| Filename | Latest commit message | Latest commit date |
|---|---|---|
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
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||
| .. | ||
| fs | ||
| RcppParallel | ||
| README.md | ||
| registry.json | ||
Patch Registry
This directory contains the curated registry of per-package build-time patches consumed by bincraft's patches argument.
Schema
The registry is defined in registry.json as an array of patch entries. Each entry specifies lightweight build-time overrides (environment variables, configure arguments, Makevars) and optionally a source diff to apply before building.
Field semantics
| Field | Type | Required | Description |
|---|---|---|---|
package |
string | yes | CRAN package name. |
versions |
string | yes | "*" for any, a constraint such as ">=5.1.0", or an exact version "5.1.11-2". Env-tier fixes are typically "*"; source diffs are normally exact or lower-bounded because a diff is pinned to the source it was generated against. |
platforms |
array of strings | yes | Matched against the running build's platform tokens — distro family (alpine, ubuntu, redhat), codename (ubuntu-2604, alpine-324), and arch (amd64, arm64). An entry matches if any listed token matches any build token. ["*"] matches all platforms. |
env |
object | no | Environment variables exported only for this package's isolated build. |
configure_args |
array | no | Arguments passed as --configure-args to the isolated build. |
makevars |
object | no | Key/value pairs written into a package-local Makevars for the isolated build. |
patch |
string or null | no | Path (relative to local/patches/) to a unified diff applied to the unpacked CRAN source before building. |
reason |
string | yes | Human explanation, surfaced in logs and metadata. |
Adding an entry
To add a new patch entry:
-
Add an object to the array in
registry.jsonwith the fields documented above. Start with lightweight overrides (environment variables, configure arguments, Makevars) before resorting to source diffs. -
If a source diff is needed, place it in
local/patches/<package>/<file>.patchand reference its path in thepatchfield. For example, a diff forRcppParallelwould go inlocal/patches/RcppParallel/fix.patchand be referenced as"patch": "RcppParallel/fix.patch". -
The
reasonfield should clearly explain why the patch is needed and what problem it solves.
Validation
The registry is validated and applied by bincraft during the build process. For manual validation, run the validator from the repo root:
Rscript local/validate-patches.R
This validates the schema, referenced patch-file existence, and checks for duplicate entries across platforms and versions.