ports/146411: [patch][maintainer] biology/migrate: update to latest version

[Glen Barber]

>Number:         146411
>Category:       ports
>Synopsis:       [patch][maintainer] biology/migrate: update to latest version
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Sat May 08 21:00:13 UTC 2010
>Closed-Date:
>Last-Modified:
>Originator:     Glen Barber
>Release:        8.0-STABLE
>Organization:
>Environment:
FreeBSD orion 8.0-STABLE FreeBSD 8.0-STABLE #89 r207326: Wed Apr 28 11:28:39 EDT 2010     root at orion:/usr/obj/usr/src/sys/ORION  amd64
>Description:
Update biology/migrate from 3.1.3 -> 3.1.4
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

diff -ruN /usr/ports/biology/migrate.orig/Makefile /usr/ports/biology/migrate/Makefile
--- /usr/ports/biology/migrate.orig/Makefile	2010-03-24 02:46:44.000000000 -0400
+++ /usr/ports/biology/migrate/Makefile	2010-05-08 16:15:19.000000000 -0400
@@ -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 -ruN /usr/ports/biology/migrate.orig/distinfo /usr/ports/biology/migrate/distinfo
--- /usr/ports/biology/migrate.orig/distinfo	2010-03-24 02:46:44.000000000 -0400
+++ /usr/ports/biology/migrate/distinfo	2010-05-08 14:42:58.000000000 -0400
@@ -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 -ruN /usr/ports/biology/migrate.orig/files/patch-Makefile.in /usr/ports/biology/migrate/files/patch-Makefile.in
--- /usr/ports/biology/migrate.orig/files/patch-Makefile.in	2009-01-14 11:00:34.000000000 -0500
+++ /usr/ports/biology/migrate/files/patch-Makefile.in	2010-05-08 16:10:34.000000000 -0400
@@ -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"


>Release-Note:
>Audit-Trail:
>Unformatted: