From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Feb 1 18:10:02 2010 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 1991D1065676 for ; Mon, 1 Feb 2010 18:10:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id D334B8FC14 for ; Mon, 1 Feb 2010 18:10:01 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id o11IA14m045034 for ; Mon, 1 Feb 2010 18:10:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id o11IA1ne045033; Mon, 1 Feb 2010 18:10:01 GMT (envelope-from gnats) Resent-Date: Mon, 1 Feb 2010 18:10:01 GMT Resent-Message-Id: <201002011810.o11IA1ne045033@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, KATO Tsuguru Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 44FDB1065676 for ; Mon, 1 Feb 2010 18:00:57 +0000 (UTC) (envelope-from tkato432@yahoo.com) Received: from msa102lp.auone-net.jp (msa102lp.auone-net.jp [222.3.140.165]) by mx1.freebsd.org (Postfix) with ESMTP id E087F8FC0C for ; Mon, 1 Feb 2010 18:00:56 +0000 (UTC) Received: from localhost.localdomain (ZT047016.ppp.dion.ne.jp [59.128.47.16]) by msa102lp.auone-net.jp (au one net msa) with ESMTP id E1A884AC036 for ; Tue, 2 Feb 2010 03:00:44 +0900 (JST) Message-Id: <20100202030008.c5c678b2.tkato432@yahoo.com> Date: Tue, 2 Feb 2010 03:00:08 +0900 From: KATO Tsuguru To: FreeBSD-gnats-submit@FreeBSD.org Cc: Subject: ports/143437: Update port: biology/migrate to 3.1.1 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 01 Feb 2010 18:10:02 -0000 >Number: 143437 >Category: ports >Synopsis: Update port: biology/migrate to 3.1.1 >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 Feb 01 18:10:01 UTC 2010 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.2-RELEASE-p6 i386 >Organization: >Environment: >Description: - Update to version 3.1.1 New file: files/patch-main.c Remove file: pkg-plist >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/migrate/Makefile biology/migrate/Makefile --- /usr/ports/biology/migrate/Makefile 2009-01-15 02:26:28.000000000 +0900 +++ biology/migrate/Makefile 2010-02-01 23:34:50.000000000 +0900 @@ -6,9 +6,9 @@ # PORTNAME= migrate -PORTVERSION= 3.0.3 +PORTVERSION= 3.1.1 CATEGORIES= biology -MASTER_SITES= http://people.scs.fsu.edu/~beerli/popgen/currentversion/ +MASTER_SITES= http://people.sc.fsu.edu/~beerli/popgen/currentversion/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= ports@FreeBSD.org @@ -20,8 +20,11 @@ CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}" MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY" -MAN1= migrate.1 -MLINKS= migrate.1 migrate-n.1 +MAN1= ${PORTNAME}.1 +MLINKS= ${PORTNAME}.1 ${PORTNAME}-n.1 +PORTDOCS= * +PORTEXAMPLES= * +PLIST_FILES= bin/${PORTNAME} bin/${PORTNAME}-n .include @@ -41,14 +44,16 @@ post-patch: @${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g ; \ s|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure + @${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h + @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin - ${LN} -sf migrate-n ${PREFIX}/bin/migrate - ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1 + ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${PREFIX}/bin + ${LN} -sf ${PORTNAME}-n ${PREFIX}/bin/${PORTNAME} + ${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${MAN1PREFIX}/man/man1 .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} -.for i in HISTORY HOWTO-PARALLEL README migrate.html +.for i in HISTORY HOWTO-PARALLEL README ${PORTNAME}.html ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR} .endfor @${MKDIR} ${DOCSDIR}/graphics diff -urN /usr/ports/biology/migrate/distinfo biology/migrate/distinfo --- /usr/ports/biology/migrate/distinfo 2009-01-15 02:26:28.000000000 +0900 +++ biology/migrate/distinfo 2010-01-24 01:13:27.000000000 +0900 @@ -1,3 +1,3 @@ -MD5 (migrate-3.0.3.src.tar.gz) = ea4a67a6320300a4df554f74a272581e -SHA256 (migrate-3.0.3.src.tar.gz) = d00c1999e7af055aca9f30565dfb610b03e42c2dcc60838c9c4367be87d0edd1 -SIZE (migrate-3.0.3.src.tar.gz) = 5660159 +MD5 (migrate-3.1.1.src.tar.gz) = 5870d5e980a4bb9b34e4ea50d86ef98a +SHA256 (migrate-3.1.1.src.tar.gz) = 2149dadb91b164aea77759b4757aa8cc6269fc50743664bef05dc32239a9ad58 +SIZE (migrate-3.1.1.src.tar.gz) = 3874625 diff -urN /usr/ports/biology/migrate/files/patch-main.c biology/migrate/files/patch-main.c --- /usr/ports/biology/migrate/files/patch-main.c 1970-01-01 09:00:00.000000000 +0900 +++ biology/migrate/files/patch-main.c 2010-02-01 23:03:12.000000000 +0900 @@ -0,0 +1,23 @@ +--- main.c.orig 2010-01-20 23:47:41.000000000 +0900 ++++ main.c 2010-02-01 23:02:52.000000000 +0900 +@@ -630,7 +630,9 @@ + { + fprintf(EARTH->outfile,"%5li %10.5f\n",locus+1,universe[locus]->averageheat); + } ++#ifdef PRETTY + pdf_print_averageheat(universe,options); ++#endif + } + #ifdef PRETTY + pdf_print_end_time(&page_height); +@@ -2443,8 +2445,10 @@ + { + fprintf(file,"\n\nLocus Raw Thermodynamic score(1a) Bezier approximated score(1b) Harmonic mean(2)\n"); + fprintf(file,"------------------------------------------------------------------------------------------\n"); ++#ifdef PRETTY + if(file==EARTH->outfile) + pdf_bayes_factor_rawscores_header(EARTH,options); ++#endif + } + if(options->heating)//-----------------------heating + { diff -urN /usr/ports/biology/migrate/pkg-descr biology/migrate/pkg-descr --- /usr/ports/biology/migrate/pkg-descr 2009-12-21 15:16:18.000000000 +0900 +++ biology/migrate/pkg-descr 2010-01-24 01:14:12.000000000 +0900 @@ -3,4 +3,4 @@ migration rates and different subpopulation sizes. The n-population migrate can use sequence data, microsatellite data or electrophoretic data. -WWW: http://popgen.csit.fsu.edu/Migrate-n.html +WWW: http://popgen.sc.fsu.edu/Migrate-n.html diff -urN /usr/ports/biology/migrate/pkg-plist biology/migrate/pkg-plist --- /usr/ports/biology/migrate/pkg-plist 2009-01-15 02:26:28.000000000 +0900 +++ biology/migrate/pkg-plist 1970-01-01 09:00:00.000000000 +0900 @@ -1,76 +0,0 @@ -bin/migrate -bin/migrate-n -%%PORTDOCS%%%%DOCSDIR%%/HISTORY -%%PORTDOCS%%%%DOCSDIR%%/HOWTO-PARALLEL -%%PORTDOCS%%%%DOCSDIR%%/README -%%PORTDOCS%%%%DOCSDIR%%/graphics/librarian.gif -%%PORTDOCS%%%%DOCSDIR%%/graphics/mail.gif -%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif -%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif -%%PORTDOCS%%%%DOCSDIR%%/migrate.html -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aicfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/datefile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mighistfile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-1 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-2 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-brown -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5-0.5 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-step -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-dated.pdf -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3.pdf -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-paral2 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-single -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-watkins-0.5-0.5 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml.pdf -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_double -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_float -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outifle-ml-3 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile-testbayes.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.gugus -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml-save -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pretty -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skylinefile.dated -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-1 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-2 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-3 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-mpi-ml -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-single -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile1 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-1 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-2 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-3 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile.dated -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% -%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics -%%PORTDOCS%%@dirrm %%DOCSDIR%% >Release-Note: >Audit-Trail: >Unformatted: