Author	SHA1	Message	Date
pat-s	fe2289af56	fix(patches): force RcppParallel to use its bundled oneTBB (#146) ... ## Why `RcppParallel` binaries built on ubuntu 22.04 still record `NEEDED libtbb.so.12` and cannot `dyn.load` without the distro TBB, although #145 landed the link-order patch and build-env-images dropped `TBB_INC`/`TBB_LIB` the same morning. The link-order fix does not survive a build image that exports those variables, and the published images still do: `.crow/images.yaml` in build-env-images triggers on `cron`/`manual` only, so every image in the registry is still the 2026-07-21 build. With `TBB_LIB` set, `configure.R` never reaches the bundled-oneTBB branch at all, `install.libs.R` fills `RcppParallel/lib` with absolute symlinks into the image's library dir, and the plain `-L` from #145 just points at the system TBB instead of the bundled one. Nothing on the pipeline side can undo this: R reads `~/.Renviron` **after** the process environment, so neither a Crow `environment:` block nor the registry `env` field wins. ``` # the image, not the Containerfile docker run --rm reg.devxy.io/rpkgs/build-env-ubuntu:jammy sh -lc 'grep TBB ~/.Renviron' TBB_INC=/usr/include/oneapi TBB_LIB=/usr/lib/x86_64-linux-gnu ``` Rather than couple correctness to image freshness for a third round-trip, the patch now forces the bundled TBB itself. ## Changes - `local/patches/RcppParallel/bundled-tbb-link-order.patch` -> `local/patches/RcppParallel/force-bundled-tbb.patch`. Keeps the `-Wl,-L` -> `-L` link-order hunk (the bundled branch has the same problem when a distro libtbb is installed) and adds an opt-out, `BINCRAFT_ALLOW_SYSTEM_TBB=TRUE`, for the ambient `TBB_ROOT`/`TBB_LIB`/`TBB_INC`. - All four read sites have to move together; patching only `configure.R` builds the bundled TBB and then **segfaults R on the post-install load test**: - `tools/config/configure.R`: branch selection. - `src/install.libs.R`: `R CMD INSTALL` runs it outside the `tbb` rule in `src/Makevars` that passes the configured values, so at install time it still sees the image environment. - `R/tbb.R` `tbbLibraryPath()`: run time. `.onLoad()` would `dyn.load` the system TBB into the global scope next to the bundled one that `RcppParallel.so` needs - two copies of the same symbols, hence the segfault. - `R/tbb.R` `tbbCxxFlags()` / `tbbLdFlags()`: otherwise dependents such as `rstan` get the system TBB handed back to them. - `local/patches/registry.json`: new patch path and a `reason` describing both failure modes. ## Verification Built through `bincraft:::prepare_patched_repo()` on the **current, unfixed** images (all three still export `TBB_INC`/`TBB_LIB`), with bincraft v5.0.1, i.e. what CI deploys: | image | `NEEDED` | rpath | `RcppParallel/lib` | load, all system `libtbb*` moved away | | --- | --- | --- | --- | --- | | `build-env-ubuntu:jammy` | `libtbb.so` | `$ORIGIN/../lib` | real `libtbb.so.2`, 5.0 MB | OK, 12 threads | | `build-env-redhat:9` | `libtbb.so` | `$ORIGIN/../lib` | real `libtbb.so.2`, 5.1 MB | OK, 12 threads | | `build-env-alpine:3.24` | `libtbb.so` | `$ORIGIN/../lib` | real `libtbb.so.2`, 4.7 MB | OK, 12 threads | For contrast, the same jammy build without this change: ``` NEEDED libtbb.so.12 RUNPATH /usr/lib/x86_64-linux-gnu:$ORIGIN/../lib lib/ libtbb.so.12.5 -> /usr/lib/x86_64-linux-gnu/libtbb.so.12.5 (dangling off the image) load libtbb.so.12: cannot open shared object file: No such file or directory ``` With `TBB_LIB` still exported, `RcppParallel::tbbLibraryPath()` resolves to the package's own `lib`, and `CxxFlags()` emits the package's own `include` plus `-DTBB_INTERFACE_NEW` - not `/usr/include/oneapi`. ## Behaviour change Published `RcppParallel` binaries carry their own oneTBB on every platform, whichever image version CI pulls. The patch content changed, so the patched-binary cache key changes with it and no stale entry is reused. The build-env-images fix is still worth rolling out (those images also carry the broken el8 `uvr` and uvr 0.4.1), but RcppParallel no longer waits on it. ## Follow-up, not in this PR The binaries already in B2 are the broken ones; they need a rebuild, and a Bunny `/purge` does not evict Perma-Cache. Reviewed-on: #146	2026-07-31 09:48:41 +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
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	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