Attachment #23618 for bug #40612

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Lines 1-10 Link Here

(-)nab/Makefile (-2 / +5 lines)
1	# New ports collection Makefile for: nab	1	# New ports collection Makefile for: nab
2	# Date created: Sept. 10, 2000	2	# Date created: Sept. 10, 2000
3	# Whom: M. L. Dodson <bdodson@scms.utmb.edu>	3	# Whom: M. L. Dodson <bdodson@scms.utmb.edu>
4	# $FreeBSD: ports/biology/nab/Makefile,v 1.5 2002/03/31 03:55:29 kris Exp $	4	# $FreeBSD$
5		5
6	PORTNAME= nab	6	PORTNAME= nab
7	PORTVERSION= 4.3.2	7	PORTVERSION= 4.4
8	CATEGORIES= biology	8	CATEGORIES= biology
9	MASTER_SITES= ftp://ftp.scripps.edu/pub/case/	9	MASTER_SITES= ftp://ftp.scripps.edu/pub/case/
10		10
Lines 30-35 Link Here
30	pre-patch:	30	pre-patch:
31	@${PERL} -pi -e 's,<malloc.h>,<stdlib.h>,' \	31	@${PERL} -pi -e 's,<malloc.h>,<stdlib.h>,' \
32	${WRKSRC}/cifparse/cifparse.c	32	${WRKSRC}/cifparse/cifparse.c
		33
		34	post-patch:
		35	@rm -f ${WRKSRC}/examples/program_7.nab.orig
33		36
34	pre-install:	37	pre-install:
35	@cd ${WRKSRC}/src && \	38	@cd ${WRKSRC}/src && \

Line 1 Link Here

(-)nab/distinfo (-1 / +1 lines)
1	MD5 (nab-4.3.2.tar.gz) = 35a706bd124a212cc8310ca1327be227	1	MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474

Lines 97-104 Link Here

(-)nab/files/config.h (-2 / +2 lines)
97	#	97	#
98	# Use these CFLAGS if AVS = 0	98	# Use these CFLAGS if AVS = 0
99	#	99	#
100	CFLAGS=	100	CFLAGS= -O -pipe
101	OCFLAGS= -O	101	OCFLAGS= -O -pipe
102	NABFLAGS=	102	NABFLAGS=
103	#	103	#
104	# Use these CFLAGS if AVS = 1	104	# Use these CFLAGS if AVS = 1




*** 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
  
  }
  




*** 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 );




*** 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 ];

Lines 1-4 Link Here

(-)nab/pkg-descr (-1 / +1 lines)
1	This is version 4.2 of nab (nucleic acid builder), a computer language that	1	This is version 4.4 of nab (nucleic acid builder), a computer language that
2	is intended for use in creating, describing and modifying macromolecules,	2	is intended for use in creating, describing and modifying macromolecules,
3	especially nucleic acids. Programs written in nab are translated into C,	3	especially nucleic acids. Programs written in nab are translated into C,
4	which in turn is compiled into machine code.	4	which in turn is compiled into machine code.




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

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

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

Return to bug 40612

Line 0 Link Here

(-)nab/files/patch-ad (+32 lines)
	1	*** src/database.c.orig Wed Nov 15 19:46:50 2000
	2	--- src/database.c Sun Jun 2 12:57:50 2002
	3	***************
	4	* 67,72 **
	5	--- 67,79 ----
	6
	7
	8
	9	+ #if (defined(__unix__) \|\| defined(unix)) && !defined(USG)
	10	+ #include <sys/param.h>
	11	+ #endif
	12	+
	13	+ #if defined(BSD)
	14	+ #include <math.h>
	15	+ #endif
	16
	17
	18	#include "stdio.h"
	19	***************
	20	* 979,985 **
	21	--- 986,996 ----
	22
	23	sDBRemoveLeadingSpaces( sLine );
	24	sDBRemoveFirstString( sLine, sHead );
	25	+ #if defined (linux) \|\| defined(BSD)
	26	+ sscanf( sHead, "%lg", dPDbl );
	27	+ #else
	28	sscanf( sHead, "%lG", dPDbl );
	29	+ #endif
	30
	31	}
	32

