Date: Wed, 29 Jan 2003 10:56:15 -0600 (CST) From: "M. L. Dodson" <bdodson@scms.utmb.EDU> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/47643: biology/nab port update by maintainer Message-ID: <200301291656.h0TGuFNH026204@histidine.utmb.edu>
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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: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Wed Jan 29 09:00:17 PST 2003 >Closed-Date: >Last-Modified: >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: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports-bugs" in the body of the message
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