Update to 5.0.

Among the many changes:

*  New MPI version
*  Now uses autoconf/automake

See the ChangeLog for full details.

6 files changed, 58 insertions, 68 deletions

diff --git a/biology/puzzle/Makefile b/biology/puzzle/Makefile
index 646de864e25..e04296d81a3 100644
--- a/biology/puzzle/Makefile
+++ b/biology/puzzle/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.2 2001/02/16 13:41:31 wiz Exp $
+# $NetBSD: Makefile,v 1.3 2001/07/08 13:36:33 jtb Exp $
 
-DISTNAME=	puzzle-402
-PKGNAME=	puzzle-4.0.2
-WRKSRC=		${WRKDIR}/${PKGNAME}/src
+DISTNAME=	tree-puzzle-5.0
+PKGNAME=	puzzle-5.0
 CATEGORIES=	biology
 MASTER_SITES=	http://members.tripod.de/korbi/puzzle/ \
 		ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle/ \
@@ -11,15 +10,19 @@ MASTER_SITES=	http://members.tripod.de/korbi/puzzle/ \
 		http://iubio.bio.indiana.edu/soft/molbio/evolve/puzzle/
 
 MAINTAINER=	babafou@babafou.eu.org
-HOMEPAGE=	http://members.tripod.de/korbi/puzzle/
+HOMEPAGE=	http://www.tree-puzzle.de
 COMMENT=	Maximum likelihood analysis of molecular sequence data
 
-MAKEFILE=	makefile
-ALL_TARGET=	puzzle
+BUILD_DEPENDS=	mpich>=1.2.1:../../parallel/mpi-ch
 
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/puzzle ${PREFIX}/bin
+GNU_CONFIGURE=	yes
+
+post-install:
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/puzzle
-	${INSTALL_DATA} ${WRKDIR}/${PKGNAME}/doc/manual.html ${PREFIX}/share/doc/puzzle
+	cd ${WRKSRC}/doc; ${INSTALL_DATA} manual.html *.gif 		\
+		${PREFIX}/share/doc/puzzle
+	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/puzzle
+	cd ${WRKSRC}/data; ${INSTALL_DATA} atp6.a globin.a		\
+		marswolf.n primates.b ${PREFIX}/share/examples/puzzle
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/puzzle/distinfo b/biology/puzzle/distinfo
index 3a66f10d15b..cf329710c3b 100644
--- a/biology/puzzle/distinfo
+++ b/biology/puzzle/distinfo
@@ -1,7 +1,6 @@
-$NetBSD: distinfo,v 1.2 2001/04/19 16:02:25 agc Exp $
+$NetBSD: distinfo,v 1.3 2001/07/08 13:36:33 jtb Exp $
 
-SHA1 (puzzle-402.tar.gz) = 4c6e6abdb4b1e6f9bfcdbb5caba9d91c18e506fa
-Size (puzzle-402.tar.gz) = 100980 bytes
-SHA1 (patch-aa) = 2537c3ad4b2ac01bce41a0aa97910993a0d2fe6b
-SHA1 (patch-ab) = 613175c3f83827bd2164735aaddcb4786eea0e91
-SHA1 (patch-ac) = f74911a9661b4ccc97427e5eccc6b4be86bc9439
+SHA1 (tree-puzzle-5.0.tar.gz) = 8c73c003a874c4c701b21b9fbdf0bbed496eda1a
+Size (tree-puzzle-5.0.tar.gz) = 190137 bytes
+SHA1 (patch-aa) = 4391e9ba6d8b01b59240f80dee09bf33b04e12ff
+SHA1 (patch-ab) = cf32c3bf87b3fba7b3e3476ae2ceb489610d2463
diff --git a/biology/puzzle/patches/patch-aa b/biology/puzzle/patches/patch-aa
index 921af783c37..22c98752f2d 100644
--- a/biology/puzzle/patches/patch-aa
+++ b/biology/puzzle/patches/patch-aa
@@ -1,20 +1,13 @@
-$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+$NetBSD: patch-aa,v 1.2 2001/07/08 13:36:33 jtb Exp $
 
---- makefile.orig	Sun May 23 15:40:28 1999
-+++ makefile	Sun May 23 15:40:42 1999
-@@ -10,11 +10,11 @@
+--- src/ml.h.orig	Thu May 24 05:12:06 2001
++++ src/ml.h
+@@ -173,7 +173,7 @@
+ /* function prototypes of all ml function */
  
- 
- # ANSI C compiler
--CC = gcc
--CFLAGS = -O3 -Wall -pedantic -ansi
-+#CC = gcc
-+#CFLAGS = -O3 -Wall -pedantic -ansi
- # Comment out for compiler other than gcc
--#CC = cc
--#CFLAGS = -O 
-+CC = cc
-+CFLAGS = -O 
- 
- # ANSI math library
- LIBFLAGS = -lm
+ void convfreq(dvector);
+-void radixsort(cmatrix, ivector, int, int, int *);
++void my_radixsort(cmatrix, ivector, int, int, int *);
+ void condenceseq(cmatrix, ivector, cmatrix, ivector, int, int, int);
+ void countconstantsites(cmatrix, ivector, int, int, int *, int*);
+ void evaluateseqs(void);
diff --git a/biology/puzzle/patches/patch-ab b/biology/puzzle/patches/patch-ab
index 343ad02a0e3..4781fa4c25c 100644
--- a/biology/puzzle/patches/patch-ab
+++ b/biology/puzzle/patches/patch-ab
@@ -1,13 +1,22 @@
-$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+$NetBSD: patch-ab,v 1.2 2001/07/08 13:36:33 jtb Exp $
 
---- ml.h.orig	Sun May 23 12:08:41 1999
-+++ ml.h	Sun May 23 12:08:49 1999
-@@ -165,7 +165,7 @@
- /* function prototypes of all ml function */
+--- src/ml1.c.orig	Thu May 24 05:12:15 2001
++++ src/ml1.c
+@@ -78,7 +78,7 @@
+ }
  
- void convfreq(dvector);
--void radixsort(cmatrix, ivector, int, int, int *);
-+void my_radixsort(cmatrix, ivector, int, int, int *);
- void condenceseq(cmatrix, ivector, cmatrix, ivector, int, int, int);
- void countconstantsites(cmatrix, ivector, int, int, int *);
- void evaluateseqs(void);
+ /* sort site patters of original input data */
+-void radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
++void my_radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
+ 	int *numptrn)
+ {
+ 	int i, j, k, l, n, pass;
+@@ -196,7 +196,7 @@
+ 
+ 	convfreq(Freqtpm); /* make all frequencies slightly different */
+ 	ali = new_ivector(Maxsite);
+-	radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
++	my_radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
+ 	Seqpat = new_cmatrix(Maxspc, Numptrn);
+ 	constpat = new_ivector(Numptrn);
+ 	Weight = new_ivector(Numptrn);
diff --git a/biology/puzzle/patches/patch-ac b/biology/puzzle/patches/patch-ac
deleted file mode 100644
index ff0797222ad..00000000000
--- a/biology/puzzle/patches/patch-ac
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
-
---- ml1.c.orig	Sun May 23 12:07:15 1999
-+++ ml1.c	Sun May 23 12:07:36 1999
-@@ -65,7 +65,7 @@
- }
- 
- /* sort site patters of original input data */
--void radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
-+void my_radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite,
- 	int *numptrn)
- {
- 	int i, j, k, l, n, pass;
-@@ -181,7 +181,7 @@
- 
- 	convfreq(Freqtpm); /* make all frequencies slightly different */
- 	ali = new_ivector(Maxsite);
--	radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
-+	my_radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn);
- 	Seqpat = new_cmatrix(Maxspc, Numptrn);
- 	constpat = new_ivector(Numptrn);
- 	Weight = new_ivector(Numptrn);
diff --git a/biology/puzzle/pkg/PLIST b/biology/puzzle/pkg/PLIST
index 3356fd35c39..d9ada87e8de 100644
--- a/biology/puzzle/pkg/PLIST
+++ b/biology/puzzle/pkg/PLIST
@@ -1,4 +1,12 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $
+@comment $NetBSD: PLIST,v 1.2 2001/07/08 13:36:34 jtb Exp $
+bin/ppuzzle
 bin/puzzle
 share/doc/puzzle/manual.html
+share/doc/puzzle/ppuzzle.gif
+share/doc/puzzle/puzzle.gif
+share/examples/puzzle/atp6.a
+share/examples/puzzle/globin.a
+share/examples/puzzle/marswolf.n
+share/examples/puzzle/primates.b
 @dirrm share/doc/puzzle
+@dirrm share/examples/puzzle