5 files changed, 22 insertions, 105 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 4e7eaf15a86f..81feb424d647 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -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>
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 8239f7cdd76c..af29c9581366 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -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
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
index 1a3ef22e54bc..6a65ce4d3ff6 100644
--- a/biology/migrate/files/patch-Makefile.in
+++ b/biology/migrate/files/patch-Makefile.in
@@ -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:
diff --git a/biology/migrate/files/patch-main.c b/biology/migrate/files/patch-main.c
deleted file mode 100644
index 2cb9bcf9e3fc..000000000000
--- a/biology/migrate/files/patch-main.c
+++ /dev/null
@@ -1,23 +0,0 @@
---- 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 --git a/biology/migrate/pkg-descr b/biology/migrate/pkg-descr
index 3aaa0693067c..4d341599607a 100644
--- a/biology/migrate/pkg-descr
+++ b/biology/migrate/pkg-descr
@@ -3,4 +3,4 @@ two or "n" populations assuming a migration matrix model with asymmetric
 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