From 659789f17c8cad81eac606d429a9a3f724bc0d2b Mon Sep 17 00:00:00 2001
From: Benjamin Demaille <benjamin.demaille@icloud.com>
Date: Tue, 8 Sep 2026 11:23:57 +0200
Subject: [PATCH] Makefiles: only force -arch x86_64 on Intel macOS

The external_libs Makefiles append `-arch x86_64` on any Darwin host. On
Apple Silicon this cross-compiles the helper libraries for the wrong
architecture, and the final link fails:

    ld: warning: ignoring file external_libs/qf/qf.a, building for
        macOS-arm64 but attempting to link with file built for macOS-x86_64
    Undefined symbols for architecture arm64: "_qf", referenced from:
        get_davies_pv(...) in SKAT.cpp.o

Guard the flag with `uname -m` so native arm64 builds keep the host
architecture, while Intel macOS builds are unchanged.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---
 external_libs/mvtnorm/Makefile  | 5 ++++-
 external_libs/pgenlib/Makefile  | 5 ++++-
 external_libs/qf/Makefile       | 5 ++++-
 external_libs/quadpack/Makefile | 5 ++++-
 external_libs/remeta/Makefile   | 5 ++++-
 5 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/external_libs/mvtnorm/Makefile b/external_libs/mvtnorm/Makefile
index ac3d3893..29f883db 100644
--- a/external_libs/mvtnorm/Makefile
+++ b/external_libs/mvtnorm/Makefile
@@ -5,8 +5,11 @@ CC   ?= gcc
 FC   ?= gfortran
 
 UNAME_S := $(shell uname -s)
+UNAME_M := $(shell uname -m)
 ifeq ($(UNAME_S),Darwin)
- FLAG += -arch x86_64
+ ifeq ($(UNAME_M),x86_64)
+  FLAG += -arch x86_64
+ endif
 endif
 
 libMvtnorm.a: mvtnorm.o mvt.o randomF77.o
diff --git a/external_libs/pgenlib/Makefile b/external_libs/pgenlib/Makefile
index 262d920b..5ed281d8 100644
--- a/external_libs/pgenlib/Makefile
+++ b/external_libs/pgenlib/Makefile
@@ -7,8 +7,11 @@ CXXFLAGS    = -O3 -Wall -std=c++11
 CFLAGS      = 
 
 UNAME_S := $(shell uname -s)
+UNAME_M := $(shell uname -m)
 ifeq ($(UNAME_S),Darwin)
- CXXFLAGS += -arch x86_64
+ ifeq ($(UNAME_M),x86_64)
+  CXXFLAGS += -arch x86_64
+ endif
 endif
 
 OBJECTS       = $(patsubst %.cc,%.o,$(wildcard ./include/*.cc)) $(patsubst %.cpp,%.o,$(wildcard *.cpp))  $(patsubst %.cc,%.o,$(wildcard *.cc))
diff --git a/external_libs/qf/Makefile b/external_libs/qf/Makefile
index 3d0341ac..f139e65f 100644
--- a/external_libs/qf/Makefile
+++ b/external_libs/qf/Makefile
@@ -3,8 +3,11 @@ CXX      ?= g++
 CXXFLAGS  = -O2 -DNDEBUG -fPIC
 
 UNAME_S := $(shell uname -s)
+UNAME_M := $(shell uname -m)
 ifeq ($(UNAME_S),Darwin)
- CXXFLAGS += -arch x86_64
+ ifeq ($(UNAME_M),x86_64)
+  CXXFLAGS += -arch x86_64
+ endif
 endif
 
 qf.a: qfc.o
diff --git a/external_libs/quadpack/Makefile b/external_libs/quadpack/Makefile
index e160de35..f70f0b1f 100644
--- a/external_libs/quadpack/Makefile
+++ b/external_libs/quadpack/Makefile
@@ -3,8 +3,11 @@ AR   ?= ar
 FC   ?= gfortran
 
 UNAME_S := $(shell uname -s)
+UNAME_M := $(shell uname -m)
 ifeq ($(UNAME_S),Darwin)
- FLAG += -arch x86_64
+ ifeq ($(UNAME_M),x86_64)
+  FLAG += -arch x86_64
+ endif
 endif
 
 OBJECTS = $(patsubst %.f,%.o,$(wildcard ./*.f))
diff --git a/external_libs/remeta/Makefile b/external_libs/remeta/Makefile
index 543c5c7e..9d5f2aad 100644
--- a/external_libs/remeta/Makefile
+++ b/external_libs/remeta/Makefile
@@ -12,8 +12,11 @@ ifneq ($(strip $(HTSLIB_PATH)),) # defined externally
 endif
 
 UNAME_S := $(shell uname -s)
+UNAME_M := $(shell uname -m)
 ifeq ($(UNAME_S),Darwin)
-	CXXFLAGS += -arch x86_64
+ ifeq ($(UNAME_M),x86_64)
+	 CXXFLAGS += -arch x86_64
+ endif
 endif
 
 OBJECTS       = bgz_writer.o regenie_ld_matrix_writer.o