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