Attachment 23618 Details for Bug 40612 – file.diff

[patch] file.diff

file.diff (text/plain), 5.42 KB, created by bdodson on 2002-07-15 20:30:01 UTC

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Creator: bdodson

Created: 2002-07-15 20:30:01 UTC

Size: 5.42 KB

patch

obsolete

>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

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Attachments on bug 40612: 23618