Author	SHA1	Message	Date
automation-bot	5dad51c76a	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.10	2026-10-12 00:32:11 +00:00
automation-bot	317990a40f	chore(deps): update pre-commit hook posit-dev/air-pre-commit to v0.12.0	2026-10-02 00:32:22 +00:00
automation-bot	b18c21aa8d	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.9	2026-09-24 00:32:00 +00:00
automation-bot	aa6e5e9dd8	chore(deps): update pre-commit hook davidanson/markdownlint-cli2 to v0.23.3	2026-09-21 00:31:54 +00:00
automation-bot	212065f5a4	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v4.0.2	2026-09-20 00:31:53 +00:00
automation-bot	caefd1131f	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.8	2026-09-19 00:32:12 +00:00
automation-bot	3325a7bda2	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.7	2026-09-17 00:32:19 +00:00
automation-bot	d3f24c89df	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v4 (#197) ... This PR contains the following updates: | Package | Type | Update | Change | |---|---|---|---| | [editorconfig-checker/editorconfig-checker](https://github.com/editorconfig-checker/editorconfig-checker) | repository | major | `v3.11.3` → `v4.0.1` | Note: The `pre-commit` manager in Renovate is not supported by the `pre-commit` maintainers or community. Please do not report any problems there, instead [create a Discussion in the Renovate repository](https://github.com/renovatebot/renovate/discussions/new) if you have any questions. --- ### Release Notes <details> <summary>editorconfig-checker/editorconfig-checker (editorconfig-checker/editorconfig-checker)</summary> ### [`v4.0.1`](https://github.com/editorconfig-checker/editorconfig-checker/releases/tag/v4.0.1) [Compare Source](https://github.com/editorconfig-checker/editorconfig-checker/compare/v4.0.0...v4.0.1) ##### Bug Fixes - bump golang.org/x/mod to v0.40.0 ([3d2215c](3d2215c10a)) - **ci:** build docker images for all our platforms ([a34a6ee](a34a6eeac7)) - update pre-commit-config to use v4 of our repo ([fcd68bf](fcd68bffda)) ### [`v4.0.0`](https://github.com/editorconfig-checker/editorconfig-checker/releases/tag/v4.0.0) [Compare Source](https://github.com/editorconfig-checker/editorconfig-checker/compare/v3.11.3...v4.0.0) ##### ⚠ BREAKING CHANGES - internalize our packages ([#&#8203;619](https://github.com/editorconfig-checker/editorconfig-checker/issues/619))<br>It will no longer be possible to import our internal packages in your code. If you rely on one of our packages please let us know by opening an issue. - migrate to goreleaser dockers\_v2. ([#&#8203;617](https://github.com/editorconfig-checker/editorconfig-checker/issues/617))<br>This means we stop publishing the arch-suffixed images like `3.11.2-amd64` or `3.11.2-arm64v8`. All these architectures are still provided in the multiarch tag `3.11.2`. - rename ec to editorconfig-checker ([#&#8203;371](https://github.com/editorconfig-checker/editorconfig-checker/issues/371)) - `.ecrc` is no longer discovered as a default config file name. Rename `.ecrc` to `.editorconfig-checker.json`, or pass the file explicitly with `--config .ecrc`. - Docker image tags no longer carry a leading `v`. Pull `3.12.0`, `3.12` and `3` instead of `v3.12.0`, `v3.12` and `v3` - the deprecated `SpacesAftertabs` configuration key has been removed, use `SpacesAfterTabs` instead. - stop accepting latin1 files as utf-8. ([#&#8203;598](https://github.com/editorconfig-checker/editorconfig-checker/issues/598))<br>Previously `charset=utf-8` was satisfied with files encoded as `latin1`. While most of the `latin1` range is identical to `utf-8`, not all is. If you request `utf-8` but have `latin1` encoded files expect these files to be reported as violations now. ##### Features - add safe EditorConfig autofixes ([#&#8203;612](https://github.com/editorconfig-checker/editorconfig-checker/issues/612)) ([2f4962c](2f4962c596)) - auto-detect `github-actions` output format in CI ([#&#8203;606](https://github.com/editorconfig-checker/editorconfig-checker/issues/606)) ([271c500](271c500a31)) - remove support for the deprecated `.ecrc` config file name ([#&#8203;603](https://github.com/editorconfig-checker/editorconfig-checker/issues/603)) ([2062751](2062751696)) ##### Bug Fixes - add missing space in wrong indentation type error message ([#&#8203;610](https://github.com/editorconfig-checker/editorconfig-checker/issues/610)) ([e0f1b56](e0f1b561a2)) - allow builds with Go 1.26 ([#&#8203;615](https://github.com/editorconfig-checker/editorconfig-checker/issues/615)) ([343018a](343018a4a3)) - consolidate error blocks that are interleaved with other errors ([#&#8203;601](https://github.com/editorconfig-checker/editorconfig-checker/issues/601)) ([76b6313](76b6313bc2)) - correct end line in codeclimate formatter output ([#&#8203;602](https://github.com/editorconfig-checker/editorconfig-checker/issues/602)) ([2476e7c](2476e7c671)) - correct the -disable-end-of-line flag description ([#&#8203;600](https://github.com/editorconfig-checker/editorconfig-checker/issues/600)) ([1615efc](1615efcaed)) - drop a path whose content type could not be read ([#&#8203;599](https://github.com/editorconfig-checker/editorconfig-checker/issues/599)) ([46995b1](46995b1db0)) - handle `unset` for `end_of_line` and `insert_final_newline` ([#&#8203;594](https://github.com/editorconfig-checker/editorconfig-checker/issues/594)) ([123ba31](123ba319dc)), closes [#&#8203;580](https://github.com/editorconfig-checker/editorconfig-checker/issues/580) - remove ambiguity between potential folder and file matches ([#&#8203;611](https://github.com/editorconfig-checker/editorconfig-checker/issues/611)) ([4c4f7d4](4c4f7d4c30)) - remove leading `v` from Docker image tags ([#&#8203;607](https://github.com/editorconfig-checker/editorconfig-checker/issues/607)) ([3827a6c](3827a6c595)) - remove retired goreportcard badge ([2a9dd32](2a9dd32f6e)) - stop accepting latin1 files as utf-8. ([#&#8203;598](https://github.com/editorconfig-checker/editorconfig-checker/issues/598))\<br>Previously `charset=utf-8` was satisfied with files encoded as `latin1`. While most of the `latin1` range is identical to `utf-8`, not all is. If you request `utf-8` but have `latin1` encoded files expect these files to be reported as violations now. ([4d84a77](4d84a778c9)) - typo in config, `SpacesAftertabs` => `SpacesAfterTabs` ([#&#8203;604](https://github.com/editorconfig-checker/editorconfig-checker/issues/604)) ([bbc3f03](bbc3f03507)) ##### Miscellaneous Chores - internalize our packages ([#&#8203;619](https://github.com/editorconfig-checker/editorconfig-checker/issues/619))\<br>It will no longer be possible to import our internal packages in your code. If you rely on one of our packages please let us know by opening an issue. ([d42bcb7](d42bcb7af0)) - rename ec to editorconfig-checker ([#&#8203;371](https://github.com/editorconfig-checker/editorconfig-checker/issues/371)) ([0e3b27f](0e3b27f7e2)) ##### Continuous Integration - migrate to goreleaser dockers\_v2. ([#&#8203;617](https://github.com/editorconfig-checker/editorconfig-checker/issues/617))\<br>This means we stop publishing the arch-suffixed images like `3.11.2-amd64` or `3.11.2-arm64v8`. All these architectures are still provided in the multiarch tag `3.11.2`. ([d4c1442](d4c14421f8)) </details> --- ### Configuration 📅 **Schedule**: (UTC) - Branch creation - Between 12:00 AM and 03:59 AM (`* 0-3 * * *`) - Automerge - Between 12:00 AM and 03:59 AM (`* 0-3 * * *`) 🚦 **Automerge**: Disabled by config. Please merge this manually once you are satisfied. ♻ **Rebasing**: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox. 🔕 **Ignore**: Close this PR and you won't be reminded about this update again. --- - [ ] <!-- rebase-check -->If you want to rebase/retry this PR, check this box --- This PR has been generated by [Mend Renovate](https://github.com/renovatebot/renovate). <!--renovate-debug:eyJjcmVhdGVkSW5WZXIiOiI0My4yODMuMCIsInVwZGF0ZWRJblZlciI6IjQzLjI4OC4wIiwidGFyZ2V0QnJhbmNoIjoibWFpbiIsImxhYmVscyI6W119--> Reviewed-on: #197	2026-09-04 09:51:46 +00:00
automation-bot	e4ba623ddc	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.11.3	2026-09-04 00:32:36 +00:00
automation-bot	f4ab6f9dc5	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.11.2	2026-08-26 00:32:02 +00:00
automation-bot	4cb8b692ab	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.11.1	2026-08-09 00:32:28 +00:00
automation-bot	6bc8213a2f	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.10.0	2026-08-08 00:32:07 +00:00
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
automation-bot	463054625a	chore(deps): update pre-commit hook posit-dev/air-pre-commit to v0.11.0	2026-07-28 02:34:05 +00:00
automation-bot	adcc74ba4f	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.6	2026-07-28 00:32:55 +00:00
automation-bot	36c963eac9	chore(deps): update pre-commit hook davidanson/markdownlint-cli2 to v0.23.2	2026-07-28 00:32:39 +00:00
automation-bot	5f10863a9c	chore(deps): update pre-commit hook davidanson/markdownlint-cli2 to v0.23.0	2026-07-02 00:32:11 +00:00
automation-bot	2cf5714ad9	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.4	2026-07-01 00:32:49 +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
automation-bot	1e910bc703	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.9.1	2026-06-29 00:31:40 +00:00
automation-bot	597f759bb2	chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker to v3.8.0	2026-06-29 00:31:27 +00:00
automation-bot	3ffa25ddac	chore(deps): update pre-commit hook rbubley/mirrors-prettier to v3.8.5	2026-06-28 00:32:21 +00:00
automation-bot	a6788f9044	chore(deps): update pre-commit hook posit-dev/air-pre-commit to v0.10.0	2026-06-20 00:31:34 +00:00
automation-bot	6c97f34cf5	chore(deps): update pre-commit hook posit-dev/air-pre-commit to v0.9.0	2026-06-15 00:31:42 +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