diff options
| -rw-r--r-- | biology/gkl/Makefile | 3 | ||||
| -rw-r--r-- | biology/gkl/distinfo | 6 | ||||
| -rw-r--r-- | biology/gkl/files/patch-CMakeLists.txt | 4 | ||||
| -rw-r--r-- | biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h | 11 | ||||
| -rw-r--r-- | biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc | 11 | ||||
| -rw-r--r-- | 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; } |