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Message-Id: <200207151922.g6FJMIj5020241@histidine.utmb.edu>
Date: Mon, 15 Jul 2002 14:22:18 -0500 (CDT)
From: "M. L. Dodson" <bdodson@scms.utmb.edu>
Reply-To: "M. L. Dodson" <bdodson@scms.utmb.edu>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: port update by maintainer
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         40612
>Category:       ports
>Synopsis:       port update by maintainer
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Jul 15 12:30:01 PDT 2002
>Closed-Date:    Mon Jul 15 23:18:42 PDT 2002
>Last-Modified:  Mon Jul 15 23:18:42 PDT 2002
>Originator:     M. L. Dodson
>Release:        FreeBSD 4.6-PRERELEASE i386
>Organization:
University of Texas Medical Branch
>Environment:
System: FreeBSD histidine.utmb.edu 4.6-PRERELEASE FreeBSD \
4.6-PRERELEASE #0: Wed May 8 15:41:49 CDT 2002 \
bdodson@histidine.utmb.edu:/usr/obj/usr/src/sys/HISTIDINE i386


>Description:
	Update of the biology/nab port to the latest version of the
	software.  The files corresponding to the patches: patch-ad,
	patch-ae, patch-af in the included diff are new files.  The
	output of "diff -ruN nab.bak nab" is included.
>How-To-Repeat:
>Fix:

diff -ruN nab.bak/Makefile nab/Makefile
--- nab.bak/Makefile	Mon Apr  1 10:41:40 2002
+++ nab/Makefile	Sun Jun  2 13:58:18 2002
@@ -1,10 +1,10 @@
 # New ports collection Makefile for: nab
 # Date created:         Sept. 10, 2000
 # Whom:                 M. L. Dodson <bdodson@scms.utmb.edu>
-# $FreeBSD: ports/biology/nab/Makefile,v 1.5 2002/03/31 03:55:29 kris Exp $
+# $FreeBSD$
 
 PORTNAME=	nab
-PORTVERSION=	4.3.2
+PORTVERSION=	4.4
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/
 
@@ -30,6 +30,9 @@
 pre-patch:
 	@${PERL} -pi -e 's,<malloc.h>,<stdlib.h>,' \
 		${WRKSRC}/cifparse/cifparse.c
+
+post-patch:
+	@rm -f ${WRKSRC}/examples/program_7.nab.orig
 
