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Sun, 17 Aug 2025 16:58:22 GMT (envelope-from git) Date: Sun, 17 Aug 2025 16:58:22 GMT Message-Id: <202508171658.57HGwMEX012973@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: 2c95e6006b12 - main - biology/hyphy: Update to 2.5.77 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 2c95e6006b12cb65d01c1d10ebd402d7985649ff Auto-Submitted: auto-generated The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=2c95e6006b12cb65d01c1d10ebd402d7985649ff commit 2c95e6006b12cb65d01c1d10ebd402d7985649ff Author: Joseph Mingrone AuthorDate: 2025-08-17 16:56:18 +0000 Commit: Joseph Mingrone CommitDate: 2025-08-17 16:56:18 +0000 biology/hyphy: Update to 2.5.77 Release notes: https://github.com/veg/hyphy/releases/tag/2.5.77 Sponsored by: The FreeBSD Foundation --- biology/hyphy/Makefile | 2 +- biology/hyphy/distinfo | 6 +++--- biology/hyphy/files/patch-CMakeLists.txt | 27 --------------------------- 3 files changed, 4 insertions(+), 31 deletions(-) diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 9c44e24985ad..e9632df3e987 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,5 @@ PORTNAME= hyphy -DISTVERSION= 2.5.76 +DISTVERSION= 2.5.77 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org 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)