From owner-svn-ports-all@freebsd.org Sat Nov 3 21:10:08 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 0672E10E833E; Sat, 3 Nov 2018 21:10:08 +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 TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id B0F276ABD6; Sat, 3 Nov 2018 21:10:07 +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 8DB5D1EFC0; Sat, 3 Nov 2018 21:10:07 +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 wA3LA7ef002243; Sat, 3 Nov 2018 21:10:07 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id wA3LA7SB002241; Sat, 3 Nov 2018 21:10:07 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <201811032110.wA3LA7SB002241@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Sat, 3 Nov 2018 21:10:07 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r483910 - in head/biology/bowtie: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/bowtie: . files X-SVN-Commit-Revision: 483910 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: Sat, 03 Nov 2018 21:10:08 -0000 Author: jwb Date: Sat Nov 3 21:10:06 2018 New Revision: 483910 URL: https://svnweb.freebsd.org/changeset/ports/483910 Log: biology/bowtie: Patch Added: head/biology/bowtie/files/patch-ebwt.h (contents, props changed) Modified: head/biology/bowtie/Makefile Modified: head/biology/bowtie/Makefile ============================================================================== --- head/biology/bowtie/Makefile Sat Nov 3 20:29:12 2018 (r483909) +++ head/biology/bowtie/Makefile Sat Nov 3 21:10:06 2018 (r483910) @@ -1,9 +1,9 @@ # $FreeBSD$ PORTNAME= bowtie -PORTVERSION= 1.1.2 -PORTREVISION= 6 DISTVERSIONPREFIX= v +DISTVERSION= 1.1.2 +PORTREVISION= 7 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -13,13 +13,14 @@ LICENSE= ART10 # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 + +USES= gmake perl5 python:run shebangfix # FIXME: bowtie-align intermittently dumps core when compiled with clang # GCC 4.2 does not provide good performance USE_GCC= yes -USES= gmake perl5 python:run shebangfix USE_PERL5= run -SHEBANG_FILES= scripts/*.pl bowtie bowtie-build \ - bowtie-inspect + +SHEBANG_FILES= scripts/*.pl bowtie bowtie-build bowtie-inspect USE_GITHUB= yes GH_ACCOUNT= BenLangmead Added: head/biology/bowtie/files/patch-ebwt.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie/files/patch-ebwt.h Sat Nov 3 21:10:06 2018 (r483910) @@ -0,0 +1,11 @@ +--- ebwt.h.orig 2018-11-03 20:51:56 UTC ++++ ebwt.h +@@ -860,7 +860,7 @@ public: + TIndexOffU* ftab() const { return _ftab; } + TIndexOffU* eftab() const { return _eftab; } + TIndexOffU* offs() const { return _offs; } +- uint32_t* isa() const { return _isa; } /* check */ ++ uint32_t* isa() const { return (uint32_t)_isa; } /* check */ + TIndexOffU* plen() const { return _plen; } + TIndexOffU* rstarts() const { return _rstarts; } + uint8_t* ebwt() const { return _ebwt; }