2 files changed, 20 insertions, 27 deletions
diff --git a/biology/hyphy/files/patch-CMakeLists.txt b/biology/hyphy/files/patch-CMakeLists.txt
deleted file mode 100644
index 0c926e529c55..000000000000
--- a/biology/hyphy/files/patch-CMakeLists.txt
+++ /dev/null
@@ -1,27 +0,0 @@
---- CMakeLists.txt.orig	2025-08-15 20:40:45 UTC
-+++ CMakeLists.txt
-@@ -83,7 +83,7 @@ int main() {
-     if(HYPHY_HAVE_NEON)
-         add_compile_definitions(_SLKP_USE_ARM_NEON)
-         if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
--            list(APPEND HYPHY_SIMD_FLAGS "-mcpu=native;-mtune=native")
-+            list(APPEND HYPHY_SIMD_FLAGS "-mtune=native")
-         endif()
-     endif()
-     set(CMAKE_REQUIRED_FLAGS ${OLD_CMAKE_REQUIRED_FLAGS})
-@@ -91,7 +91,7 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_CO
- 
- if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-     if(NOT HYPHY_HAVE_NEON AND NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
--        list(APPEND COMMON_COMPILE_FLAGS "-march=native" "-mcpu=native" "-mtune=native")
-+        list(APPEND COMMON_COMPILE_FLAGS "-march=native" "-mtune=native")
-     endif()
-     if(NOT NOAVX)
-         set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
-@@ -332,4 +332,4 @@ add_test(NAME GARD COMMAND hyphy tests/hbltests/libv3/
- add_test(CONTRAST-FEL hyphy tests/hbltests/libv3/CFEL.wbf)
- add_test(FADE hyphy tests/hbltests/libv3/FADE.wbf)
- add_test(NAME GARD COMMAND hyphy tests/hbltests/libv3/GARD.wbf "ENV=TOLERATE_NUMERICAL_ERRORS=1;")
--add_test(ABSREL hyphy tests/hbltests/libv3/ABSREL.wbf)
-\ No newline at end of file
-+add_test(ABSREL hyphy tests/hbltests/libv3/ABSREL.wbf)
diff --git a/biology/hyphy/files/patch-src_core_global__things.cpp b/biology/hyphy/files/patch-src_core_global__things.cpp
new file mode 100644
index 000000000000..397be8520ae5
--- /dev/null
+++ b/biology/hyphy/files/patch-src_core_global__things.cpp
@@ -0,0 +1,20 @@
+--- src/core/global_things.cpp.orig	2025-08-22 19:21:44 UTC
++++ src/core/global_things.cpp
+@@ -173,7 +173,7 @@ hyPointer MemAllocate(size_t bytes, bool zero, size_t 
+   result = (hyPointer)zero ? calloc(bytes, 1) : malloc(bytes);
+ 
+   if (result == nil) {
+-    HandleApplicationError(_String("Failed to allocate '") & bytes & "' bytes'",
++    HandleApplicationError(_String("Failed to allocate '") & (unsigned long)bytes & "' bytes'",
+                            true);
+   }
+   return result;
+@@ -186,7 +186,7 @@ hyPointer MemReallocate(hyPointer old_pointer, size_t 
+ 
+   if (result == nil) {
+     HandleApplicationError(
+-        _String("Failed to resize memory to '") & new_size & "' bytes'", true);
++        _String("Failed to resize memory to '") & (unsigned long)new_size & "' bytes'", true);
+   }
+ 
+   return result;