git: 25848df4724c - main - biology/gkl: update 0.8.11-9 → 0.9.1

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=25848df4724ce501e9d6966f5b5547a8d459c9b2

commit 25848df4724ce501e9d6966f5b5547a8d459c9b2
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-08-23 18:26:47 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-08-23 18:26:47 +0000

    biology/gkl: update 0.8.11-9 → 0.9.1
---
 biology/gkl/Makefile                                          |  3 +--
 biology/gkl/distinfo                                          |  6 +++---
 biology/gkl/files/patch-CMakeLists.txt                        |  4 ++--
 .../files/patch-src_main_native_pdhmm_pdhmm-implementation.h  | 11 +++++++++++
 biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc | 11 +++++++++++
 biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h         |  4 ++--
 6 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/biology/gkl/Makefile b/biology/gkl/Makefile
index 7c4c025158c6..128a190d5839 100644
--- a/biology/gkl/Makefile
+++ b/biology/gkl/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	gkl
-DISTVERSION=	0.8.11-9
-DISTVERSIONSUFFIX=	-g25670d8
+DISTVERSION=	0.9.1
 CATEGORIES=	biology devel
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/biology/gkl/distinfo b/biology/gkl/distinfo
index 35c01c063547..d1758a9bcd7a 100644
--- a/biology/gkl/distinfo
+++ b/biology/gkl/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1722788727
-SHA256 (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 743d1eb48c2629454a6dcb98d9adca3aaedfe9c658e6f89e890b03b6e029df61
-SIZE (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 5310668
+TIMESTAMP = 1755972512
+SHA256 (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 8e32bc3c63013ca6468c65fbbb6af80a433652b640be868d0cb82cb70a919799
+SIZE (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 5363673
diff --git a/biology/gkl/files/patch-CMakeLists.txt b/biology/gkl/files/patch-CMakeLists.txt
index 2cda423767df..a05193ec57f9 100644
--- a/biology/gkl/files/patch-CMakeLists.txt
+++ b/biology/gkl/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig	2024-08-04 17:44:32 UTC
+--- CMakeLists.txt.orig	2025-07-07 07:42:12 UTC
 +++ CMakeLists.txt
-@@ -24,6 +24,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native)
+@@ -28,6 +28,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native)
  # add CMakeLists.txt in subdirectories
  set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native)
  
diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h
new file mode 100644
index 000000000000..b47595807911
--- /dev/null
+++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h
@@ -0,0 +1,11 @@
+--- src/main/native/pdhmm/pdhmm-implementation.h.orig	2025-08-23 18:25:35 UTC
++++ src/main/native/pdhmm/pdhmm-implementation.h
+@@ -31,7 +31,7 @@
+ #include "avx512_impl.h"
+ #endif
+ 
+-#if defined(__linux__)
++#if defined(__linux__) || defined(__FreeBSD__)
+ #include <omp.h>
+ #endif
+ 
diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc
new file mode 100644
index 000000000000..ebe9e8d41887
--- /dev/null
+++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc
@@ -0,0 +1,11 @@
+--- src/main/native/pdhmm/pdhmm-serial.cc.orig	2025-08-23 18:12:32 UTC
++++ src/main/native/pdhmm/pdhmm-serial.cc
+@@ -24,7 +24,7 @@
+ #include "pdhmm-serial.h"
+ #include "MathUtils.h"
+ #include <cstdio>
+-#if defined(__linux__)
++#if defined(__linux__) || defined(__FreeBSD__)
+ #include <omp.h>
+ #endif
+ 
diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h
index 4896be46607f..b4afa8fb6791 100644
--- a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h
+++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h
@@ -1,4 +1,4 @@
---- src/main/native/pdhmm/pdhmm.h.orig	2024-08-04 16:31:53 UTC
+--- src/main/native/pdhmm/pdhmm.h.orig	2025-07-07 07:42:12 UTC
 +++ src/main/native/pdhmm/pdhmm.h
 @@ -27,6 +27,9 @@
  #ifdef linux
@@ -8,5 +8,5 @@
 +#include <omp.h>
 +#endif
  
- inline INT_TYPE roundDownToNearestMultipleOf(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; }
+ inline INT_TYPE CONCAT(roundDownToNearestMultipleOf_, SIMD_ENGINE)(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; }