diff options
Diffstat (limited to 'biology/hyphy')
| -rw-r--r-- | biology/hyphy/Makefile | 11 | ||||
| -rw-r--r-- | biology/hyphy/distinfo | 6 | ||||
| -rw-r--r-- | biology/hyphy/files/patch-CMakeLists.txt | 27 | ||||
| -rw-r--r-- | biology/hyphy/files/patch-src_core_global__things.cpp | 20 |
4 files changed, 30 insertions, 34 deletions
diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 9c44e24985ad..0e827bd9239e 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,6 @@ PORTNAME= hyphy -DISTVERSION= 2.5.76 +DISTVERSION= 2.5.77 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org @@ -20,9 +21,11 @@ USES= cmake:insource,testing localbase:ldflags # tests fail in outsource build, USE_GITHUB= yes GH_ACCOUNT= veg -OPTIONS_DEFINE= AVX -AVX_DESC= Advanced vector extensions support +OPTIONS_DEFINE= AVX TARGET_NATIVE +AVX_DESC= Advanced vector extensions support +TARGET_NATIVE_DESC= Enable CPU-specific instructions and tuning for build machine -AVX_CMAKE_BOOL_OFF= NOAVX +AVX_CMAKE_BOOL_OFF= NOAVX +TARGET_NATIVE_CMAKE_BOOL= TARGET_NATIVE .include <bsd.port.mk> diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index 3bcc8e9eb6fe..7a055e3a0004 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1755289798 -SHA256 (veg-hyphy-2.5.76_GH0.tar.gz) = d3f649b304e6ed408ee25f568de8361d43fb0a20d689243eba227d63fe6926ae -SIZE (veg-hyphy-2.5.76_GH0.tar.gz) = 4027248 +TIMESTAMP = 1755447505 +SHA256 (veg-hyphy-2.5.77_GH0.tar.gz) = 5012efd40938caeb9894bbd480565f95d735840f8eac67c6e84884a347e32e76 +SIZE (veg-hyphy-2.5.77_GH0.tar.gz) = 4027226 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; |