Date: Mon, 15 Jul 2002 14:22:18 -0500 (CDT) From: "M. L. Dodson" <bdodson@scms.utmb.edu> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/40612: port update by maintainer Message-ID: <200207151922.g6FJMIj5020241@histidine.utmb.edu>
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>Number: 40612 >Category: ports >Synopsis: port update by maintainer >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Jul 15 12:30:01 PDT 2002 >Closed-Date: >Last-Modified: >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: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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