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kalign: 3.4.0 -> 3.5.1 (#492312)

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OTABI Tomoya
2026-04-23 11:55:36 +00:00
committed by GitHub
parent df3735cd30 3111f21eec
commit 00e46caec3
2 changed files with 56 additions and 2 deletions
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pkgs/by-name/ka/kalign/macos-openmp-config.patch
+46
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@@ -0,0 +1,46 @@
From fb223fceeb81f481316694560ceacc473ad04b4a Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 23 Apr 2026 16:46:54 +0900
Subject: [PATCH] cmake: allow overriding hardcoded libomp path on macOS
The OpenMP workaround hardcoded /opt/homebrew/opt/libomp, which locked
out a custom build.
Introduce LIBOMP_ROOT (defaulting to Homebrew) so the prefix can be
overridden on the cmake command line.
While here, restrict the block to AppleClang. The flags inside are
AppleClang-specific (-Xpreprocessor -fopenmp, linking against the LLVM
libomp runtime) and were previously forced on any compiler targeting
Apple Silicon, silently breaking GCC and mis-configuring Homebrew LLVM
Clang builds.
---
CMakeLists.txt | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5a7d3f0..d76453d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -75,15 +75,15 @@ set(KALIGN_KMEANS_UPGMA_THRESHOLD "50" CACHE STRING "Number of sequences thresho
if(USE_OPENMP)
- # Configure OpenMP for macOS with Homebrew (only for arm64 native builds)
- if(APPLE AND CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "arm64" AND NOT CMAKE_OSX_ARCHITECTURES MATCHES "x86_64")
- list(APPEND CMAKE_PREFIX_PATH /opt/homebrew)
- # Set OpenMP flags for Apple Clang + Homebrew libomp
- set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include")
+ # Configure OpenMP for macOS with external libomp (only for Apple Clang on arm64 native builds)
+ if(APPLE AND CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "arm64" AND NOT CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" AND CMAKE_C_COMPILER_ID STREQUAL "AppleClang")
+ # Defaults to Homebrew
+ set(LIBOMP_ROOT "/opt/homebrew/opt/libomp" CACHE PATH "libomp install prefix")
+ set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I${LIBOMP_ROOT}/include")
set(OpenMP_C_LIB_NAMES "omp")
- set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include")
+ set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${LIBOMP_ROOT}/include")
set(OpenMP_CXX_LIB_NAMES "omp")
- set(OpenMP_omp_LIBRARY /opt/homebrew/opt/libomp/lib/libomp.dylib)
+ set(OpenMP_omp_LIBRARY "${LIBOMP_ROOT}/lib/libomp.dylib")
endif()
find_package(OpenMP)
pkgs/by-name/ka/kalign/package.nix
+10 -2
View File
@@ -11,15 +11,23 @@
stdenv.mkDerivation (finalAttrs: {
pname = "kalign";
version = "3.4.0";
version = "3.5.1";
src = fetchFromGitHub {
owner = "TimoLassmann";
repo = "kalign";
tag = "v${finalAttrs.version}";
hash = "sha256-QcFNaCTqj6CFiOzQ6ezfBL0mu8PDU11hyNdkcsLOPzA=";
hash = "sha256-wcVzKedd8IFKql+TU4wJ4jEGDPdDfpyC5iGXrPYa0oY=";
};
patches = [
# Allow overriding the hardcoded Homebrew libomp path on macOS and
# restrict the workaround to AppleClang so other compilers fall back
# to the standard OpenMP detection path.
# https://github.com/TimoLassmann/kalign/pull/65
./macos-openmp-config.patch
];
nativeBuildInputs = [
cmake
];