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Filename Latest commit message Latest commit date
pat-s 2561bed5e7
 fix(patches): add rstan entry to skip removed tbb_stddef.h 
StanHeaders' init_threadpool_tbb.hpp unconditionally includes the legacy
<tbb/tbb_stddef.h> for TBB version detection, but that header was removed
in oneTBB 2021+ (the version StanHeaders now bundles), so rstan's Module.cpp
fails to compile when rstan is pulled in as a transitive dependency (e.g. of
ctsem).

Pre-define TBB_INTERFACE_NEW via CPPFLAGS so the header's own guard skips the
removed include and selects the modern tbb/global_control.h + tbb/task_arena.h
path that the bundled TBB provides. Preserve -I/usr/local/include since the
CPPFLAGS override replaces the R default.
2026-07-14 13:37:29 +00:00
..
RcppParallel fix: RcppParallel disable-TBB source patch (env var was a no-op) (#106) 2026-06-30 13:27:01 +00:00
README.md feat: patch registry + wiring for per-package patching (#103) 2026-06-30 08:50:19 +00:00
registry.json fix(patches): add rstan entry to skip removed tbb_stddef.h 2026-07-14 13:37:29 +00:00

README.md

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:

  1. Add an object to the array in registry.json with the fields documented above. Start with lightweight overrides (environment variables, configure arguments, Makevars) before resorting to source diffs.

  2. If a source diff is needed, place it in local/patches/<package>/<file>.patch and reference its path in the patch field. For example, a diff for RcppParallel would go in local/patches/RcppParallel/fix.patch and be referenced as "patch": "RcppParallel/fix.patch".

  3. The reason field 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.