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Message-Id: <200301291656.h0TGuFNH026204@histidine.utmb.edu>
Date: Wed, 29 Jan 2003 10:56:15 -0600 (CST)
From: "M. L. Dodson" <bdodson@scms.utmb.EDU>
Reply-To: "M. L. Dodson" <bdodson@scms.utmb.EDU>
To: FreeBSD-gnats-submit@freebsd.org
Subject: biology/nab port update by maintainer
X-Send-Pr-Version: 3.113
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>Number:         47643
>Category:       ports
>Synopsis:       biology/nab port update by maintainer
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Jan 29 09:00:17 PST 2003
>Closed-Date:    Wed Feb 12 08:44:10 PST 2003
>Last-Modified:  Wed Feb 12 08:44:10 PST 2003
>Originator:     M. L. Dodson
>Release:        FreeBSD 4.7-STABLE i386
>Organization:
University of Texas Medical Branch
>Environment:
System: FreeBSD histidine.utmb.edu 4.7-STABLE FreeBSD 4.7-STABLE #1: Wed Nov 20 14:04:16 CST 2002 bdodson@histidine.utmb.edu:/usr/obj/usr/src/sys/HISTIDINE i386


>Description:
	biology/nab port update by maintainer
>How-To-Repeat:
>Fix:

Remove files/patch-nabgrm.y and files/patch-parser.y
diff -ruN nab.bak nab :

diff -ruN nab.bak/Makefile nab/Makefile
--- nab.bak/Makefile	Mon Nov  4 14:57:05 2002
+++ nab/Makefile	Wed Jan 29 10:09:57 2003
@@ -2,11 +2,11 @@
 # Date created:         Sept. 10, 2000
 # Whom:                 M. L. Dodson <bdodson@scms.utmb.edu>
 #
-# $FreeBSD: ports/biology/nab/Makefile,v 1.8 2002/11/04 01:55:06 edwin Exp $
+# $FreeBSD:$
 #
 
 PORTNAME=	nab
-PORTVERSION=	4.4
+PORTVERSION=	4.5
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
 		http://www.scripps.edu/case/
@@ -15,7 +15,6 @@
 
 MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH}
 
-USE_BISON=	yes
 MAN1=		nab.1
 MANCOMPRESSED=	yes
 USE_REINPLACE=	yes
diff -ruN nab.bak/distinfo nab/distinfo
--- nab.bak/distinfo	Tue Jul 16 01:18:16 2002
+++ nab/distinfo	Wed Jan 29 09:55:48 2003
@@ -1 +1 @@
-MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474
+MD5 (nab-4.5.tar.gz) = 57a5ff89c0c8c990403c18e482e426d1
diff -ruN nab.bak/files/config.h nab/files/config.h
--- nab.bak/files/config.h	Tue Jul 16 01:18:16 2002
+++ nab/files/config.h	Wed Jan 29 10:04:52 2003
@@ -78,12 +78,9 @@
 #          are not used.
 #
 #          For RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
-#
-#	   For FreeBSD 4.2-STABLE, there seems to be a dependency
-#	   on bison.  Berkeley yacc was very problematic.
 CC=		cc
 LEX=    	flex
-YACC=   	bison -y -t
+YACC=   	yacc
 AR=		ar
 #
 #  Set the C-preprocessor.  Code for a small preprocessor is in
diff -ruN nab.bak/files/patch-tleap:database.c nab/files/patch-tleap:database.c
--- nab.bak/files/patch-tleap:database.c	Tue Jul 16 01:18:16 2002
+++ nab/files/patch-tleap:database.c	Wed Jan 29 10:01:07 2003
@@ -1,35 +1,16 @@
-*** 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 );
+--- tleap/database.c.orig	Sat Nov  9 18:36:58 2002
++++ tleap/database.c	Wed Jan 29 09:56:46 2003
+@@ -185,6 +185,13 @@
+ }
+ 
+ 
++#if (defined(__unix__) || defined(unix)) && !defined(USG)
++#include <sys/param.h>
++#endif
++
++#if defined(BSD)
++#include <math.h>
++#endif
+ 
+ 
+ 
diff -ruN nab.bak/pkg-plist nab/pkg-plist
--- nab.bak/pkg-plist	Tue Jul 16 01:18:16 2002
+++ nab/pkg-plist	Wed Jan 29 10:25:02 2003
@@ -101,8 +101,28 @@
 share/nab/test/duplex.nab
 share/nab/test/ltest.out.check
 share/nab/test/dg_gyrate.out.check
+share/nab/test/duplex.exe
+share/nab/test/gbtrx.nab
+share/nab/test/gbtrx.out.check
+share/nab/test/prmtop.gb2
+share/nab/test/rattle_md.nab
+share/nab/test/rattle_md.out.check
+share/nab/test/rattle_min.nab
+share/nab/test/rattle_min.out.check
+share/nab/test/rembed.nab
+share/nab/test/rembed.out.check
+share/nab/test/trxox.2.4ns.pdb
+share/nab/test/trxox.2.4ns.x
 share/nab/suppose/suppose.1
 share/nab/suppose/suppose.nab
+share/nab/suppose/ccmath.h
+share/nab/suppose/eigen.c
+share/nab/suppose/housev.c
+share/nab/suppose/Makefile
+share/nab/suppose/matutl.h
+share/nab/suppose/PCA_suppose.nab
+share/nab/suppose/qrevec.c
+share/nab/suppose/trnm.c
 share/nab/dgdb/adna.basepair.db
 share/nab/dgdb/adna.nucleotide.db
 share/nab/dgdb/adna.stack.db
@@ -173,7 +193,6 @@
 share/nab/reslib/leap/ions91.lib
 share/nab/reslib/leap/pro-dna91.nmr.lib
 share/nab/reslib/leap/pro-dna91.nmr.prepin
-share/nab/reslib/leap/WW7.lib
 share/nab/reslib/bdna.std/bdna.std.bnd
 share/nab/reslib/bdna.std/bdna.std.chi
 share/nab/reslib/bdna.std/bdna.std.pdb
>Release-Note:
>Audit-Trail:

From: Christian Weisgerber <naddy@mips.inka.de>
To: bdodson@scms.utmb.EDU
Cc: freebsd-gnats-submit@freebsd.org
Subject: Re: ports/47643: biology/nab port update by maintainer
Date: Wed, 12 Feb 2003 01:40:02 +0100 (CET)

 In article <200301291656.h0TGuFNH026204@histidine.utmb.edu> you write:
 
 > >Number:         47643
 > >Category:       ports
 > >Synopsis:       biology/nab port update by maintainer
 
 This does not build on alpha:
 
   ...
   cc -c -O -pipe NAB_ainit.c
   ./nab  -c  allatom_to_dna3.nab
   nab2c failed!
   *** Error code 1
   ...
 
 There are numerous 64-bit-related warnings earlier in the build.
 
 In the port Makefile, you can replace "-mkdir -p" with "${MKDIR}".
 We also have a ${TAR} macro.
 
 -- 
 Christian "naddy" Weisgerber                          naddy@mips.inka.de
State-Changed-From-To: open->closed 
State-Changed-By: naddy 
State-Changed-When: Wed Feb 12 08:43:24 PST 2003 
State-Changed-Why:  
Submitter requests PR to be closed.  More work is required. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=47643 
>Unformatted:
