From owner-svn-ports-head@FreeBSD.ORG Mon Jan 14 08:04:39 2013 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.FreeBSD.org [8.8.178.115]) by hub.freebsd.org (Postfix) with ESMTP id 18ED77C6; Mon, 14 Jan 2013 08:04:39 +0000 (UTC) (envelope-from araujo@FreeBSD.org) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) by mx1.freebsd.org (Postfix) with ESMTP id 03C1FAC4; Mon, 14 Jan 2013 08:04:39 +0000 (UTC) Received: from svn.freebsd.org (svn.FreeBSD.org [8.8.178.70]) by svn.freebsd.org (8.14.5/8.14.5) with ESMTP id r0E84cjG092779; Mon, 14 Jan 2013 08:04:38 GMT (envelope-from araujo@svn.freebsd.org) Received: (from araujo@localhost) by svn.freebsd.org (8.14.5/8.14.5/Submit) id r0E84cl4092776; Mon, 14 Jan 2013 08:04:38 GMT (envelope-from araujo@svn.freebsd.org) Message-Id: <201301140804.r0E84cl4092776@svn.freebsd.org> From: Marcelo Araujo Date: Mon, 14 Jan 2013 08:04:38 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r310361 - in head/biology/t_coffee: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 14 Jan 2013 08:04:39 -0000 Author: araujo Date: Mon Jan 14 08:04:38 2013 New Revision: 310361 URL: http://svnweb.freebsd.org/changeset/ports/310361 Log: - Update to 9.03. PR: ports/172499 Submitted by: KATO Tsuguru Added: head/biology/t_coffee/files/patch-dev3.c (contents, props changed) Deleted: head/biology/t_coffee/files/patch-Makefile head/biology/t_coffee/pkg-plist Modified: head/biology/t_coffee/Makefile head/biology/t_coffee/distinfo (contents, props changed) Modified: head/biology/t_coffee/Makefile ============================================================================== --- head/biology/t_coffee/Makefile Mon Jan 14 07:17:13 2013 (r310360) +++ head/biology/t_coffee/Makefile Mon Jan 14 08:04:38 2013 (r310361) @@ -2,36 +2,40 @@ # $FreeBSD$ PORTNAME= t_coffee -PORTVERSION= 5.68 +PORTVERSION= 9.03 +DISTVERSIONSUFFIX= .r1318 CATEGORIES= biology -MASTER_SITES= http://www.tcoffee.org/Packages/ -DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION} +MASTER_SITES= http://www.tcoffee.org/Packages/Stable/%SUBDIR%/ +MASTER_SITE_SUBDIR= Version_${PORTVERSION}${DISTVERSIONSUFFIX} +DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX} MAINTAINER= ports@FreeBSD.org COMMENT= A multiple DNA or protein sequence alignment package -BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw -RUN_DEPENDS:= ${BUILD_DEPENDS} +LICENSE= GPLv2 + +RUN_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw + +OPTIONS_DEFINE= EXAMPLES BUILD_WRKSRC= ${WRKSRC}/t_coffee_source -MAKE_ENV= MV=${MV} USER_BIN=${PREFIX}/bin \ - CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw +USE_FORTRAN= yes +MAKE_ENV= FCC="${FC} ${FFLAGS}" MAKEFILE= makefile +MAKE_JOBS_SAFE= yes -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin +PORTEXAMPLES= * +PLIST_FILES= bin/TMalign bin/t_coffee -post-install: -.if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCSDIR}/html - ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/license.txt ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/html/* ${DOCSDIR}/html -.endif -.if !defined(NOPORTEXAMPLES) - @ ${MKDIR} ${EXAMPLESDIR} - cd ${WRKSRC}/example && ${COPYTREE_SHARE} \* ${EXAMPLESDIR} +.include + +do-install: + (cd ${BUILD_WRKSRC} \ + && ${INSTALL_PROGRAM} TMalign t_coffee ${PREFIX}/bin) +.if ${PORT_OPTIONS:MEXAMPLES} + @${MKDIR} ${EXAMPLESDIR} + @(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${EXAMPLESDIR}) .endif .include Modified: head/biology/t_coffee/distinfo ============================================================================== --- head/biology/t_coffee/distinfo Mon Jan 14 07:17:13 2013 (r310360) +++ head/biology/t_coffee/distinfo Mon Jan 14 08:04:38 2013 (r310361) @@ -1,2 +1,2 @@ -SHA256 (T-COFFEE_distribution_Version_5.68.tar.gz) = 137d188cef6f33a42cbd656482eb961d1588fef3091d2457ee0ef23fab16a6de -SIZE (T-COFFEE_distribution_Version_5.68.tar.gz) = 2875438 +SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c +SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629 Added: head/biology/t_coffee/files/patch-dev3.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/t_coffee/files/patch-dev3.c Mon Jan 14 08:04:38 2013 (r310361) @@ -0,0 +1,10 @@ +--- t_coffee_source/dev3.c.orig 2012-07-13 02:06:31.000000000 +0900 ++++ t_coffee_source/dev3.c 2012-10-04 22:14:10.000000000 +0900 +@@ -3,6 +3,7 @@ + #include + #include + #include ++#include + #include + #include "dev3_lib_header.h" + /******************************COPYRIGHT NOTICE*******************************/