From nobody Wed Mar 26 07:34:47 2025 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 4ZMz8772tNz5rWvJ; Wed, 26 Mar 2025 07:34:47 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4ZMz876bd9z3tn7; Wed, 26 Mar 2025 07:34:47 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1742974487; 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=iF+MGFA9tFaEceTR9IPo42hjkJJCoAsw+jZdxpPROns=; b=WhKTyI5sxSA1eD/98iRV8xNDCw4Bwba6Vrhetcn8qJyjO8cLwJ70ptjH5elctPofvdkpME 5HjTodPoEoxrhUhTFdokuAet/l1nfCYnVJcn5WSLuZk/XKIF5zKDCmkDrAGo/cm2BMm5gn 4DpqXAuNyQw67SFXxemyZqsEuyd4BfpdkJlFt6TC1hbsPfPcQ549E15eGMsbg3as6Q2QL+ Ss9bXbKc9GSc4kd1sz3uY/UdLXyopDbe1BJ7MAwBx/jj1u1KDI6VEDADoqa0+KLW4VUtsz G+2DW+6OoMlFvtUxX8Xy3l2otiGVWPSdmZrD+WfF7fO6fOWPX3dBVC5qlKbcMw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1742974487; a=rsa-sha256; cv=none; b=X6KTgH2ejw++UlHIshedVTotMQPBmRbUwmwIzB4qOE889AK2Z5bswhY8J3GKcagWsVaDBu JCil1KXQLvnnPTZO7CeX7CxdLMcfJyuNqS8n04y49KNc5/yHvGhJDvI0A7a0adEN8EgHWe 7u3TGoyw1eTvtp9ugjIvDHfh5l7Uaaap649s6pl3dR3zHEyGj391Q/ydPZLxPP7lKD+atr dwNV2o6kWri0Ch7uh1aLma4u65Q2lbm8IfKho6nRfzzzR1M4sXdJd2jTE8P0UfCLM3CFgh 2TVQvF36x8kwhhNMnNwLgVuDnfunIE3xvWp3uCTdoi+anZlGVVLvoUO3OU0qLg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1742974487; 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=iF+MGFA9tFaEceTR9IPo42hjkJJCoAsw+jZdxpPROns=; b=jiUyH6HGiK3LmuBWtaasmU1vMu1k9b5Li89RsqcsgfF/inFAJKoRr68RoHTDy/nk1Oa9FG fpWNaMRfAz68fzjBC+OL2mo6seDImCzzIttFbCFX4hFDlPkZejW5yNp28jNvjorCydu+o2 GeHr8qEhBtBddpYqJ+TbknUUw6M/z+EANvJrn6iASyHkvuARqo0ULN+mrjZH6pBXtxMZl1 GIgV9ZSb5VAWLzQPgK022SDHJMUTf6HFHV4hMRQ0e0AOYXutIQnV4xOQfKPSPOhGWdupSF y5lRq24vDwBwged1S9zeL1lse59M7MTrt/J88kyNMry5kOEjVyaMQOpfwULWVA== 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 4ZMz8766vNz1G5J; Wed, 26 Mar 2025 07:34:47 +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 52Q7YlXF037474; Wed, 26 Mar 2025 07:34:47 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 52Q7YluO037471; Wed, 26 Mar 2025 07:34:47 GMT (envelope-from git) Date: Wed, 26 Mar 2025 07:34:47 GMT Message-Id: <202503260734.52Q7YluO037471@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Fernando =?utf-8?Q?Apestegu=C3=ADa?= Subject: git: b66379cdc662 - main - biology/bwa: update 0.7.18 => 0.7.19 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: fernape X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: b66379cdc6620acb33e1e3bc32b77be597cad24b Auto-Submitted: auto-generated The branch main has been updated by fernape: URL: https://cgit.FreeBSD.org/ports/commit/?id=b66379cdc6620acb33e1e3bc32b77be597cad24b commit b66379cdc6620acb33e1e3bc32b77be597cad24b Author: Älven AuthorDate: 2025-03-24 18:13:29 +0000 Commit: Fernando Apesteguía CommitDate: 2025-03-26 07:34:34 +0000 biology/bwa: update 0.7.18 => 0.7.19 ChangeLog: https://github.com/lh3/bwa/blob/master/NEWS.md#release-0719-22-march-2025 Notable changes: * Bugfix: internal @HD lines. The bug was introduced in 0.7.18. * Merged #414, #391, #346, #312, #311, #308, #291, #288, #286 and #212 PR: 285620 Reported by: alster@vinterdalen.se (maintainer) --- biology/bwa/Makefile | 2 +- biology/bwa/distinfo | 6 +++--- biology/bwa/files/patch-Makefile | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index 13316b89e355..3481077c3af3 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -1,6 +1,6 @@ PORTNAME= bwa DISTVERSIONPREFIX= v -DISTVERSION= 0.7.18 +DISTVERSION= 0.7.19 CATEGORIES= biology MAINTAINER= alster@vinterdalen.se diff --git a/biology/bwa/distinfo b/biology/bwa/distinfo index b9b0548bf588..d6325d94fb62 100644 --- a/biology/bwa/distinfo +++ b/biology/bwa/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1732300398 -SHA256 (lh3-bwa-v0.7.18_GH0.tar.gz) = 194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870 -SIZE (lh3-bwa-v0.7.18_GH0.tar.gz) = 238036 +TIMESTAMP = 1742771512 +SHA256 (lh3-bwa-v0.7.19_GH0.tar.gz) = cdff5db67652c5b805a3df08c4e813a822c65791913eccfb3cf7d528588f37bc +SIZE (lh3-bwa-v0.7.19_GH0.tar.gz) = 238518 diff --git a/biology/bwa/files/patch-Makefile b/biology/bwa/files/patch-Makefile index e7d704d5e0b3..a48f921d7ddf 100644 --- a/biology/bwa/files/patch-Makefile +++ b/biology/bwa/files/patch-Makefile @@ -1,11 +1,11 @@ ---- Makefile.orig 2014-05-19 13:11:41 UTC +--- Makefile.orig 2025-03-22 18:55:09 UTC +++ Makefile @@ -1,6 +1,6 @@ -CC= gcc +CC?= gcc #CC= clang --analyze --CFLAGS= -g -Wall -Wno-unused-function -O2 -+CFLAGS?= -g -Wall -Wno-unused-function -O2 +-CFLAGS= -g -Wall -Wno-unused-function -O3 ++CFLAGS?= -g -Wall -Wno-unused-function -O3 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS AR= ar DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)