From owner-svn-ports-all@freebsd.org Fri Mar 20 18:14:24 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 DA18E26EE8F; Fri, 20 Mar 2020 18:14:24 +0000 (UTC) (envelope-from jwb@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) server-signature RSA-PSS (4096 bits) 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 48kX3h5WnPz48GR; Fri, 20 Mar 2020 18:14:24 +0000 (UTC) (envelope-from jwb@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 B6E1E27970; Fri, 20 Mar 2020 18:14:24 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 02KIEOtq043601; Fri, 20 Mar 2020 18:14:24 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 02KIEOKq043598; Fri, 20 Mar 2020 18:14:24 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <202003201814.02KIEOKq043598@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Fri, 20 Mar 2020 18:14:24 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r528792 - head/biology/canu X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: head/biology/canu X-SVN-Commit-Revision: 528792 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: 2.1.29 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, 20 Mar 2020 18:14:24 -0000 Author: jwb Date: Fri Mar 20 18:14:23 2020 New Revision: 528792 URL: https://svnweb.freebsd.org/changeset/ports/528792 Log: biology/canu: Upgrade to 2.0 Several routine enhancements and bug fixes Reported by: portscout Modified: head/biology/canu/Makefile head/biology/canu/distinfo head/biology/canu/pkg-plist Modified: head/biology/canu/Makefile ============================================================================== --- head/biology/canu/Makefile Fri Mar 20 17:44:37 2020 (r528791) +++ head/biology/canu/Makefile Fri Mar 20 18:14:23 2020 (r528792) @@ -2,8 +2,7 @@ PORTNAME= canu DISTVERSIONPREFIX= v -DISTVERSION= 1.9 -PORTREVISION= 1 +DISTVERSION= 2.0 CATEGORIES= biology java perl5 MAINTAINER= jwb@FreeBSD.org @@ -41,9 +40,6 @@ pre-configure: -e 's|-funroll-loops||g' \ -e 's|-fexpensive-optimizations||g' \ ${WRKSRC}/Makefile - @${REINPLACE_CMD} \ - -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \ - ${WRKSRC}/pipelines/canu/OverlapMhap.pm @${REINPLACE_CMD} \ -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \ ${WRKSRC}/pipelines/canu.pl Modified: head/biology/canu/distinfo ============================================================================== --- head/biology/canu/distinfo Fri Mar 20 17:44:37 2020 (r528791) +++ head/biology/canu/distinfo Fri Mar 20 18:14:23 2020 (r528792) @@ -1,3 +1,3 @@ -TIMESTAMP = 1573142752 -SHA256 (marbl-canu-v1.9_GH0.tar.gz) = 6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385 -SIZE (marbl-canu-v1.9_GH0.tar.gz) = 3410307 +TIMESTAMP = 1584624503 +SHA256 (marbl-canu-v2.0_GH0.tar.gz) = e2e6e8b5ec4dd4cfba5e372f4a64b2c01fbd544d4b5867746021f10771a6f4ef +SIZE (marbl-canu-v2.0_GH0.tar.gz) = 3443777 Modified: head/biology/canu/pkg-plist ============================================================================== --- head/biology/canu/pkg-plist Fri Mar 20 17:44:37 2020 (r528791) +++ head/biology/canu/pkg-plist Fri Mar 20 18:14:23 2020 (r528792) @@ -41,7 +41,6 @@ bin/sequence bin/splitHaplotype bin/splitReads bin/sqStoreCreate -bin/sqStoreCreatePartition bin/sqStoreDumpFASTQ bin/sqStoreDumpMetaData bin/tgStoreCompress