From nobody Sat Jan 21 22:31:41 2023 X-Original-To: dev-commits-ports-main@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 4Nzrgy27pmz2v9r4; Sat, 21 Jan 2023 22:31:42 +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 4Nzrgy1N63z3Nl5; Sat, 21 Jan 2023 22:31:42 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1674340302; 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=+OJvmx4GWJw9uehmZip/ldoOvVBbwpmW5u4KyH+heJk=; b=CzRTDfNx98NMOz9soKYE8yGnjquG/SKe5J491sOK85RUzPe8sd7/Z1BSonDDzoe5r0rCpa afVlRv3jk8TjVn3+KgwbMENS4AFb8x8pNX3QbcNfycIsb9DHYv0tWvQLriQL4FFvSanBz3 CqBL8+LqC8W4eQ01WKt5q8yN5IxWdF7YTf9AM0Inv1vkjEQShJ64bjigwa7okq4wvFOzcs U3oEHgPqxWAdFbuStvb0amaJnHmYJs2zzoRT4BIGzGSUyuqfd7AQzHaKfAI+f4pWInKPVC L9i2CxwkDmfFzek/XJJ2YB3CoEOnyitEjuX6aacse8OARwINFxS9y5KXWc4iHg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1674340302; 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=+OJvmx4GWJw9uehmZip/ldoOvVBbwpmW5u4KyH+heJk=; b=HPY2I3jNNb+Xdu4VnpUNpj/3Ji9wlVUreKuZ1qNwTdln3dLGTNiPT+exHxDklR9fyRFmC6 jb2PfGtT+wVdTt3V5EYctwKZW6c/lJHaKMJTHZwCA7/8f1t/FxPB+mpmB0dI7c8Bn2qWmi th4KmlMXXsnU/50J9NPhEZ7/81oWtjPK71fRdXRjQflHX8GG2N6X47hlvAYl4XuP09AEoS P8/nKdUoSuIXSSIgPrVzy3m6g3SL4zCxLH0j/zJX/yS/8HdNDu51XphdjIgkxGjirkDQG/ fsQTElQ2DCx+8vgZPhH74PBqiFoATKLu858oL1+Khf9+uHm3U+T8E5St0hJLRw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1674340302; a=rsa-sha256; cv=none; b=h7jbWWfu4I51slzL6z/ZhhldkDIknZ8kE1LNnQ9koJQxokcKGcoOZYWmA/iFpsnotKjjsh P7JhkFoooBMIF9tojnSM35dyC2ik62x7Ye3wJrHNVnVqMSucB+dNFhtFAvsWw+RX6ukDyt wQTlNNo+Z66wESTcIftF7NnEYXSk9nU/fw1Qr81lHlsA4Xeh32Huog+2hGBk7JpUu5Cglq N5kzg4IriuyhoZfNyLatLxBAsTGwLTMPWSFxessCklZYEBcu/LmrVfwRBGySbNr4gTIkKV IH0C2l/ByOOy2vxSliHImElWn+sU5COqirvIwrWSqe8bRq2FcKTpEL4B1ZZlaA== 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 4Nzrgy0QnLzRYK; Sat, 21 Jan 2023 22:31:42 +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 30LMVfXu034045; Sat, 21 Jan 2023 22:31:41 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 30LMVfXb034044; Sat, 21 Jan 2023 22:31:41 GMT (envelope-from git) Date: Sat, 21 Jan 2023 22:31:41 GMT Message-Id: <202301212231.30LMVfXb034044@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: 65ce3f1684bc - main - biology/bowtie2: Update to 2.5.1 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: 65ce3f1684bc6a0457bfc55feb059baf76bbee2a Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=65ce3f1684bc6a0457bfc55feb059baf76bbee2a commit 65ce3f1684bc6a0457bfc55feb059baf76bbee2a Author: Jason W. Bacon AuthorDate: 2023-01-21 22:30:48 +0000 Commit: Jason W. Bacon CommitDate: 2023-01-21 22:30:48 +0000 biology/bowtie2: Update to 2.5.1 A few minor fixes and enhancements Changes: https://github.com/BenLangmead/bowtie2/tags Reported by: portscout --- biology/bowtie2/Makefile | 2 +- biology/bowtie2/distinfo | 6 +++--- biology/bowtie2/files/patch-Makefile | 28 +++++----------------------- 3 files changed, 9 insertions(+), 27 deletions(-) diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index b227373a69b0..14777fb43760 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -1,6 +1,6 @@ PORTNAME= bowtie2 DISTVERSIONPREFIX= v -DISTVERSION= 2.5.0 +DISTVERSION= 2.5.1 CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo index 1ebf87291129..69c8b6900f9a 100644 --- a/biology/bowtie2/distinfo +++ b/biology/bowtie2/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1667400686 -SHA256 (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 55dedeba8bea240d3ce3f46211d6e14310035c1de5a3e9ac33f72f739165fea0 -SIZE (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 10598633 +TIMESTAMP = 1674338476 +SHA256 (BenLangmead-bowtie2-v2.5.1_GH0.tar.gz) = 3fe00f4f89b5dd85fd9317e2168ec93f30dbb75d7950a08516c767d21eca7c27 +SIZE (BenLangmead-bowtie2-v2.5.1_GH0.tar.gz) = 10598627 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 23bb0fae0c58..abbe01f5f982 100644 --- a/biology/bowtie2/files/patch-Makefile +++ b/biology/bowtie2/files/patch-Makefile @@ -1,29 +1,11 @@ ---- Makefile.orig 2022-11-01 01:53:08 UTC +--- Makefile.orig 2023-01-21 21:59:18 UTC +++ Makefile -@@ -32,7 +32,7 @@ BOWTIE_SHARED_MEM := - - CXXFLAGS += -std=c++11 - --ARCH = $(shell uname -m) -+ARCH = $(shell uname -p) - NGS_VER ?= 2.9.2 - VDB_VER ?= 2.9.2-1 - -@@ -62,7 +62,7 @@ ifneq (,$(findstring Darwin,$(shell uname))) +@@ -61,7 +61,7 @@ ifneq (,$(findstring Darwin,$(shell uname))) endif BITS := 32 --ifneq (,$(findstring $(shell uname -m), x86_64 amd64)) -+ifneq (,$(findstring $(shell uname -p), x86_64 amd64)) +-ARCH ?= $(shell uname -m) ++ARCH ?= $(shell uname -p) + ifneq (,$(findstring $(ARCH), x86_64 amd64)) BITS := 64 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 ppc64 ppc64le)) - BITS := 64 - SSE_FLAG := - CXXFLAGS += -fopenmp-simd