6 files changed, 122 insertions, 57 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 7cd19b3030c8..18457f50637d 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,11 +6,9 @@
 #
 
 PORTNAME=	migrate
-PORTVERSION=	2.4.3
-PORTREVISION=	1
+PORTVERSION=	3.0.3
 CATEGORIES=	biology
-MASTER_SITES=	http://popgen.csit.fsu.edu/%SUBDIR%/
-MASTER_SITE_SUBDIR=	currentversion oldversions/${PORTVERSION}
+MASTER_SITES=	http://people.scs.fsu.edu/~beerli/popgen/currentversion/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
 MAINTAINER=	ports@FreeBSD.org
@@ -18,10 +16,9 @@ COMMENT=	A program to estimate population sizes and migration rates
 
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
 
-USE_GNOME=	gnometarget
 GNU_CONFIGURE=	yes
-MAKE_ARGS=	HARDWARECFLAGS="${CFLAGS}" \
-		MYCPPFLAGS="${CFLAGS} -DNOJPEG -DNOPNG -DNOZLIB"
+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
@@ -42,8 +39,8 @@ ALL_TARGET=	all
 .endif
 
 post-patch:
-	@${REINPLACE_CMD} -e \
-		's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g ; \
+		 s|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
@@ -59,7 +56,7 @@ do-install:
 .endif
 .if !defined(NOPORTEXAMPLES)
 	@${MKDIR} ${EXAMPLESDIR}
-	${INSTALL_DATA} ${WRKSRC}/../example/* ${EXAMPLESDIR}
+	${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* ${EXAMPLESDIR}
 .endif
 
 .include <bsd.port.post.mk>
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index d35c3659dac2..df9ec6b2ae18 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-MD5 (migrate-2.4.3.src.tar.gz) = 3cf0e169191826c657fc1fbcedecb32d
-SHA256 (migrate-2.4.3.src.tar.gz) = 6732fc8c97373e6f08b9e43a78902a9a313fc37841e58752dbd9c7a924a708d4
-SIZE (migrate-2.4.3.src.tar.gz) = 1958543
+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
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
index deccc333af92..765eb15bc0bb 100644
--- a/biology/migrate/files/patch-Makefile.in
+++ b/biology/migrate/files/patch-Makefile.in
@@ -1,40 +1,66 @@
---- Makefile.in.orig	Thu Jan 10 10:33:23 2008
-+++ Makefile.in	Sun Jan 13 04:43:42 2008
-@@ -56,11 +56,11 @@
- # machines or ./configure --enable-altivec on PowerPC architectures, this will then set the option 
- # correctly
- HARDWARECFLAGS    = @HARDWARECFLAGS@
--COMMONFLAGS       = $(ARCH) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
-+COMMONFLAGS       = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
+--- 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 @@
+ # -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)
  #
  # combine the common flags with the version number and subversion number
  COMMONVFLAGS      =  $(COMMONFLAGS)  -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" 
--CFLAGS            = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" 
-+CFLAGS            = $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" 
- # IBM xlc compiler
- # CC              = xlc
- # CFLAGS_XLC      = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded 
-@@ -151,8 +151,8 @@
- 	@echo "----------------------------------------------------"
- 	$(MAKE) all
+@@ -195,22 +195,21 @@
+ 	@echo '  make install (installs the executables and man page)'
+ 	@echo '  [there are other targets for debugging purposes, check the Makefile]'
  
 -all::   haru
--	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 
-+all::   
-+	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 
+-	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" 
++all::
++	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" 
  
- debug::   
- 	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)"
-@@ -274,10 +274,10 @@
- 	-/bin/chmod +x $(CONFIGUREEXEC) 	
  
- haru::
--	(cd ./haru ; make -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=$(ARCH)")
-+	(cd ./haru ; $(MAKE) -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=")
+ pretty:: haru   
+ 	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" 
  
- haru-clean::
--	(cd ./haru ; make -f makefile.osx clean)
-+	(cd ./haru ; $(MAKE) -f makefile.osx clean)
+-thread:: haru   
++thread-pretty:: haru   
+ 	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) $(EXCEPTIONS)" 
  
- distrib::
- 	$(MAKE) srcdistrib;
+ 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)"
+@@ -398,22 +397,22 @@
+ 	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) ;
+ 
+ 
+ #----------------------------------------------------------------
diff --git a/biology/migrate/files/patch-src-pretty-win32.cpp b/biology/migrate/files/patch-src-pretty-win32.cpp
deleted file mode 100644
index c6e2321db136..000000000000
--- a/biology/migrate/files/patch-src-pretty-win32.cpp
+++ /dev/null
@@ -1,12 +0,0 @@
---- pretty-win32.cpp.orgi	2008-02-27 08:15:26.000000000 +0100
-+++ pretty-win32.cpp	2008-02-27 08:16:07.000000000 +0100
-@@ -13,9 +13,3 @@
-   _set_new_handler(throw_new_handler);
- }
- #endif
--
--int dummy_function(int do_nothing)
--{
--  print("Some computer fail to compile MIGRATE with empty files\n");
--  return 0;
--}
diff --git a/biology/migrate/pkg-descr b/biology/migrate/pkg-descr
index 413ec6dea6c3..98f93e85d5bf 100644
--- a/biology/migrate/pkg-descr
+++ b/biology/migrate/pkg-descr
@@ -4,4 +4,4 @@ migration rates and different subpopulation sizes.  The n-population migrate
 can use sequence data, microsatellite data or electrophoretic data.
 
 Author: Peter Beerli <beerli@scs.fsu.edu>
-WWW:    http://popgen.scs.fsu.edu/Migrate-n.html
+WWW:    http://popgen.csit.fsu.edu/Migrate-n.html
diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist
index 7f737002f50c..bccdc40fe777 100644
--- a/biology/migrate/pkg-plist
+++ b/biology/migrate/pkg-plist
@@ -9,14 +9,68 @@ bin/migrate-n
 %%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%%