Fix master sites, un-deprecate and update biology/recombine to 1.41.

4 files changed, 19 insertions, 86 deletions

diff --git a/biology/recombine/Makefile b/biology/recombine/Makefile
index 0b0daa69e8d2..50bcfff4b0c3 100644
--- a/biology/recombine/Makefile
+++ b/biology/recombine/Makefile
@@ -6,28 +6,26 @@
 #
 
 PORTNAME=	recombine
-PORTVERSION=	1.40
+PORTVERSION=	1.41
 CATEGORIES=	biology
-MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/recombine/
-DISTNAME=	${PORTNAME}${PORTVERSION}
+MASTER_SITES=	http://evolution.gs.washington.edu/lamarc/recombine/
+DISTNAME=	${PORTNAME}${PORTVERSION}.src.doc
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A program to fit population models across sites
 
-DEPRECATED=	distfile disappeared from homepage
-EXPIRATION_DATE=	2007-01-07
+WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
 
-NO_WRKSUBDIR=	yes
 ALL_TARGET=	${PORTNAME}
 
 do-install:
-	@ ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/
-	@ ${INSTALL_SCRIPT} ${WRKSRC}/filetran ${PREFIX}/bin/
+	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${PREFIX}/bin/
+	${INSTALL_SCRIPT} ${WRKSRC}/filetran ${PREFIX}/bin/
 
 post-install:
 .if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCSDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/*.doc ${DOCSDIR}/
+	${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/recombine.txt ${DOCSDIR}/
 .endif
 
 .include <bsd.port.mk>
diff --git a/biology/recombine/distinfo b/biology/recombine/distinfo
index aac3425f6e44..4205cb639d47 100644
--- a/biology/recombine/distinfo
+++ b/biology/recombine/distinfo
@@ -1,3 +1,3 @@
-MD5 (recombine1.40.tar.gz) = 78f308f69c35610fbd31a091b8d17e2f
-SHA256 (recombine1.40.tar.gz) = 9601f94d1fd41233fa8470a03d53fb48bcb3f2e7358b756eebbde278114f1c35
-SIZE (recombine1.40.tar.gz) = 140331
+MD5 (recombine1.41.src.doc.tar.gz) = c833be133188d2482c846a596ae35cb8
+SHA256 (recombine1.41.src.doc.tar.gz) = e247810ef31414f500f9c118b6462b549c761562140519f7c57f305fcb284643
+SIZE (recombine1.41.src.doc.tar.gz) = 149129
diff --git a/biology/recombine/files/patch-Makefile b/biology/recombine/files/patch-Makefile
index de759e7d7bf9..338b70873c8c 100644
--- a/biology/recombine/files/patch-Makefile
+++ b/biology/recombine/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig	Wed Oct 25 23:39:34 2000
-+++ Makefile	Mon Aug  6 16:13:02 2001
-@@ -1,105 +1,37 @@
+--- Makefile.orig	Thu Jan 25 13:59:21 2007
++++ Makefile	Thu Jan 25 14:02:58 2007
+@@ -1,11 +1,6 @@
  LIBS    = -lm
  BINDIR  = ./bin
 -#CFLAGS  = -Wall -Wshadow -g
@@ -13,12 +13,7 @@
  DCC     = gcc -g -Wall -DDMALLOC_FUNC_CHECK -ansi -pedantic
  PLUSCC    = g++ $(CFLAGS)
  LIBS   = -lm -L/usr/local/lib
- DLIBS   = -lm -L/usr/local/lib -ldmalloc
- CGCC    = checkergcc -g -Wall
- CGLIBS  = -lm
--# -O
- PROGS   =           recombine
- 
+@@ -18,29 +13,29 @@
  # The big banana
  recombine : recombine.o jdrop.o rec_modellike.o jworld.o getdata.o \
  	traitlike.o getmsatdata.o
@@ -52,66 +47,7 @@
  
  traitlike.o : traitlike.c
 -	$(CC) -c traitlike.c
--
--rectreedna : rectreedna.c
--	$(CC) -o rectreedna rectreedna.c $(LIBS)
--
--hapdna : hapdna.c
--	$(CC) -o hapdna hapdna.c $(LIBS)
--
--mhapdna : mhapdna.c
--	$(CC) -o mhapdna mhapdna.c $(LIBS)
--
--drecombine.o : recombine.c
--	$(CC) -o drecombine.o -c recombine.c
--
--djdrop.o : jdrop.c
--	$(CC)  -o djdrop.o -c jdrop.c
--
--drec_modellike.o : rec_modellike.c
--	$(CC) -o drec_modellike.o -c rec_modellike.c
--
--djworld.o : jworld.c
--	$(CC) -o djworld.o -c jworld.c
--
--dgetdata.o : getdata.c
--	$(CC) -o dgetdata.o -c getdata.c
--
--dgetmsatdata.o : getmsatdata.c
--	$(CC) -o dgetmsatdata.o -c getmsatdata.c
--
--drecombine:  drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o memdebug.o memalpha.o memfree.o \
--        dgetmsatdata.o
--	$(CC) drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o memdebug.o memalpha.o memfree.o \
--	dgetmsatdata.o $(LIBS) -o drecombine
--
--dclean: 
--	rm drecombine.o djdrop.o drec_modellike.o djworld.o dgetdata.o dgetmsatdata.o
--
--clean :
--	rm -f *.o
--
--gentrees.o : gentrees.c
--	$(CC) -c gentrees.c
--
--segtre_mig.o : segtre_mig.c
--	$(CC) -c segtre_mig.c
--
--rectree : gentrees.o segtre_mig.o
--	$(CC) gentrees.o segtre_mig.o $(LIBS) -o rectree
--
--jrectree : simrectree.c
--	$(CC) simrectree.c $(LIBS) -o jrectree
--
--snp : snp.c
--	$(CC) snp.c $(LIBS) -o snp
--
--panelmaker : panelmaker.c
--	$(CC) panelmaker.c $(LIBS) -o panelmaker
--
--variance : variance.c
--	$(CC) variance.c $(LIBS) -o variance
--
--distree : distree.c
--	$(CC) distree.c $(LIBS) -o distree
 +	$(CC) $(CFLAGS) -c traitlike.c
+ 
+ rectreedna : rectreedna.c
+ 	$(CC) -o rectreedna rectreedna.c $(LIBS)
diff --git a/biology/recombine/pkg-plist b/biology/recombine/pkg-plist
index 3a78fcf0ba0e..9df8ac3cf76e 100644
--- a/biology/recombine/pkg-plist
+++ b/biology/recombine/pkg-plist
@@ -1,5 +1,4 @@
 bin/filetran
 bin/recombine
-%%PORTDOCS%%%%DOCSDIR%%/rec_errors.doc
-%%PORTDOCS%%%%DOCSDIR%%/recombine.doc
+%%PORTDOCS%%%%DOCSDIR%%/recombine.txt
 %%PORTDOCS%%@dirrm %%DOCSDIR%%