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authorVasil Dimov <vd@FreeBSD.org>2007-01-25 12:22:50 +0000
committerVasil Dimov <vd@FreeBSD.org>2007-01-25 12:22:50 +0000
commit885510efe14d17ddffe87697792076e92660ca0d (patch)
tree26153ce1875e7daaa4ab51abbe2b1f7a3715d251 /biology
parent35aff202d519b3daee2750d5ef17c497edefd756 (diff)
downloadports-885510efe14d17ddffe87697792076e92660ca0d.tar.gz
ports-885510efe14d17ddffe87697792076e92660ca0d.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/recombine/Makefile18
-rw-r--r--biology/recombine/distinfo6
-rw-r--r--biology/recombine/files/patch-Makefile78
-rw-r--r--biology/recombine/pkg-plist3
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%%