From nobody Sat Aug 23 18:27:00 2025 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4c8QWS2hsCz66FSm; Sat, 23 Aug 2025 18:27:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R12" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4c8QWS1vB1z3dsL; Sat, 23 Aug 2025 18:27:00 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1755973620; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=IVpLj7ZI+WjCObf1Fv1QBlu20lJ0hjk/JiwybHSYBZI=; b=mS/TZ8GldWXEQ2iFar1mFyjujg0fS7Gt1xbypMdVdJvgPTwjm3h6LaZOrf7hEmACTMtpN7 edBgFDldVwXwPiz88BRBG2GgpEzI/5rQEW8dOq7kUW+952uQSe8o9aqh7uYhf92371ABbb goQ85b5QbndCq8+J2nThMEXG6vUcrBxvFQfmR2f7kO0nTC0kVrvGmmJIyCqZ9qPZbDQsdj GFNfGUgEOvqMsJsC99xiW/keRZd/Awn3sbwxV+T13TwCJ4/7BeUA8ZIYqm11dnOCqdqESA dGsvRKQFV2Ft1abudOMi4nnsSUY7wHGfd7rgns/HO897Mu9ykOj60uXY54qmmg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1755973620; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=IVpLj7ZI+WjCObf1Fv1QBlu20lJ0hjk/JiwybHSYBZI=; b=A4kOozpts+VzVcCqFT0Mpu3cT5XQXYkZitcRdAFqu6OhwHhjJ5V2opLi84P4r0Mc9p63z+ oWNtkGF6N/5fCmcFcnfQmSCkmPtCwuBLgMDaLPWSbNqmTbEfIp+W+bDbSj7sj8BtxOmbFG mggSvrgKmeQubEQzg6a2NsYtYXI7luHcijEojZ355Uh2ZpdLpT9+Gzis2MLFxWifa5L37j 8tX+lx4Ps8Am0GPQsgovOQZzXjZNyRM5KImzgIBKDSDXWFn27w7wyF4+qhg9qiPTyB3NCj S/D0eq3bR6po2WsBBSfWUcDV5vDlzt2TAxzBIBVtNnJTvOnhudTJ/ecFKdEQFQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1755973620; a=rsa-sha256; cv=none; b=Lc/YU8Ej3hKG8EuUHLT8bieE7y7J9oX21uqcr4cc5QAS8ACnWsi/gqlCWT4YVRBIds/KYc Up6EwBG3axPtBxfekTpeoBX/HAu8C/RVS/VUS1k8gRZy7ViKhBfe+JV4FMCm/8cjIo6RBr yJWNFgzYzpqKfQnEJqD8CUAx5zqY+Hf4vbmEuA05Qo4rACGBTXgvbhP2HySxkUaklPBbqW PRzuXKizna2dMac/sO9YgJom5NtrEiLkBXZ9FNYFHRMfFOYHRJ/Wf86LMeI9+sEWJlB30O RSTq6/tXKpeyAN37HleCX490sSKTPVv24ydLp5bNDc8M+MWoLma6m/bLuucyrw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4c8QWS137tzB6p; Sat, 23 Aug 2025 18:27:00 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 57NIR02D058760; Sat, 23 Aug 2025 18:27:00 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 57NIR0rx058757; Sat, 23 Aug 2025 18:27:00 GMT (envelope-from git) Date: Sat, 23 Aug 2025 18:27:00 GMT Message-Id: <202508231827.57NIR0rx058757@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 25848df4724c - main - =?utf-8?Q?biology/gkl: update 0.8.11-9 =E2=86=92 0.9.1?= List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 25848df4724ce501e9d6966f5b5547a8d459c9b2 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=25848df4724ce501e9d6966f5b5547a8d459c9b2 commit 25848df4724ce501e9d6966f5b5547a8d459c9b2 Author: Yuri Victorovich AuthorDate: 2025-08-23 18:26:47 +0000 Commit: Yuri Victorovich 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 + #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 +-#if defined(__linux__) ++#if defined(__linux__) || defined(__FreeBSD__) + #include + #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 +#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; }