Re: git: 2c95e6006b12 - main - biology/hyphy: Update to 2.5.77

On Sun, 2025-08-17 at 19:13, Daniel Engberg <diizzy@FreeBSD.org> wrote:

> On 2025-08-17 18:58, Joseph Mingrone wrote:
>> The branch main has been updated by jrm:

>> URL:https://cgit.FreeBSD.org/ports/commit/?id=2c95e6006b12cb65d01c1d10ebd402d7985649ff

>> commit 2c95e6006b12cb65d01c1d10ebd402d7985649ff
>> Author:     Joseph Mingrone<jrm@FreeBSD.org>
>> AuthorDate: 2025-08-17 16:56:18 +0000
>> Commit:     Joseph Mingrone<jrm@FreeBSD.org>
>> 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()
>> ....

> Hi Joseph,

> This port needs a bit more love,

> It hardcodes -march=native -mtune=native on at least amd64, this is a no go and will produce broken packages as host and target may not share the same CPU features. Preferably it shouldn't set any feature flags at all and only test based on what CPUTYPE (--=march=XXX)
> provides.

> Best regards,
> Daniel

Hello Daniel,

Yeah, that's not good.

https://reviews.freebsd.org/D51977

Thanks,
Joe