensitive_pkgs.rds`, and `s3_cache.rds`. That cache volume is **per-agent**, so a build job scheduled on a different (fresh) agent than the one that ran install-deps finds the snapshot absent and dies at `readRDS` (`cannot open compressed file '/mnt/cache/packages/pkgs_to_build.rds'`). This adds a conditional guard at the top of `build-all.R`: when any of the three files is missing, it sources `local/packages-to-build.R` (which has all needed creds via `PGPASS` / `B2_S3_*` env, already present in the build step) and writes the derived `.rds` files — exactly mirroring the install-deps command. - The first build job on a fresh agent repopulates the shared cache, so subsequent jobs on that agent reuse it. - Concurrent jobs that also miss simply redo the work (accepted tradeoff vs. slow shared storage like NFS). - Saves use a temp-file + atomic `file.rename`, so a concurrent reader never sees a half-written `.rds`. Reviewed-on: #95	2026-06-17 17:49:04 +00:00
pat-s	1cd86b65e1	feat(build): skip already-built package versions on workflow restart (#91) ... ## Summary When a `build-all-*` workflow is restarted, the build job re-reads the static `pkgs_to_build.rds` that the install-deps step produced once, so it cycles over every package an interrupted run already built. This adds a DB-based skip filter so a restart only processes what is genuinely left. - At job start, `build-all.R` queries the `single_builds` metadata table for `(name, tag)` already built successfully (`error_occurred = FALSE`) on this `platform`/`arch`, and drops those pairs from the chunk before the build loop. It logs how many it skipped. - One indexed query, one round trip, run before the pak forks — no extra S3 listing and no new Python/s3fs memory pressure (`RPostgres`/`DBI` are already used in the container). - Errored versions are intentionally **not** skipped, so transient failures still get retried on restart. ## Dependency Correctness depends on a `error_occurred = FALSE` row meaning the binary is actually published. That guarantee is added in rpkgs/bincraft#56 (success row written only after a confirmed S3 upload). This PR should land together with / after a bincraft release including that fix. Reviewed-on: #91	2026-06-16 07:27:20 +00:00
pat-s	7e01f481c0	perf(local): skip per-minor passes for non-r-minor-sensitive packages ... A package's ABI sensitivity is the same across R minors, so for a non-sensitive package the per-minor loop only ran `ensure_bincraft` (a ~14s bincraft/cranlike install per minor) before build-one.R classified and skipped it. The primary pass now writes a .r_minor_sensitive sentinel when it builds a sensitive package, and the wrapper gates the whole per-minor loop (installs included) on that file — non-sensitive rebuilds no longer touch other minors' libraries.	2026-06-14 14:50:40 +02:00
pat-s	a9ad907f9c	chore(local): add S3 migration and CRAN-source helper scripts ... - migrate-s3-hetzner-to-backblaze.sh: rclone-based bucket migration helper. - find-R-api-packages.sh: scan CRAN package sources for a C-API usage pattern. - query-pkgs-without-old-versions.R, test-package-loading.R: ad-hoc helpers.	2026-06-14 13:02:48 +02:00
pat-s	3ae4672d66	feat(local): just rebuild builds across all installed R minors ... - Dockerfile: install bincraft into each R minor, run a primary pass plus a sensitive-only pass under every other /opt/R/[0-9]* minor (deduped by minor), probe/skip xvfb, set GIT_TERMINAL_PROMPT=0; extra-minor failures are non-fatal. - build-one.R: add --sensitive-only mode, log + shallow-clone the ABI classify step, and clear cranlike's stale ./PACKAGES.db before each index refresh (workaround for the "table packages already exists" bug; pending cranlike fix).	2026-06-14 13:02:48 +02:00
pat-s	1224bd74fe	feat(local): just rebuild recipe for targeted builds via remote buildx (#87) ... ## Summary Adds a local `just rebuild` recipe to (re)build specific versions of a single package on a given OS/arch, dispatching to a remote buildx builder (the build runs there, not locally). - `just rebuild <os> <tag> <arch> <package> <version>...` → `docker buildx build --builder <artemis|gaia> --platform linux/<arch> …` (amd64→artemis, arm64→gaia; names + `R_VERSION` env-overridable). - `docker/build-one.Dockerfile` runs `build-one.R` as a secret-mounted `RUN`, built `--no-cache --output type=cacheonly` (pure side-effect: the S3 upload; no image kept). - `local/build-one.R` auto-classifies each version via the ABI classifier (risky → per-minor slot `contrib/<x.y>/`, else generic), force-rebuilds + uploads + stores metadata, then refreshes the touched slot's `PACKAGES` index. ## Prerequisites - buildx builders named `artemis` (amd64) and `gaia` (arm64) registered (`docker buildx create --name artemis ssh://…`). - Exported secrets: `B2_S3_ACCESS_KEY`, `B2_S3_SECRET_KEY`, `PGPASS` (`GITHUB_PAT` optional). - bincraft `v4.2.0` tag must exist (the build installs `@v4.2.0` and uses its classifier + per-minor index API). Reviewed-on: #87	2026-06-14 09:03:45 +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	53da568749	refactor: single source of truth for excluded packages (#79) ... ## Summary `local/build-all.R` had a 75-name hardcoded `exclude <- c(...)