Line 0 Link Here

(-)nab/files/patch-ae (+35 lines)
	1	*** tleap/database.c.orig Wed Mar 27 15:41:01 2002
	2	--- tleap/database.c Sun Jun 2 12:59:14 2002
	3	***************
	4	* 97,102 **
	5	--- 97,109 ----
	6
	7
	8
	9	+ #if (defined(__unix__) \|\| defined(unix)) && !defined(USG)
	10	+ #include <sys/param.h>
	11	+ #endif
	12	+
	13	+ #if defined(BSD)
	14	+ #include <math.h>
	15	+ #endif
	16
	17
	18	#include "basics.h"
	19	***************
	20	* 563,569 **
	21
	22	sRemoveLeadingSpaces( sLine );
	23	sRemoveFirstString( sLine, sHead );
	24	! #ifdef linux
	25	sscanf( sHead, "%lg", dPDbl );
	26	#else
	27	sscanf( sHead, "%lG", dPDbl );
	28	--- 570,576 ----
	29
	30	sRemoveLeadingSpaces( sLine );
	31	sRemoveFirstString( sLine, sHead );
	32	! #if defined(linux) \|\| defined(BSD)
	33	sscanf( sHead, "%lg", dPDbl );
	34	#else
	35	sscanf( sHead, "%lG", dPDbl );

Line 0 Link Here

(-)nab/files/patch-af (+19 lines)
	1	*** examples/program_7.nab Wed Mar 10 18:57:51 1999
	2	--- examples/program_7.nab Sun Jun 2 13:40:36 2002
	3	***************
	4	* 9,15 **
	5	cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
	6
	7	m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
	8	! "dna", 2.25, -4.96, 36.0, 4.38, "" );
	9
	10	b = newbounds(m, "");
	11	allocate xyz[ 4*m.natoms ];
	12	--- 9,15 ----
	13	cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
	14
	15	m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
	16	! "dna", 2.25, -4.96, 36.0, 3.38, "" );
	17
	18	b = newbounds(m, "");
	19	allocate xyz[ 4*m.natoms ];

Lines 101-117 Link Here

(-)nab/pkg-plist (-11 / +3 lines)
101	share/nab/test/duplex.nab	101	share/nab/test/duplex.nab
102	share/nab/test/ltest.out.check	102	share/nab/test/ltest.out.check
103	share/nab/test/dg_gyrate.out.check	103	share/nab/test/dg_gyrate.out.check
104	share/nab/peptide/COPYING
105	share/nab/peptide/aaaa.pdb
106	share/nab/peptide/lprot.nab
107	share/nab/peptide/write_pdb.nab
108	share/nab/peptide/README
109	share/nab/peptide/Makefile
110	share/nab/peptide/conf.lib
111	share/nab/peptide/peptide.nab
112	share/nab/peptide/match_template.nab
113	share/nab/peptide/peptide.c
114	share/nab/peptide/fix_angles.nab
115	share/nab/suppose/suppose.1	104	share/nab/suppose/suppose.1
116	share/nab/suppose/suppose.nab	105	share/nab/suppose/suppose.nab
117	share/nab/dgdb/adna.basepair.db	106	share/nab/dgdb/adna.basepair.db
Lines 131-136 Link Here
131	share/nab/dgdb/zdna.basepair.db	120	share/nab/dgdb/zdna.basepair.db
132	share/nab/dgdb/zdna.nucleotide.db	121	share/nab/dgdb/zdna.nucleotide.db
133	share/nab/dgdb/zdna.stack.db	122	share/nab/dgdb/zdna.stack.db
		123	share/nab/peptide/peptide.nab
		124	share/nab/peptide/README
134	share/nab/reslib/leap.log	125	share/nab/reslib/leap.log
135	share/nab/reslib/hetatm.amber94/hetatm.amber94.chi	126	share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
136	share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd	127	share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
Lines 301-306 Link Here
301	share/nab/fd_data/abdna.dat	292	share/nab/fd_data/abdna.dat
302	share/nab/fd_data/aprna.dat	293	share/nab/fd_data/aprna.dat
303	share/nab/fd_data/lbdna.dat	294	share/nab/fd_data/lbdna.dat
		295	share/nab/fd_data/abdna.dat.old
304	share/nab/coords	296	share/nab/coords
305	share/nab/lib/cifparse.a	297	share/nab/lib/cifparse.a
306	share/nab/lib/libnab.a	298	share/nab/lib/libnab.a