Date: Sun, 26 May 2013 07:49:48 +0000 (UTC) From: Wen Heping <wen@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r319096 - in head/biology/migrate: . files Message-ID: <201305260749.r4Q7nmRE015451@svn.freebsd.org>
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Author: wen Date: Sun May 26 07:49:47 2013 New Revision: 319096 URL: http://svnweb.freebsd.org/changeset/ports/319096 Log: - Update to 3.5.1 - Trim Makefile headers - Convert to optionsNG - Update WWW, MASTER_SITES and COMMENT Deleted: head/biology/migrate/files/patch-main.c Modified: head/biology/migrate/Makefile head/biology/migrate/distinfo head/biology/migrate/files/patch-Makefile.in (contents, props changed) head/biology/migrate/pkg-descr Modified: head/biology/migrate/Makefile ============================================================================== --- head/biology/migrate/Makefile Sun May 26 07:22:39 2013 (r319095) +++ head/biology/migrate/Makefile Sun May 26 07:49:47 2013 (r319096) @@ -1,25 +1,20 @@ -# New ports collection makefile for: migrate -# Date created: 6 August 2001 -# Whom: Johann Visagie <wjv@FreeBSD.org> -# +# Created by: Johann Visagie <wjv@FreeBSD.org> # $FreeBSD$ -# PORTNAME= migrate -PORTVERSION= 3.1.6 +PORTVERSION= 3.5.1 CATEGORIES= biology -MASTER_SITES= http://people.sc.fsu.edu/~beerli/popgen/currentversion/ \ - https://www.glenbarber.us/ports/${CATEGORIES}/${PORTNAME}/ +MASTER_SITES= http://popgen.sc.fsu.edu/currentversions/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= wen@FreeBSD.org -COMMENT= A program to estimate population sizes and migration rates +COMMENT= Program to estimate population sizes and migration rates WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src GNU_CONFIGURE= yes CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}" -MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY" +MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++" MAN1= ${PORTNAME}.1 MLINKS= ${PORTNAME}.1 ${PORTNAME}-n.1 @@ -27,7 +22,7 @@ PORTDOCS= * PORTEXAMPLES= * PLIST_FILES= bin/${PORTNAME} bin/${PORTNAME}-n -.include <bsd.port.pre.mk> +.include <bsd.port.options.mk> NOT_FOR_ARCHS= alpha ONLY_FOR_ARCHS_REASON= Does not compile @@ -52,17 +47,17 @@ do-install: ${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) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} -.for i in HISTORY HOWTO-PARALLEL README ${PORTNAME}.html +.for i in HISTORY README README_PARALLEL_GENERAL ${PORTNAME}.html ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR} .endfor @${MKDIR} ${DOCSDIR}/graphics ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics .endif -.if !defined(NOPORTEXAMPLES) +.if ${PORT_OPTIONS:MEXAMPLES} @${MKDIR} ${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* ${EXAMPLESDIR} .endif -.include <bsd.port.post.mk> +.include <bsd.port.mk> Modified: head/biology/migrate/distinfo ============================================================================== --- head/biology/migrate/distinfo Sun May 26 07:22:39 2013 (r319095) +++ head/biology/migrate/distinfo Sun May 26 07:49:47 2013 (r319096) @@ -1,2 +1,2 @@ -SHA256 (migrate-3.1.6.src.tar.gz) = 03bd8668d620b3db16b7da63b3ba4a09d343c1e36133c267e9ceee397775d032 -SIZE (migrate-3.1.6.src.tar.gz) = 2808609 +SHA256 (migrate-3.5.1.src.tar.gz) = b2ade170567f31fe64b6ad7ca427833820c56f03a6007cd5f832324d826dd76c +SIZE (migrate-3.5.1.src.tar.gz) = 27875680 Modified: head/biology/migrate/files/patch-Makefile.in ============================================================================== --- head/biology/migrate/files/patch-Makefile.in Sun May 26 07:22:39 2013 (r319095) +++ head/biology/migrate/files/patch-Makefile.in Sun May 26 07:49:47 2013 (r319096) @@ -1,70 +1,15 @@ ---- Makefile.in.orig 2010-05-01 16:14:26.000000000 -0400 -+++ Makefile.in 2010-05-08 16:08:49.000000000 -0400 -@@ -80,7 +80,7 @@ - # -DNEXUSTREE print nexus tree instead of plain newick trees - # -UEP calculates unique event polymorphism - NEWSTUFF = -DNEWVERSION -DBFDEBUG --COMMONFLAGS = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) -+COMMONFLAGS = $(MACOSVERSION) $(NEWSTUFF) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) +--- Makefile.in.orig 2013-05-25 14:59:22.000000000 +0000 ++++ Makefile.in 2013-05-25 14:59:37.000000000 +0000 +@@ -89,7 +89,7 @@ + # -DINTEGRATEDLIKE may be used to get a marginal likelihood different to the current thermodynamic integr and harmonic mean [does not work] + # -UEP calculates unique event polymorphism [not checked in a long time -- most likely does not work] + NEWSTUFF = -DNEXUSTREE +-COMMONFLAGS = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) ++COMMONFLAGS = $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) # # combine the common flags with the version number and subversion number COMMONVFLAGS = $(COMMONFLAGS) -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" -@@ -202,22 +202,21 @@ - @echo ' make install (installs the executables and man page [out of date])' - @echo ' [there are other targets for debugging purposes, check the Makefile]' - --all:: haru -- $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" -+all:: -+ $(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" - - - pretty:: haru - $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" - --thread:: haru -+thread-pretty:: haru - $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" - - debug:: haru - $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS)" - - thread:: -- $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(LIBS)";\ -- strip $(NAME) -+ $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(LIBS)" - - mpis-thread:: haru - $(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" -@@ -405,22 +404,22 @@ - else echo Must define $@; exit 1; fi - - $(NAME): $(PRODUCT_DEPENDS) -- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(LIBS) ; -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(LIBS) ; - - $(WINNAME): $(PRODUCT_DEPENDS) -- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(OTHERLIBS) $(WINLIBS) ; -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(OTHERLIBS) $(WINLIBS) ; - - - $(EFENCENAME): $(PRODUCT_DEPENDS) -- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(EFENCELIBS) $(LIBS) ; -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(EFENCELIBS) $(LIBS) ; - - - $(MEMDEBUGNAME): $(PRODUCT_DEPENDS) -- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(MEMDEBUGLIBS) $(LIBS) ; -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(MEMDEBUGLIBS) $(LIBS) ; - - - $(DMALLOCNAME): $(PRODUCT_DEPENDS) -- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(DMALLOCLIBS) $(LIBS) ; -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(DMALLOCLIBS) $(LIBS) ; - - - #---------------------------------------------------------------- -@@ -473,4 +472,4 @@ +@@ -544,4 +544,4 @@ #---------------------------------------------------------------- # BEAGLE beagle: Modified: head/biology/migrate/pkg-descr ============================================================================== --- head/biology/migrate/pkg-descr Sun May 26 07:22:39 2013 (r319095) +++ head/biology/migrate/pkg-descr Sun May 26 07:49:47 2013 (r319096) @@ -3,4 +3,4 @@ two or "n" populations assuming a migrat migration rates and different subpopulation sizes. The n-population migrate can use sequence data, microsatellite data or electrophoretic data. -WWW: http://popgen.sc.fsu.edu/Migrate-n.html +WWW: http://popgen.sc.fsu.edu/Migrate/Migrate-n.html
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