From b5dabfb20dc5ba66969b8548e8657973fc54aac0 Mon Sep 17 00:00:00 2001
From: Sylvio Cesar Teixeira <sylvio@FreeBSD.org>
Date: Sun, 9 May 2010 13:59:34 +0000
Subject: [PATCH] - Update to 3.1.4

PR:		ports/146411
Submitted by:	Glen Barber <glen.j.barber@gmail.com> (maintainer)
---
 biology/migrate/Makefile                |  2 +-
 biology/migrate/distinfo                |  6 +++---
 biology/migrate/files/patch-Makefile.in | 21 ++++++++++++++-------
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index a5f912eb1551..2b2c6f6e2753 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	migrate
-PORTVERSION=	3.1.3
+PORTVERSION=	3.1.4
 CATEGORIES=	biology
 MASTER_SITES=	http://people.sc.fsu.edu/~beerli/popgen/currentversion/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index c2aaa89d30e8..672e54d04486 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-MD5 (migrate-3.1.3.src.tar.gz) = 20b07feaeb3624769d6befec640a30e2
-SHA256 (migrate-3.1.3.src.tar.gz) = 176f516c8dec12b5370230e91dbc454b2ab6740656fdbb1a2475a5377fee630d
-SIZE (migrate-3.1.3.src.tar.gz) = 2021127
+MD5 (migrate-3.1.4.src.tar.gz) = a1ffa3baa8a78b17b2dcb387de7801ee
+SHA256 (migrate-3.1.4.src.tar.gz) = f09d35f544865f1cde3677b9b347b8a5de9e907f81d4f509e8f15c2fd28ea110
+SIZE (migrate-3.1.4.src.tar.gz) = 2227530
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
index 765eb15bc0bb..971ff5683425 100644
--- a/biology/migrate/files/patch-Makefile.in
+++ b/biology/migrate/files/patch-Makefile.in
@@ -1,16 +1,16 @@
---- Makefile.in.orig	2008-12-06 03:19:25.000000000 +0900
-+++ Makefile.in	2008-12-09 15:17:10.000000000 +0900
-@@ -79,7 +79,7 @@
+--- 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
+ NEWSTUFF          =  
 -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)
  #
  # combine the common flags with the version number and subversion number
  COMMONVFLAGS      =  $(COMMONFLAGS)  -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" 
-@@ -195,22 +195,21 @@
- 	@echo '  make install (installs the executables and man page)'
+@@ -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
@@ -36,7 +36,7 @@
  
  mpis-thread:: haru   
  	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)"
-@@ -398,22 +397,22 @@
+@@ -405,22 +404,22 @@
  	else echo Must define $@; exit 1; fi
  
  $(NAME): $(PRODUCT_DEPENDS)
@@ -64,3 +64,10 @@
  
  
  #----------------------------------------------------------------
+@@ -473,4 +472,4 @@
+ #----------------------------------------------------------------
+ # BEAGLE
+ beagle:
+-	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)"  "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"
+\ No newline at end of file
++	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)"  "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"