- Update to 2.4.1

PR:		119719
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

4 files changed, 46 insertions, 15 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index fc2f5228ea2d..0b4f00327de2 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,9 +6,10 @@
 #
 
 PORTNAME=	migrate
-PORTVERSION=	2.3
+PORTVERSION=	2.4.1
 CATEGORIES=	biology
-MASTER_SITES=	http://popgen.csit.fsu.edu/currentversion/
+MASTER_SITES=	http://popgen.csit.fsu.edu/%SUBDIR%/
+MASTER_SITE_SUBDIR=	currentversion oldversions/${PORTVERSION}
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
 MAINTAINER=	ports@FreeBSD.org
@@ -42,8 +43,6 @@ ALL_TARGET=	all
 post-patch:
 	@${REINPLACE_CMD} -e \
 		's|-lpthread|${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
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 5530898c1b28..c781822e7123 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-MD5 (migrate-2.3.src.tar.gz) = 12dbf7bd9d69b6ba87a9ba16b68ff7e5
-SHA256 (migrate-2.3.src.tar.gz) = 3407a92b41f23d036a6ef5fd11f77e6d1aa8ee39fa4f61c65b0f71670b8b8f62
-SIZE (migrate-2.3.src.tar.gz) = 1952466
+MD5 (migrate-2.4.1.src.tar.gz) = cd0e1d2bb551d09b553d833bb90a5df5
+SHA256 (migrate-2.4.1.src.tar.gz) = 09cb370f6911794d94b721e0f2a1a26c5f3bde5b2e55256f52ad57e9a0c0cdee
+SIZE (migrate-2.4.1.src.tar.gz) = 1950793
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
new file mode 100644
index 000000000000..deccc333af92
--- /dev/null
+++ b/biology/migrate/files/patch-Makefile.in
@@ -0,0 +1,40 @@
+--- 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)
+ #
+ # 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
+ 
+-all::   haru
+-	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 
++all::   
++	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 
+ 
+ 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=")
+ 
+ haru-clean::
+-	(cd ./haru ; make -f makefile.osx clean)
++	(cd ./haru ; $(MAKE) -f makefile.osx clean)
+ 
+ distrib::
+ 	$(MAKE) srcdistrib;
diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist
index 2d4ed78b2f2d..7f737002f50c 100644
--- a/biology/migrate/pkg-plist
+++ b/biology/migrate/pkg-plist
@@ -9,20 +9,12 @@ bin/migrate-n
 %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
 %%PORTDOCS%%%%DOCSDIR%%/migrate.html
 %%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%%