4 files changed, 19 insertions, 33 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 351bc6e5966b..0be9c9a3be0e 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,9 +6,9 @@
 #
 
 PORTNAME=	migrate
-PORTVERSION=	2.0.3
+PORTVERSION=	2.1.3
 CATEGORIES=	biology
-MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/
+MASTER_SITES=	http://popgen.csit.fsu.edu/currentversion/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
 MAINTAINER=	ports@FreeBSD.org
@@ -17,17 +17,18 @@ COMMENT=	A program to estimate population sizes and migration rates
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
 GNU_CONFIGURE=	yes
 CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+MAKE_ARGS=	CFLAGS="${CFLAGS}"
 
 MAN1=		migrate.1
 MLINKS=		migrate.1 migrate-n.1
 
 DOCS=		HISTORY HOWTO-PARALLEL README migrate.html
-EXAMPLES=	README infile.benchmark infile.ep infile.msat infile.seq \
-		parmfile parmfile.benchmark parmfile.ep parmfile.msat \
-		parmfile.seq
+EXAMPLES=	README infile.ep infile.msat infile.seq \
+		outfile-bayes-saved outfile-ml-saved \
+		parmfile parmfile.testbayes parmfile.testml
 
 post-patch:
-		@${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure
 
 do-install:
 	@ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
@@ -35,12 +36,12 @@ do-install:
 	@ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
 .if !defined(NOPORTDOCS)
 	@ ${MKDIR} ${DOCSDIR}/graphics
-.for file in ${DOCS}
-	@ ${INSTALL_DATA} ${WRKSRC}/../${file} ${DOCSDIR}
+.for i in ${DOCS}
+	@ ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
 .endfor
 	@ ${MKDIR} ${EXAMPLESDIR}
-.for file in ${EXAMPLES}
-	@ ${INSTALL_DATA} ${WRKSRC}/../example/${file} ${EXAMPLESDIR}
+.for i in ${EXAMPLES}
+	@ ${INSTALL_DATA} ${WRKSRC}/../example/${i} ${EXAMPLESDIR}
 .endfor
 	@ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
 .endif
@@ -48,7 +49,7 @@ do-install:
 .include <bsd.port.pre.mk>
 
 .if ${ARCH} == "alpha"
-BROKEN=		"Does not compile"
+BROKEN=		Does not compile
 .endif
 
 .include <bsd.port.post.mk>
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 5de258062d1f..915a48e0a13f 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-MD5 (migrate-2.0.3.src.tar.gz) = 8e8e93790cb66093ad5297dcbfc83439
-SHA256 (migrate-2.0.3.src.tar.gz) = f1210cf94e6b67cd762eae5949f97316b082b9f052b4188cf024afc7d8c1db56
-SIZE (migrate-2.0.3.src.tar.gz) = 467274
+MD5 (migrate-2.1.3.src.tar.gz) = fdff82f3dd509811fa4780287a554931
+SHA256 (migrate-2.1.3.src.tar.gz) = 91c8636c5b7a189fd693ddb9a863ff5995abf7157f10bf005e8e3e2497d56023
+SIZE (migrate-2.1.3.src.tar.gz) = 1637715
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
deleted file mode 100644
index 67bb12994344..000000000000
--- a/biology/migrate/files/patch-Makefile.in
+++ /dev/null
@@ -1,14 +0,0 @@
-
-$FreeBSD$
-
---- Makefile.in.orig
-+++ Makefile.in
-@@ -40,7 +40,7 @@
- COMMONFLAGS =  -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DBAYESUPDATE
- #COMMONFLAGS =  -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER
- COMMONVFLAGS =  $(COMMONFLAGS)
--CFLAGS = @CFLAGS@ $(COMMONVFLAGS)  -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\" 
-+CFLAGS += @CFLAGS@ $(COMMONVFLAGS)  -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\" 
- # IBM PowerPC compiler on macosx needs also CC=xlc
- #CFLAGS = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded -Dpowerpc $(COMMONVFLAGS)  -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
- THREADCFLAGS= @THREADCFLAGS@
diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist
index 62135c58c177..66649c66e5f1 100644
--- a/biology/migrate/pkg-plist
+++ b/biology/migrate/pkg-plist
@@ -9,15 +9,14 @@ bin/migrate-n
 %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
 %%PORTDOCS%%%%DOCSDIR%%/migrate.html
 %%PORTDOCS%%%%EXAMPLESDIR%%/README
-%%PORTDOCS%%%%EXAMPLESDIR%%/infile.benchmark
 %%PORTDOCS%%%%EXAMPLESDIR%%/infile.ep
 %%PORTDOCS%%%%EXAMPLESDIR%%/infile.msat
 %%PORTDOCS%%%%EXAMPLESDIR%%/infile.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/outfile-bayes-saved
+%%PORTDOCS%%%%EXAMPLESDIR%%/outfile-ml-saved
 %%PORTDOCS%%%%EXAMPLESDIR%%/parmfile
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.benchmark
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.ep
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.msat
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testbayes
+%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testml
 %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
 %%PORTDOCS%%@dirrm %%DOCSDIR%%