From owner-svn-ports-all@freebsd.org Fri Jul 3 11:22:50 2020 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 6508D34B3A5; Fri, 3 Jul 2020 11:22:50 +0000 (UTC) (envelope-from jrm@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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 49ysyL24JHz48nm; Fri, 3 Jul 2020 11:22:50 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 2A687AFE2; Fri, 3 Jul 2020 11:22:50 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 063BMoeX018764; Fri, 3 Jul 2020 11:22:50 GMT (envelope-from jrm@FreeBSD.org) Received: (from jrm@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 063BMnIW018762; Fri, 3 Jul 2020 11:22:49 GMT (envelope-from jrm@FreeBSD.org) Message-Id: <202007031122.063BMnIW018762@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jrm set sender to jrm@FreeBSD.org using -f From: Joseph Mingrone Date: Fri, 3 Jul 2020 11:22:49 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r541097 - in head/biology/diamond: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jrm X-SVN-Commit-Paths: in head/biology/diamond: . files X-SVN-Commit-Revision: 541097 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 03 Jul 2020 11:22:50 -0000 Author: jrm Date: Fri Jul 3 11:22:49 2020 New Revision: 541097 URL: https://svnweb.freebsd.org/changeset/ports/541097 Log: biology/diamond: Update to version 0.9.36 Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36 Added: head/biology/diamond/files/ head/biology/diamond/files/patch-src_search_collision.cpp (contents, props changed) Modified: head/biology/diamond/Makefile (contents, props changed) head/biology/diamond/distinfo (contents, props changed) Modified: head/biology/diamond/Makefile ============================================================================== --- head/biology/diamond/Makefile Fri Jul 3 10:39:06 2020 (r541096) +++ head/biology/diamond/Makefile Fri Jul 3 11:22:49 2020 (r541097) @@ -2,7 +2,7 @@ PORTNAME= diamond DISTVERSIONPREFIX= v -DISTVERSION= 0.9.35 +DISTVERSION= 0.9.36 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org Modified: head/biology/diamond/distinfo ============================================================================== --- head/biology/diamond/distinfo Fri Jul 3 10:39:06 2020 (r541096) +++ head/biology/diamond/distinfo Fri Jul 3 11:22:49 2020 (r541097) @@ -1,3 +1,3 @@ -TIMESTAMP = 1593274744 -SHA256 (bbuchfink-diamond-v0.9.35_GH0.tar.gz) = 21d25780de6dacf4f965a1c583cf511b19f04def9289387c793e5a175061452d -SIZE (bbuchfink-diamond-v0.9.35_GH0.tar.gz) = 1102711 +TIMESTAMP = 1593736895 +SHA256 (bbuchfink-diamond-v0.9.36_GH0.tar.gz) = 870af89606330f6c0b57ed478d2d8237334ce8f5630eac770399ff431948bd59 +SIZE (bbuchfink-diamond-v0.9.36_GH0.tar.gz) = 1104423 Added: head/biology/diamond/files/patch-src_search_collision.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/diamond/files/patch-src_search_collision.cpp Fri Jul 3 11:22:49 2020 (r541097) @@ -0,0 +1,10 @@ +--- src/search/collision.cpp.orig 2020-07-03 10:58:27 UTC ++++ src/search/collision.cpp +@@ -92,7 +92,6 @@ bool is_primary_hit(const Letter *query, + const unsigned sid, + const unsigned len) + { +- assert(len > 0 && len <= config.window * 2); + const bool chunked(config.lowmem > 1); + uint64_t mask = reduced_match32(query, subject, len); + unsigned i = 0;