From nobody Fri Nov 04 23:49:03 2022 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 4N3y5D2frqz4h5w5; Fri, 4 Nov 2022 23:49:04 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4N3y5D29mmz3Gf5; Fri, 4 Nov 2022 23:49:04 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1667605744; 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=1YQPVy91/m6ZED2m0aCdWvZNf9Yl/E55H0bpagFM8PY=; b=u0EaU/PO1FbK56QNg5e78fhc+G71Qs1+0VgGYIwPGLCYF9h/3CmThKuPYBV9tuvBdCyIiI t8zVZKaTYXsScrxA6a68Pakp/v85m7QdgoJ6GuCenfzhKEZyGIU1vrw4kyVmaVYCmNFE6Y NBkyT84WNTdDDb1wa/OV+7QVScCR5Ar/S4zLxwntI0zvnEdBRIaZ8EwWUgq5eX1xNosdNp UtxA8wOzUEldRj4OVEHcq17rC8wpqfJhl3hebsW63hA/yKwbTXpXe8IcyoOT/7AHfyYk1E gWSEA+VOJW/U6VPHGX1Gh6vPwIJo9P4bVFULlxezxdTZ4+VG3otdhjzTVtp7Mw== 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 4N3y5D0zzvzL0P; Fri, 4 Nov 2022 23:49:04 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 2A4Nn39h004370; Fri, 4 Nov 2022 23:49:03 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2A4Nn30Z004369; Fri, 4 Nov 2022 23:49:03 GMT (envelope-from git) Date: Fri, 4 Nov 2022 23:49:03 GMT Message-Id: <202211042349.2A4Nn30Z004369@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: f2f8bd75c4ac - main - biology/bowtie2: Update to 2.5.0 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: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1667605744; 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=1YQPVy91/m6ZED2m0aCdWvZNf9Yl/E55H0bpagFM8PY=; b=WaCoaATmix/YacEVCE4j+tQZBK1B/TNYx3/pDfMVUDjeXb8heyvwKpa4aQKFx2gZCEzEFd 1TSzQEYiuvFrJ5PhPZMJDdLFoyvG9p0EdsDJh1XflQeLO+h01Qw4sDFhEy3UJAqW6gzz68 i2LV5jb7zwGITJSxlXIlvRMfk4mwQCyd008QBPdO4ob/8vr/k2Pty5891KuDjdgWn5tyZb tm6kEfN4Re/23fZe9yhfu6g479qLLLV1D3x5twXI8Sruvr8oDQQzu8//Y6rxIk40n9FJ0E QXkqedKXAs/aN5d92XGJhdukJdML8vDQdZZDVYQdfzyGYiT0aWv2OYlcFrlRsg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1667605744; a=rsa-sha256; cv=none; b=RDOmSTlre3bTGExADNFu/28ajjG2C2N6JPoNRl/yu2HkWrj5nGpwQnk2d95fFc/fR/McAL w36CG6GpsxWnE74jDX27rnrG5HSCIBzLfXjUl8cPuFxDFL7I3w5Ku3RICyT//UVaVckmHw AjFz5lB3GhIsszVwsl4Ji8n5haNu9zdD4ScI6uQJsphjdQ1M2WLkR+9kqTj5WUmWEuGOfS I7kbLdOgLMFtuG6E9/wBc/SKjiUFvLB6eUGLchrWMs12sVyi7fVY2RVyRPUNF9nGyN8++R DglFQK1UUPJunysYqTqY2K3zYGXTi5r6aH/gz8fVO7+HV+h/TqXnM38o8wF9jQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa commit f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa Author: Jason W. Bacon AuthorDate: 2022-11-04 23:47:34 +0000 Commit: Jason W. Bacon CommitDate: 2022-11-04 23:49:02 +0000 biology/bowtie2: Update to 2.5.0 Performance improvements and minor improvements Changes: https://github.com/BenLangmead/bowtie2/tags Reported by: portscout --- biology/bowtie2/Makefile | 2 +- biology/bowtie2/distinfo | 6 +++--- biology/bowtie2/files/patch-Makefile | 12 ++++++++---- 3 files changed, 12 insertions(+), 8 deletions(-) diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index 6ca11a69916f..b227373a69b0 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -1,6 +1,6 @@ PORTNAME= bowtie2 DISTVERSIONPREFIX= v -DISTVERSION= 2.4.5 +DISTVERSION= 2.5.0 CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo index afe87ffa42f1..1ebf87291129 100644 --- a/biology/bowtie2/distinfo +++ b/biology/bowtie2/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1642699775 -SHA256 (BenLangmead-bowtie2-v2.4.5_GH0.tar.gz) = db101391b54a5e0eeed7469b05aee55ee6299558b38607f592f6b35a7d41dcb6 -SIZE (BenLangmead-bowtie2-v2.4.5_GH0.tar.gz) = 10585723 +TIMESTAMP = 1667400686 +SHA256 (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 55dedeba8bea240d3ce3f46211d6e14310035c1de5a3e9ac33f72f739165fea0 +SIZE (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 10598633 SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743 diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile index fb68d5913e52..491fd10e7b79 100644 --- a/biology/bowtie2/files/patch-Makefile +++ b/biology/bowtie2/files/patch-Makefile @@ -1,4 +1,4 @@ ---- Makefile.orig 2021-05-15 20:10:26 UTC +--- Makefile.orig 2022-11-02 14:50:38 UTC +++ Makefile @@ -32,7 +32,7 @@ BOWTIE_SHARED_MEM := @@ -9,17 +9,21 @@ NGS_VER ?= 2.9.2 VDB_VER ?= 2.9.2-1 -@@ -59,11 +59,11 @@ ifneq (,$(findstring Darwin,$(shell uname))) +@@ -62,7 +62,7 @@ ifneq (,$(findstring Darwin,$(shell uname))) endif BITS := 32 -ifneq (,$(findstring $(shell uname -m), x86_64 amd64)) +ifneq (,$(findstring $(shell uname -p), x86_64 amd64)) BITS := 64 - SSE_FLAG := -msse2 + ifeq (1, $(SSE_AVX2)) + SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2 +@@ -71,7 +71,7 @@ ifneq (,$(findstring $(shell uname -m), x86_64 amd64)) + endif + POPCNT_CAPABILITY ?= 1 -else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le)) -+else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x powerpc64 powerpc64le)) ++else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x ppc64 ppc64le)) BITS := 64 SSE_FLAG := CXXFLAGS += -fopenmp-simd