From owner-svn-ports-all@FreeBSD.ORG Fri Dec 13 09:34:41 2013 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 4E431239; Fri, 13 Dec 2013 09:34:41 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 39A481675; Fri, 13 Dec 2013 09:34:41 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.7/8.14.7) with ESMTP id rBD9YfMW055918; Fri, 13 Dec 2013 09:34:41 GMT (envelope-from gerald@svn.freebsd.org) Received: (from gerald@localhost) by svn.freebsd.org (8.14.7/8.14.7/Submit) id rBD9Yerx055911; Fri, 13 Dec 2013 09:34:40 GMT (envelope-from gerald@svn.freebsd.org) Message-Id: <201312130934.rBD9Yerx055911@svn.freebsd.org> From: Gerald Pfeifer Date: Fri, 13 Dec 2013 09:34:40 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r336328 - in head/biology/plink: . 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-all@freebsd.org X-Mailman-Version: 2.1.17 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, 13 Dec 2013 09:34:41 -0000 Author: gerald Date: Fri Dec 13 09:34:40 2013 New Revision: 336328 URL: http://svnweb.freebsd.org/changeset/ports/336328 Log: Fix the build with more standards-compliant compilers such as GCC 4.7. [1] On the way replace USE_GMAKE by USES=gmake. PR: 184566 [1], 182136 Submitted by: Christoph Moench-Tegeder [1] Approved by: maintainer (Jason Bacon ) [1] Added: head/biology/plink/files/patch-elf.cpp (contents, props changed) head/biology/plink/files/patch-idhelp.cpp (contents, props changed) head/biology/plink/files/patch-sets.cpp (contents, props changed) Modified: head/biology/plink/Makefile Modified: head/biology/plink/Makefile ============================================================================== --- head/biology/plink/Makefile Fri Dec 13 09:03:57 2013 (r336327) +++ head/biology/plink/Makefile Fri Dec 13 09:34:40 2013 (r336328) @@ -15,8 +15,8 @@ LICENSE= GPLv2 LIB_DEPENDS= liblapack.so:${PORTSDIR}/math/lapack +USES= gmake USE_ZIP= yes -USE_GMAKE= yes USE_FORTRAN= yes # Make it use the same compiler as lapack PLIST_FILES= bin/plink Added: head/biology/plink/files/patch-elf.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/files/patch-elf.cpp Fri Dec 13 09:34:40 2013 (r336328) @@ -0,0 +1,25 @@ +--- elf.cpp.orig 2013-11-16 17:09:56.000000000 +0100 ++++ elf.cpp 2013-11-16 17:10:24.000000000 +0100 +@@ -1175,10 +1175,10 @@ + << setw(8) << gcnt << " " + << setw(8) << (double)cnt / (double)gcnt << "\n"; + +- map::iterator i = chr_cnt.begin(); +- while ( i != chr_cnt.end() ) ++ map::iterator ichr = chr_cnt.begin(); ++ while ( ichr != chr_cnt.end() ) + { +- int c = i->first; ++ int c = ichr->first; + int x = chr_cnt.find( c )->second; + int y = chr_gcnt.find( c )->second; + +@@ -1189,7 +1189,7 @@ + << setw(8) << y << " " + << setw(8) << (double)x / (double)y << "\n"; + +- ++i; ++ ++ichr; + } + + } Added: head/biology/plink/files/patch-idhelp.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/files/patch-idhelp.cpp Fri Dec 13 09:34:40 2013 (r336328) @@ -0,0 +1,19 @@ +--- idhelp.cpp.orig 2013-11-16 17:11:42.000000000 +0100 ++++ idhelp.cpp 2013-11-16 17:12:53.000000000 +0100 +@@ -772,12 +772,12 @@ + for (int j = 0 ; j < jointField.size(); j++ ) + { + set & jf = jointField[j]; +- set::iterator j = jf.begin(); ++ set::iterator jfit = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( jfit != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*jfit)->name + " " ); ++ ++jfit; + } + PP->printLOG(" }"); + } Added: head/biology/plink/files/patch-sets.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/files/patch-sets.cpp Fri Dec 13 09:34:40 2013 (r336328) @@ -0,0 +1,18 @@ +--- sets.cpp.orig 2013-11-16 17:06:29.000000000 +0100 ++++ sets.cpp 2013-11-16 17:07:12.000000000 +0100 +@@ -768,11 +768,11 @@ + ////////////////////////////////////////////// + // Reset original missing status + +- vector::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector::iterator ipp = PP->sample.begin(); ++ while ( ipp != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*ipp)->missing = (*ipp)->flag; ++ ++ipp; + } + + ////////////////////////////////////////////////