pat-s
04059f20e3
## 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
34 lines
1.9 KiB
JSON
34 lines
1.9 KiB
JSON
[
|
|
{
|
|
"package": "RcppParallel",
|
|
"versions": "*",
|
|
"platforms": ["alpine", "ubuntu-2604"],
|
|
"env": {},
|
|
"configure_args": [],
|
|
"makevars": {},
|
|
"patch": "RcppParallel/disable-tbb.patch",
|
|
"reason": "bundled Intel TBB build hangs/fails on musl (Alpine) and newer toolchains (g++ 15 on ubuntu-2604); patch unsets USE_TBB and forces -DRCPP_PARALLEL_USE_TBB=0 so RcppParallel skips the bundled build and uses the TinyThread backend"
|
|
},
|
|
{
|
|
"package": "fs",
|
|
"versions": "*",
|
|
"platforms": ["*"],
|
|
"env": {},
|
|
"configure_args": [],
|
|
"makevars": {},
|
|
"patch": "fs/force-vendored-libuv.patch",
|
|
"reason": "fs 2.x configure links system libuv whenever pkg-config finds libuv-devel (installed as a build-time sysreq), producing an fs.so with NEEDED libuv.so.1. That binary fails to dyn.load on consumer machines lacking runtime libuv, because install.packages/renv do not install SystemRequirements (only pak does, and only in the build container). The patch short-circuits configure to copy src/Makevars.vendor and build the bundled static libuv (needs cmake) so the binary is self-contained on every platform. An env/pkg-config override was tried first but the rebuilt binary still linked libuv.so.1, so a source patch is used instead."
|
|
},
|
|
{
|
|
"package": "rstan",
|
|
"versions": "*",
|
|
"platforms": ["*"],
|
|
"env": {},
|
|
"configure_args": [],
|
|
"makevars": {
|
|
"CPPFLAGS": "-DTBB_INTERFACE_NEW -I/usr/local/include"
|
|
},
|
|
"patch": null,
|
|
"reason": "StanHeaders' init_threadpool_tbb.hpp unconditionally includes the legacy <tbb/tbb_stddef.h> (removed in oneTBB 2021+) for version detection, breaking compilation of Module.cpp against the bundled oneTBB. Pre-defining TBB_INTERFACE_NEW skips that include and selects the modern tbb/global_control.h + tbb/task_arena.h path that the bundled TBB provides (-I/usr/local/include preserves the default CPPFLAGS the override replaces)"
|
|
}
|
|
]
|