 pre-install:
 	@cd ${WRKSRC}/src && \
diff -ruN nab.bak/distinfo nab/distinfo
--- nab.bak/distinfo	Fri Jun  1 13:11:28 2001
+++ nab/distinfo	Sun Jun  2 12:52:56 2002
@@ -1 +1 @@
-MD5 (nab-4.3.2.tar.gz) = 35a706bd124a212cc8310ca1327be227
+MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474
diff -ruN nab.bak/files/config.h nab/files/config.h
--- nab.bak/files/config.h	Fri Jun  1 13:11:28 2001
+++ nab/files/config.h	Sun Jun  2 13:05:27 2002
@@ -97,8 +97,8 @@
 #
 #  Use these CFLAGS if AVS = 0
 #
-CFLAGS= 
-OCFLAGS= -O
+CFLAGS= -O -pipe
+OCFLAGS= -O -pipe
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1
diff -ruN nab.bak/files/patch-ad nab/files/patch-ad
--- nab.bak/files/patch-ad	Wed Dec 31 18:00:00 1969
+++ nab/files/patch-ad	Sun Jun  2 12:59:56 2002
@@ -0,0 +1,32 @@
+*** src/database.c.orig	Wed Nov 15 19:46:50 2000
+--- src/database.c	Sun Jun  2 12:57:50 2002
+***************
+*** 67,72 ****
+--- 67,79 ----
+  
+  
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  
+  #include	"stdio.h"
+***************
+*** 979,985 ****
+--- 986,996 ----
+  
+      sDBRemoveLeadingSpaces( sLine );
+      sDBRemoveFirstString( sLine, sHead );
++ #if defined (linux) || defined(BSD)
++     sscanf( sHead, "%lg", dPDbl );
++ #else
+      sscanf( sHead, "%lG", dPDbl );
++ #endif
+  
+  }
+  
diff -ruN nab.bak/files/patch-ae nab/files/patch-ae
--- nab.bak/files/patch-ae	Wed Dec 31 18:00:00 1969
+++ nab/files/patch-ae	Sun Jun  2 13:00:33 2002
@@ -0,0 +1,35 @@
+*** tleap/database.c.orig	Wed Mar 27 15:41:01 2002
+--- tleap/database.c	Sun Jun  2 12:59:14 2002
+***************
+*** 97,102 ****
+--- 97,109 ----
+  
+  
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  
+  #include	"basics.h"
+***************
+*** 563,569 ****
+  
+      sRemoveLeadingSpaces( sLine );
+      sRemoveFirstString( sLine, sHead );
+! #ifdef linux
+      sscanf( sHead, "%lg", dPDbl );
+  #else
+      sscanf( sHead, "%lG", dPDbl );
+--- 570,576 ----
+  
+      sRemoveLeadingSpaces( sLine );
+      sRemoveFirstString( sLine, sHead );
+! #if defined(linux) || defined(BSD)
+      sscanf( sHead, "%lg", dPDbl );
+  #else
+      sscanf( sHead, "%lG", dPDbl );
diff -ruN nab.bak/files/patch-af nab/files/patch-af
--- nab.bak/files/patch-af	Wed Dec 31 18:00:00 1969
+++ nab/files/patch-af	Sun Jun  2 13:45:11 2002
@@ -0,0 +1,19 @@
+*** examples/program_7.nab	Wed Mar 10 18:57:51 1999
+--- examples/program_7.nab	Sun Jun  2 13:40:36 2002
+***************
+*** 9,15 ****
+  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
+  
+  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
+!          "dna", 2.25, -4.96, 36.0, 4.38, "" );
+  
+  b = newbounds(m, "");
+  allocate xyz[ 4*m.natoms ];
+--- 9,15 ----
+  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
+  
+  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
+!          "dna", 2.25, -4.96, 36.0, 3.38, "" );
+  
+  b = newbounds(m, "");
+  allocate xyz[ 4*m.natoms ];
diff -ruN nab.bak/pkg-descr nab/pkg-descr
--- nab.bak/pkg-descr	Tue Nov 27 15:21:07 2001
+++ nab/pkg-descr	Sun Jun  2 13:15:59 2002
@@ -1,4 +1,4 @@
-This is version 4.2 of nab (nucleic acid builder), a computer language that
+This is version 4.4 of nab (nucleic acid builder), a computer language that
 is intended for use in creating, describing and modifying macromolecules,
 especially nucleic acids. Programs written in nab are translated into C,
 which in turn is compiled into machine code.
diff -ruN nab.bak/pkg-plist nab/pkg-plist
--- nab.bak/pkg-plist	Wed Sep 12 11:07:54 2001
+++ nab/pkg-plist	Sun Jun  2 13:26:57 2002
@@ -101,17 +101,6 @@
 share/nab/test/duplex.nab
 share/nab/test/ltest.out.check
 share/nab/test/dg_gyrate.out.check
-share/nab/peptide/COPYING
-share/nab/peptide/aaaa.pdb
-share/nab/peptide/lprot.nab
-share/nab/peptide/write_pdb.nab
-share/nab/peptide/README
-share/nab/peptide/Makefile
-share/nab/peptide/conf.lib
-share/nab/peptide/peptide.nab
-share/nab/peptide/match_template.nab
-share/nab/peptide/peptide.c
-share/nab/peptide/fix_angles.nab
 share/nab/suppose/suppose.1
 share/nab/suppose/suppose.nab
 share/nab/dgdb/adna.basepair.db
@@ -131,6 +120,8 @@
 share/nab/dgdb/zdna.basepair.db
 share/nab/dgdb/zdna.nucleotide.db
 share/nab/dgdb/zdna.stack.db
+share/nab/peptide/peptide.nab
+share/nab/peptide/README
 share/nab/reslib/leap.log
 share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
 share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
@@ -301,6 +292,7 @@
 share/nab/fd_data/abdna.dat
 share/nab/fd_data/aprna.dat
 share/nab/fd_data/lbdna.dat
+share/nab/fd_data/abdna.dat.old
 share/nab/coords
 share/nab/lib/cifparse.a
 share/nab/lib/libnab.a
>Release-Note:
>Audit-Trail:
State-Changed-From-To: open->closed 
State-Changed-By: ijliao 
State-Changed-When: Mon Jul 15 23:18:25 PDT 2002 
State-Changed-Why:  
committed, thanks 

http://www.freebsd.org/cgi/query-pr.cgi?pr=40612 
>Unformatted:
