diff --git a/local/patches/RcppParallel/bundled-tbb-link-order.patch b/local/patches/RcppParallel/bundled-tbb-link-order.patch deleted file mode 100644 index 45114a8..0000000 --- a/local/patches/RcppParallel/bundled-tbb-link-order.patch +++ /dev/null @@ -1,46 +0,0 @@ -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/) -+# 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)" - ) diff --git a/local/patches/RcppParallel/force-bundled-tbb.patch b/local/patches/RcppParallel/force-bundled-tbb.patch new file mode 100644 index 0000000..c46a05e --- /dev/null +++ b/local/patches/RcppParallel/force-bundled-tbb.patch @@ -0,0 +1,154 @@ +diff --git a/R/aaa.R b/R/aaa.R +index 568a2aa..bfdab4c 100644 +--- a/R/aaa.R ++++ b/R/aaa.R +@@ -5,4 +5,21 @@ TBB_LIB <- "" + TBB_INC <- "" + + TBB_NAME <- "tbb" +-TBB_MALLOC_NAME <- "tbbmalloc" +\ No newline at end of file ++TBB_MALLOC_NAME <- "tbbmalloc" ++ ++# bincraft patch: our build images (and plenty of user environments) export ++# TBB_ROOT / TBB_LIB / TBB_INC. A binary we publish always carries its own ++# oneTBB in RcppParallel/lib -- see the companion changes in ++# tools/config/configure.R and src/install.libs.R -- so honouring those ++# variables at run time is actively harmful: .onLoad() would dyn.load() a ++# second, unrelated TBB into the process next to the bundled one (two copies ++# of the same symbols in the global scope, which segfaults R on load), and ++# RcppParallelLibs() / CxxFlags() would hand that system TBB to dependents ++# such as rstan, putting NEEDED libtbb.so.12 back into their binaries. Read ++# the variables only when explicitly opted back in. ++bincraftGetenv <- function(name, unset = "") { ++ if (Sys.getenv("BINCRAFT_ALLOW_SYSTEM_TBB", unset = "FALSE") == "TRUE") ++ Sys.getenv(name, unset = unset) ++ else ++ unset ++} +\ No newline at end of file +diff --git a/R/tbb.R b/R/tbb.R +index 6f6a745..e407986 100644 +--- a/R/tbb.R ++++ b/R/tbb.R +@@ -17,7 +17,7 @@ tbbLibraryPath <- function(name = NULL) { + sysname <- Sys.info()[["sysname"]] + + # find root for TBB install +- tbbRoot <- Sys.getenv("TBB_LIB", unset = tbbRoot()) ++ tbbRoot <- bincraftGetenv("TBB_LIB", unset = tbbRoot()) + if (is.null(name)) + return(tbbRoot) + +@@ -58,7 +58,7 @@ tbbCxxFlags <- function() { + flags <- c("-DRCPP_PARALLEL_USE_TBB=1") + + # if TBB_INC is set, apply those library paths +- tbbInc <- Sys.getenv("TBB_INC", unset = TBB_INC) ++ tbbInc <- bincraftGetenv("TBB_INC", unset = TBB_INC) + if (!file.exists(tbbInc)) { + tbbInc <- system.file("include", package = "RcppParallel") + } +@@ -117,7 +117,7 @@ tbbLdFlags <- function() { + } + + # shortcut if TBB_LIB defined +- tbbLib <- Sys.getenv("TBB_LINK_LIB", Sys.getenv("TBB_LIB", unset = TBB_LIB)) ++ tbbLib <- bincraftGetenv("TBB_LINK_LIB", bincraftGetenv("TBB_LIB", unset = TBB_LIB)) + if (nzchar(tbbLib)) { + if (R.version$os == "emscripten") { + fmt <- "-L%1$s -l%2$s" +diff --git a/src/install.libs.R b/src/install.libs.R +index 3b3cfda..c0e6f3e 100644 +--- a/src/install.libs.R ++++ b/src/install.libs.R +@@ -477,6 +477,18 @@ prependFlags <- function(prependFlags, toFlags) { + tbbLib <- Sys.getenv("TBB_LIB") + tbbInc <- Sys.getenv("TBB_INC") + ++# bincraft patch: the companion change in tools/config/configure.R stops an ++# ambient TBB_LIB / TBB_INC from selecting a system TBB, but this script is ++# also run directly by `R CMD INSTALL` (not only through the `tbb` rule in ++# src/Makevars, which passes the configured values), so at install time it ++# still sees the image's environment and would symlink the system libraries ++# into RcppParallel/lib. Drop them here for the same reason, under the same ++# opt-out. ++if (Sys.getenv("BINCRAFT_ALLOW_SYSTEM_TBB", unset = "FALSE") != "TRUE") { ++ tbbLib <- "" ++ tbbInc <- "" ++} ++ + args <- commandArgs(trailingOnly = TRUE) + if (identical(args, "build")) { + if (nzchar(tbbLib) && nzchar(tbbInc)) { +diff --git a/tools/config/configure.R b/tools/config/configure.R +index 6293fe1..eae4aaa 100644 +--- a/tools/config/configure.R ++++ b/tools/config/configure.R +@@ -40,6 +40,24 @@ tbbRoot <- Sys.getenv("TBB_ROOT", unset = NA) + tbbLib <- Sys.getenv("TBB_LIB", unset = NA) + tbbInc <- Sys.getenv("TBB_INC", unset = NA) + ++# bincraft patch: ignore an ambient TBB_ROOT / TBB_LIB / TBB_INC. Several of ++# our build images export these (a leftover from RcppParallel 5.x, whose ++# bundled Intel TBB would not build on musl or with modern g++), and any of ++# them switches the branches below to a system TBB. The published binary then ++# records NEEDED libtbb.so.12 (or libtbb.so.2 for the classic Intel TBB) and ++# gets a RcppParallel/lib full of absolute symlinks into the image's library ++# dir, so it cannot dyn.load on a consumer machine without that exact TBB. ++# 6.x bundles oneTBB 2022 and builds it with cmake on every platform we ship, ++# so the bundled copy is always the right choice here; forcing it in the ++# package rather than relying on the image environment keeps the binary ++# correct whichever image version CI happens to pull. Set ++# BINCRAFT_ALLOW_SYSTEM_TBB=TRUE to restore the upstream behaviour. ++if (Sys.getenv("BINCRAFT_ALLOW_SYSTEM_TBB", unset = "FALSE") != "TRUE") { ++ tbbRoot <- NA ++ tbbLib <- NA ++ tbbInc <- NA ++} ++ + tbbName <- Sys.getenv("TBB_NAME", unset = "tbb") + tbbMallocName <- Sys.getenv("TBB_MALLOC_NAME", unset = "tbbmalloc") + +@@ -186,12 +204,23 @@ 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/) ++# 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$(TBB_NAME)", +@@ -201,14 +230,14 @@ pkgLibs <- if (!is.na(tbbLib)) { + } else if (R.version$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)" + ) diff --git a/local/patches/registry.json b/local/patches/registry.json index fe0d387..a7e29dd 100644 --- a/local/patches/registry.json +++ b/local/patches/registry.json @@ -6,8 +6,8 @@ "env": {}, "configure_args": [], "makevars": {}, - "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/) 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." + "patch": "RcppParallel/force-bundled-tbb.patch", + "reason": "RcppParallel 6.x bundles oneTBB 2022 and builds it with cmake on every platform we ship, so the system-TBB workaround needed for 5.x is gone, but two things still steer the build back to a system TBB. (1) Ambient TBB_ROOT/TBB_LIB/TBB_INC: several build images still export these (build-env-images dropped them, but the images are rebuilt only by cron/manual runs, so a stale image keeps them), and R reads ~/.Renviron *after* the process environment, so no pipeline-side env override can undo it. configure.R then takes the system-TBB branch, install.libs.R symlinks the image's libraries into RcppParallel/lib as absolute paths, and the binary records NEEDED libtbb.so.12 (libtbb.so.2 for the classic Intel TBB on el8/el9) -- it cannot dyn.load on a consumer machine without that exact TBB. Both files are patched to ignore those variables (opt out with BINCRAFT_ALLOW_SYSTEM_TBB=TRUE); install.libs.R needs it separately because R CMD INSTALL runs it outside the src/Makevars rule that passes the configured values. (2) Link order: the bundled branch passes its build dir as '-Wl,-Ltbb/build/lib_release', and gcc expands its own search dirs (/usr/lib64, /usr/lib/) into '-L' options ahead of anything forwarded with '-Wl,', so '-ltbb' would still resolve to a distro TBB when one is installed; a plain '-L' puts the bundled dir first. Verified on the current build-env-ubuntu:jammy image (which still exports TBB_INC/TBB_LIB): NEEDED libtbb.so, RUNPATH $ORIGIN/../lib, real libtbb.so.2 in RcppParallel/lib, and the package loads with every system libtbb moved away." }, { "package": "fs",