.pre-commit-config.yaml

@@ -7,12 +7,20 @@ exclude: |
     benchmark/|
     docker/reprex/
   )
+# The `^local/patches/.*\.patch$` excludes below keep unified diffs byte-exact:
+# a context line for a blank line is a single space, and stripping it (or
+# appending a newline) makes `git apply` reject the patch, which surfaces as
+# "patch did not apply cleanly" at build time rather than as a lint failure
+# here. The exclusions are per-hook, not global, so `validate patch registry`
+# still runs when a patch changes.
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
+        exclude: ^local/patches/.*\.patch$
       - id: trailing-whitespace
+        exclude: ^local/patches/.*\.patch$
         args:
           - --markdown-linebreak-ext=md
   - repo: https://github.com/DavidAnson/markdownlint-cli2
@@ -31,6 +39,7 @@ repos:
     rev: v3.8.0
     hooks:
       - id: editorconfig-checker
+        exclude: ^local/patches/.*\.patch$
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.38.0
     hooks:

README.md

@@ -56,7 +56,7 @@ For every package+tag combination:
 ## Patching packages
 
 Some CRAN packages fail to compile on specific platforms due to compiler- or OS-specific issues unrelated to the package itself.
-The canonical example is `RcppParallel`, whose bundled TBB sources fail on musl (Alpine) and newer compiler/OS combinations.
+The canonical example is `RcppParallel`, whose bundled TBB is linked in a way that lets a system TBB on the build host shadow it, so the published binary depends on a library the consumer does not have.
 Because such packages are often transitive dependencies of many others, a single failure cascades: all dependents fail even though nothing is wrong with the dependent itself.
 
 To address this, frequently-failing packages can be "patched" before they are installed — whether as a direct build target or a transitive dependency pulled in by `pak`.

local/patches/RcppParallel/bundled-tbb-link-order.patch

@@ -0,0 +1,46 @@
+diff --git a/tools/config/configure.R b/tools/config/configure.R
+index 6293fe1..2f84337 100644
+--- a/tools/config/configure.R
++++ b/tools/config/configure.R
+@@ -186,12 +186,23 @@ define(
+ )
+ 
+ # set PKG_LIBS
++#
++# bincraft patch: the library directories below are passed as plain '-L', not
++# '-Wl,-L'. gcc expands its own search dirs (/usr/lib64, /usr/lib/<triplet>)
++# into explicit '-L' options ahead of anything forwarded verbatim with '-Wl,',
++# so with '-Wl,-L' a system libtbb.so wins over the one named here: on a 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) instead of the bundled 'libtbb.so'. The binary then loads
++# the system TBB rather than the copy shipped in RcppParallel/lib, and fails
++# outright on a machine that has no system TBB. gcc places a plain '-L' before
++# its built-in dirs, so the intended library is found first.
+ pkgLibs <- if (!is.na(tbbLib)) {
+ 
+    # a TBB supplied via TBB_LIB / TBB_ROOT. an rpath is meaningless on Windows,
+    # where the loader has no equivalent -- see R/zzz.R for how we resolve there
+    c(
+-      "-Wl,-L\"$(TBB_LIB)\"",
++      "-L\"$(TBB_LIB)\"",
+       if (.Platform$OS.type != "windows")
+          sprintf("-Wl,-rpath,%s", shQuote(tbbLib)),
+       "-l$(TBB_NAME)",
+@@ -201,14 +212,14 @@ pkgLibs <- if (!is.na(tbbLib)) {
+ } else if (R.version$os == "emscripten") {
+ 
+    c(
+-      "-Wl,-Ltbb/build/lib_release",
++      "-Ltbb/build/lib_release",
+       "-l$(TBB_NAME)"
+    )
+ 
+ } else {
+ 
+    c(
+-      "-Wl,-Ltbb/build/lib_release",
++      "-Ltbb/build/lib_release",
+       "-l$(TBB_NAME)",
+       "-l$(TBB_MALLOC_NAME)"
+    )

local/patches/RcppParallel/system-tbb.patch

@@ -1,19 +0,0 @@
-diff --git a/src/Makevars.in b/src/Makevars.in
-index be8445f..7cb6c9e 100644
---- a/src/Makevars.in
-+++ b/src/Makevars.in
-@@ -60,7 +60,13 @@ else
- 	endif
- 
- 	ifeq ($(UNAME), Linux)
--		USE_TBB=Linux
-+		# bincraft patch: link the system oneTBB (installed in the build-env images)
-+		# instead of building the bundled Intel TBB, which fails on musl (Alpine) and
-+		# newer toolchains (g++ 15). Leaving USE_TBB unset skips the bundled build;
-+		# -DRCPP_PARALLEL_USE_TBB=1 keeps the TBB backend so dependents (rstan, ...)
-+		# link TBB, and -ltbb/-ltbbmalloc pull the system library from default paths.
-+		PKG_CXXFLAGS += -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -DTBB_INTERFACE_NEW
-+		PKG_LIBS += -ltbb -ltbbmalloc
- 	endif
- 
- 	ifeq ($(UNAME), SunOS)

local/patches/registry.json

@@ -1,42 +1,22 @@
 [
   {
     "package": "RcppParallel",
-    "versions": "*",
-    "platforms": [
-      "alpine",
-      "ubuntu",
-      "redhat"
-    ],
+    "versions": ">=6.0.0",
+    "platforms": ["*"],
     "env": {},
     "configure_args": [],
     "makevars": {},
-    "patch": "RcppParallel/system-tbb.patch",
-    "reason": "RcppParallel bundles an old Intel TBB whose build fails on musl and modern toolchains (g++ 8-15 + modern make); link the system oneTBB (2021+) instead, keeping the TBB backend so dependents (rstan, ...) link TBB. All build-env platforms now provide oneTBB 2021+: native on alpine/ubuntu/el10, built from source into /usr/local on el8/el9 (their stock TBB is classic 2018/2020, too old)."
+    "patch": "RcppParallel/bundled-tbb-link-order.patch",
+    "reason": "RcppParallel 6.x bundles oneTBB 2022 and builds it with cmake, which works on musl and g++ 8-15, so the system-TBB workaround needed for 5.x is gone. What remains broken is the link order: configure.R passes the TBB directory as '-Wl,-L', and gcc expands its own search dirs (/usr/lib64, /usr/lib/<triplet>) into '-L' options ahead of anything forwarded with '-Wl,'. On a build host with a distro TBB installed, '-ltbb' therefore resolves to the system 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'. The published binary then loads the system TBB rather than the copy in RcppParallel/lib and fails to dyn.load on a consumer machine without one, the same way fs did with libuv. Passing a plain '-L' puts the bundled build dir ahead of gcc's defaults; verified on alpine 3.24, el8 and ubuntu noble to produce NEEDED libtbb.so + RPATH $ORIGIN/../lib, loading with every system libtbb removed."
   },
   {
     "package": "fs",
     "versions": "*",
-    "platforms": [
-      "*"
-    ],
+    "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)"
   }
 ]