- Update to version 2.3

PR:		ports/116019
Submitted by:	KATO Tsuguru

4 files changed, 57 insertions, 46 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 0be9c9a3be0e..fc2f5228ea2d 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	migrate
-PORTVERSION=	2.1.3
+PORTVERSION=	2.3
 CATEGORIES=	biology
 MASTER_SITES=	http://popgen.csit.fsu.edu/currentversion/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
@@ -15,41 +15,51 @@ MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A program to estimate population sizes and migration rates
 
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
+
+USE_GNOME=	gnometarget
 GNU_CONFIGURE=	yes
-CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
-MAKE_ARGS=	CFLAGS="${CFLAGS}"
+MAKE_ARGS=	HARDWARECFLAGS="${CFLAGS}" \
+		MYCPPFLAGS="${CFLAGS} -DNOJPEG -DNOPNG -DNOZLIB"
 
 MAN1=		migrate.1
 MLINKS=		migrate.1 migrate-n.1
 
-DOCS=		HISTORY HOWTO-PARALLEL README migrate.html
-EXAMPLES=	README infile.ep infile.msat infile.seq \
-		outfile-bayes-saved outfile-ml-saved \
-		parmfile parmfile.testbayes parmfile.testml
+.include <bsd.port.pre.mk>
+
+NOT_FOR_ARCHS=	alpha
+ONLY_FOR_ARCHS_REASON=	Does not compile
+
+.if defined(WITH_THREAD_PRETTY)
+ALL_TARGET=	thread-pretty
+.elif defined(WITH_PRETTY)
+ALL_TARGET=	pretty
+.elif defined(WITH_THREAD)
+ALL_TARGET=	thread
+.else
+ALL_TARGET=	all
+.endif
 
 post-patch:
-	@${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e \
+		's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e 's|@CFLAGS@||g ; \
+		 s|make -f|$$(MAKE) -f|g' ${WRKSRC}/Makefile.in
 
 do-install:
-	@ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
-	@ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate
-	@ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
+	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
+	${LN} -sf migrate-n ${PREFIX}/bin/migrate
+	${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
 .if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCSDIR}/graphics
-.for i in ${DOCS}
-	@ ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
+	@${MKDIR} ${DOCSDIR}
+.for i in HISTORY HOWTO-PARALLEL README migrate.html
+	${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
 .endfor
-	@ ${MKDIR} ${EXAMPLESDIR}
-.for i in ${EXAMPLES}
-	@ ${INSTALL_DATA} ${WRKSRC}/../example/${i} ${EXAMPLESDIR}
-.endfor
-	@ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
+	@${MKDIR} ${DOCSDIR}/graphics
+	${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
 .endif
-
-.include <bsd.port.pre.mk>
-
-.if ${ARCH} == "alpha"
-BROKEN=		Does not compile
+.if !defined(NOPORTEXAMPLES)
+	@${MKDIR} ${EXAMPLESDIR}
+	${INSTALL_DATA} ${WRKSRC}/../example/* ${EXAMPLESDIR}
 .endif
 
 .include <bsd.port.post.mk>
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 915a48e0a13f..5530898c1b28 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-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
+MD5 (migrate-2.3.src.tar.gz) = 12dbf7bd9d69b6ba87a9ba16b68ff7e5
+SHA256 (migrate-2.3.src.tar.gz) = 3407a92b41f23d036a6ef5fd11f77e6d1aa8ee39fa4f61c65b0f71670b8b8f62
+SIZE (migrate-2.3.src.tar.gz) = 1952466
diff --git a/biology/migrate/pkg-descr b/biology/migrate/pkg-descr
index 7ffe5d4c8b6f..413ec6dea6c3 100644
--- a/biology/migrate/pkg-descr
+++ b/biology/migrate/pkg-descr
@@ -3,12 +3,5 @@ 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.
 
-Migrate forms part of the Lamarc (Likelihood Analysis with Metropolis
-Algorithm using Random Coalescence) suite.  See:
-
-  http://evolution.genetics.washington.edu/lamarc.html
-
-Author: Peter Beerli <beerli@genetics.washington.edu>
-WWW:    http://evolution.genetics.washington.edu/lamarc/migrate.html
-
--- Johann Visagie <wjv@FreeBSD.org>
+Author: Peter Beerli <beerli@scs.fsu.edu>
+WWW:    http://popgen.scs.fsu.edu/Migrate-n.html
diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist
index 66649c66e5f1..2d4ed78b2f2d 100644
--- a/biology/migrate/pkg-plist
+++ b/biology/migrate/pkg-plist
@@ -8,15 +8,23 @@ bin/migrate-n
 %%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
 %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
 %%PORTDOCS%%%%DOCSDIR%%/migrate.html
-%%PORTDOCS%%%%EXAMPLESDIR%%/README
-%%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.testbayes
-%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testml
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
 %%PORTDOCS%%@dirrm %%DOCSDIR%%