From owner-freebsd-ports-bugs@FreeBSD.ORG Mon May 31 17:30:34 2004 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 3B87D16A4CE for ; Mon, 31 May 2004 17:30:34 -0700 (PDT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 2FAEA43D2D for ; Mon, 31 May 2004 17:30:34 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) i510UMki076787 for ; Mon, 31 May 2004 17:30:22 -0700 (PDT) (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.11/8.12.11/Submit) id i510UMPM076781; Mon, 31 May 2004 17:30:22 -0700 (PDT) (envelope-from gnats) Resent-Date: Mon, 31 May 2004 17:30:22 -0700 (PDT) Resent-Message-Id: <200406010030.i510UMPM076781@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Roman Neuhauser Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id A1AAE16A4CF for ; Mon, 31 May 2004 17:25:25 -0700 (PDT) Received: from smtp.dkm.cz (smtp.dkm.cz [62.24.64.34]) by mx1.FreeBSD.org (Postfix) with SMTP id 93C4B43D3F for ; Mon, 31 May 2004 17:25:24 -0700 (PDT) (envelope-from neuhauser@chello.cz) Received: (qmail 73925 invoked by uid 0); 1 Jun 2004 00:25:23 -0000 Received: from r3al16.mistral.cz (HELO isis.wad.cz) (213.220.229.16) by smtp.dkm.cz with SMTP; 1 Jun 2004 00:25:23 -0000 Received: by isis.wad.cz (Postfix, from userid 1001) id D57862FDA01; Tue, 1 Jun 2004 02:25:22 +0200 (CEST) Message-Id: <20040601002522.D57862FDA01@isis.wad.cz> Date: Tue, 1 Jun 2004 02:25:22 +0200 (CEST) From: Roman Neuhauser To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 cc: wjv@FreeBSD.org Subject: ports/67429: [PATCH] biology/migrate update to 1.7.6.1 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list Reply-To: Roman Neuhauser List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 01 Jun 2004 00:30:34 -0000 >Number: 67429 >Category: ports >Synopsis: [PATCH] biology/migrate update to 1.7.6.1 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon May 31 17:30:21 PDT 2004 >Closed-Date: >Last-Modified: >Originator: Roman Neuhauser >Release: FreeBSD 4.9-RELEASE-p2 i386 >Organization: >Environment: System: FreeBSD isis.wad.cz 4.9-RELEASE-p2 FreeBSD 4.9-RELEASE-p2 #3: Sun Mar 7 02:11:16 CET 2004 root@isis.wad.cz:/usr/obj/usr/src/sys/FREEPUPPY2_6 i386 >Description: in case there's anything wrong with the software (I can't really tell), 1.2.4 moved to ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/oldversions/1.2.4/ maintainer cc'd >How-To-Repeat: >Fix: --- biology::migrate-1.7.6.1.patch begins here --- Index: biology/migrate/Makefile =================================================================== RCS file: /home/ncvs/ports/biology/migrate/Makefile,v retrieving revision 1.4 diff -u -r1.4 Makefile --- biology/migrate/Makefile 23 Feb 2004 03:59:05 -0000 1.4 +++ biology/migrate/Makefile 1 Jun 2004 00:16:55 -0000 @@ -6,7 +6,7 @@ # PORTNAME= migrate -PORTVERSION= 1.2.4 +PORTVERSION= 1.7.6.1 CATEGORIES= biology MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src @@ -14,22 +14,32 @@ MAINTAINER= wjv@FreeBSD.org COMMENT= A program to estimate population sizes and migration rates -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} -CONFIGURE_WRKSRC= ${WRKSRC}/src -BUILD_WRKSRC= ${CONFIGURE_WRKSRC} -INSTALL_WRKSRC= ${CONFIGURE_WRKSRC} +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src GNU_CONFIGURE= yes +CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL} MAN1= migrate.1 +MLINKS= migrate.1 migrate-n.1 -post-install: +DOCS= HISTORY HOWTO-PARALLEL README migrate.html +EXAMPLES= README infile.benchmark infile.ep infile.msat infile.seq \ + parmfile parmfile.benchmark parmfile.ep parmfile.msat \ + parmfile.seq + +do-install: + @ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin @ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate + @ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1 .if !defined(NOPORTDOCS) @ ${MKDIR} ${DOCSDIR}/graphics -.for docfile in HISTORY HOWTO-PARALLEL README migrate.html - @ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR} +.for file in ${DOCS} + @ ${INSTALL_DATA} ${WRKSRC}/../${file} ${DOCSDIR} +.endfor + @ ${MKDIR} ${EXAMPLESDIR} +.for file in ${EXAMPLES} + @ ${INSTALL_DATA} ${WRKSRC}/../example/${file} ${EXAMPLESDIR} .endfor - @ ${INSTALL_DATA} ${WRKSRC}/graphics/* ${DOCSDIR}/graphics + @ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics .endif .include Index: biology/migrate/distinfo =================================================================== RCS file: /home/ncvs/ports/biology/migrate/distinfo,v retrieving revision 1.3 diff -u -r1.3 distinfo --- biology/migrate/distinfo 31 Mar 2004 03:06:19 -0000 1.3 +++ biology/migrate/distinfo 31 May 2004 22:48:00 -0000 @@ -1,2 +1,2 @@ -MD5 (migrate-1.2.4.src.tar.gz) = d5b90497336bee7d559ac3a654043e13 -SIZE (migrate-1.2.4.src.tar.gz) = 312245 +MD5 (migrate-1.7.6.1.src.tar.gz) = 5e8f03923ca2a12e7d3dd460c17679a1 +SIZE (migrate-1.7.6.1.src.tar.gz) = 384925 Index: biology/migrate/pkg-plist =================================================================== RCS file: /home/ncvs/ports/biology/migrate/pkg-plist,v retrieving revision 1.2 diff -u -r1.2 pkg-plist --- biology/migrate/pkg-plist 22 Oct 2003 09:29:51 -0000 1.2 +++ biology/migrate/pkg-plist 31 May 2004 23:45:34 -0000 @@ -8,5 +8,16 @@ %%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif %%PORTDOCS%%%%DOCSDIR%%/migrate.html +%%PORTDOCS%%%%EXAMPLESDIR%%/README +%%PORTDOCS%%%%EXAMPLESDIR%%/infile.benchmark +%%PORTDOCS%%%%EXAMPLESDIR%%/infile.ep +%%PORTDOCS%%%%EXAMPLESDIR%%/infile.msat +%%PORTDOCS%%%%EXAMPLESDIR%%/infile.seq +%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile +%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.benchmark +%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.ep +%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.msat +%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.seq +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% %%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics %%PORTDOCS%%@dirrm %%DOCSDIR%% Index: biology/migrate/files/patch-Makefile.in =================================================================== RCS file: biology/migrate/files/patch-Makefile.in diff -N biology/migrate/files/patch-Makefile.in --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ biology/migrate/files/patch-Makefile.in 1 Jun 2004 00:20:44 -0000 @@ -0,0 +1,11 @@ +--- Makefile.in.orig Mon May 10 15:58:32 2004 ++++ Makefile.in Tue Jun 1 01:44:25 2004 +@@ -39,7 +39,7 @@ + COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DNEWSTYLE + #COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DNEWSTYLE -DMERSENNE_TWISTER + COMMONVFLAGS = $(COMMONFLAGS) +-CFLAGS = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\" ++CFLAGS += @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\" + # IBM PowerPC compiler on macosx needs also CC=xlc + #CFLAGS = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded -Dpowerpc $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\" + THREADCFLAGS= @THREADCFLAGS@ --- biology::migrate-1.7.6.1.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted: