From afa3475a3e7768b1a926973c0fee16566e2e87a0 Mon Sep 17 00:00:00 2001 From: jtb Date: Sun, 8 Jul 2001 13:36:33 +0000 Subject: Update to 5.0. Among the many changes: * New MPI version * Now uses autoconf/automake See the ChangeLog for full details. --- biology/puzzle/Makefile | 23 +++++++++++++---------- biology/puzzle/distinfo | 11 +++++------ biology/puzzle/patches/patch-aa | 29 +++++++++++------------------ biology/puzzle/patches/patch-ab | 31 ++++++++++++++++++++----------- biology/puzzle/patches/patch-ac | 22 ---------------------- biology/puzzle/pkg/PLIST | 10 +++++++++- 6 files changed, 58 insertions(+), 68 deletions(-) delete mode 100644 biology/puzzle/patches/patch-ac (limited to 'biology') 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 -- cgit v1.2.3