` vector that had drifted from `local/excluded-packages.json` — `RcmdrPlugin.ROC` was in the R vector but missing from the JSON. `.crow/weekly-rebuild-missing-*.yaml` already reads the JSON via `jsonlite::fromJSON(...)[["package"]]`. This brings `build-all.R` in line with that pattern. Changes: - **`local/excluded-packages.json`**: add the missing `RcmdrPlugin.ROC` entry (reason `"hang"`, matching siblings). - **`local/build-all.R`**: replace the 16-line hardcoded vector with one `jsonlite::fromJSON(...)` call. - **`.crow/build-all-versions-install-deps-{amd,arm}64.yaml`**: add `jsonlite` to the install-deps `pak::pak()` list so it's available in `/mnt/cache/R-pkgs` for the build step. - **`.crow/build-all-versions-arm64.yaml`**: drop the dead base64-encoded `SKIP_PKGS` docs comment that nobody was passing as a `--var` anyway; replace with a one-line pointer to the JSON. Reviewed-on: #79	2026-06-08 08:30:19 +00:00
pat-s	fb95042d16	chore: drop stale Hetzner-pointing helpers (#77) ... ## Summary Both helpers still point at the old Hetzner storage: - `Justfile` — all 3 recipes (`build-all`, `build-single`, `process-updates`) hit `hel1.your-objectstorage.com` / bucket `devxy-r-package-binaries-hel1` using `HETZNER_S3_*_K3S` env vars. - `local/manual-package-index-update.R` — same endpoint + bucket, hardcoded into `s3fs::s3_dir_ls()` / `s3_file_delete()` calls. Storage moved to Backblaze (`s3.eu-central-003.backblazeb2.com` / `devxy-rpkgs-binaries`) a while back, so running either of these today would write to the wrong bucket or fail outright. No callers reference them in-tree, deleting outright. A one-off rebuild can just call `bincraft::upload_package_index()` directly with current Backblaze settings. Reviewed-on: #77	2026-06-08 08:29:40 +00:00
pat-s	84c59d1984	fix: audit workflows	2026-04-21 21:54:48 +02:00
pat-s	8a98cf96a6	fix: save S3 listing in precompute step, avoid loading s3fs in build step ... s3fs uses reticulate/Python which significantly increases R process memory. When pak tries to fork R to install package dependencies, the enlarged process can't be duplicated within the container memory limit. Now the install-deps step saves the S3 file listing as s3_cache.rds, and the build step reads it with readRDS() — no s3fs loading needed.	2026-04-17 20:05:26 +02:00
pat-s	bc3dbd6126	fix: map x86_64/aarch64 to amd64/arm64 for S3 cache path	2026-04-17 19:04:18 +02:00
pat-s	9b27b3e650	refactor: extract build-all R one-liner into local/build-all.R ... - Load bincraft eagerly via library() to avoid lazy-load memory spike - Do bulk S3 listing upfront and pass as s3_package_cache to avoid per-package S3 calls that accumulate memory and trigger fork failures - Consolidate amd64/arm64 exclude lists into single script - Much easier to read and maintain than a YAML-embedded one-liner	2026-04-17 19:01:08 +02:00
pat-s	87d3f54b21	fix: pass NULL to set_codename() which requires an explicit argument	2026-04-17 18:55:40 +02:00
pat-s	92084e51ed	fix: use bincraft::set_codename() for S3 path in precompute step ... The precompute script was constructing S3 paths as "redhat10" while bincraft uses "rhel10" as the codename. This mismatch caused the precompute to find no existing packages in S3, producing ~77K false positive package versions that all get skipped at build time. Now uses bincraft::set_codename() to ensure path alignment. Also fixes nrow() vs length() in install-deps summary message.	2026-04-17 18:54:29 +02:00
pat-s	21ec8a67dd	feat: save package+version pairs instead of just package names ... packages-to-build.R now saves the full (Package, Version) data.table so the build step can pass specific tags to build_binary_package(), eliminating redundant per-package tag discovery and S3 checks. Also reduces archive versions from 9 to 4 (+ 1 release = 5 total).	2026-04-17 18:20:00 +02:00
pat-s	ffb8c42511	feat: add weekly missing binaries audit R script	2026-04-11 21:41:59 +02:00
pat-s	84f59682eb	feat: add excluded-packages.json for weekly missing binaries workflow	2026-04-11 21:41:55 +02:00
pat-s	aa2a6edef4	fix: write error message to stdout so it appears in CI logs	2026-04-09 23:06:10 +02:00
pat-s	852f732933	fix: compute platform for all distros and add error handler to surface failures ... platform was only set inside an alpine-specific if block, causing undefined variable errors for ubuntu/redhat builds that silently exited with code 1.	2026-04-09 22:59:46 +02:00
pat-s	9568d4dbfa	fix: migrate packages-to-build.R S3 config from Hetzner to Backblaze ... The S3 credentials, endpoint, and bucket name were still pointing to the old Hetzner storage after the Backblaze migration, causing silent build failures.	2026-04-09 22:53:49 +02:00
pat-s	30753d8871	use new postgres db and user	2025-06-25 15:53:40 +02:00
pat-s	6b1ae4e555	chore: cleanup workflows	2025-06-17 21:03:49 +02:00
pat-s	05e0ecdae5	new build approach	2025-06-17 01:15:56 +02:00