From owner-freebsd-ports-bugs@FreeBSD.ORG Thu Jul 1 16:11:41 2004 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id BE85716A4CE for ; Thu, 1 Jul 2004 16:11:41 +0000 (GMT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id B0DF843D3F for ; Thu, 1 Jul 2004 16:11:41 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) i61GAGSv061184 for ; Thu, 1 Jul 2004 16:10:16 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.11/8.12.11/Submit) id i61GAGEn061182; Thu, 1 Jul 2004 16:10:16 GMT (envelope-from gnats) Resent-Date: Thu, 1 Jul 2004 16:10:16 GMT Resent-Message-Id: <200407011610.i61GAGEn061182@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, "M. L. Dodson" Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 3B52B16A4CE for ; Thu, 1 Jul 2004 16:05:37 +0000 (GMT) Received: from e500-gw1.utmb.edu (mx1.utmb.edu [129.109.195.3]) by mx1.FreeBSD.org (Postfix) with ESMTP id AB9EF43D1D for ; Thu, 1 Jul 2004 16:05:36 +0000 (GMT) (envelope-from bdodson@scms.utmb.EDU) Received: from mx1.utmb.edu(129.109.195.3) by e500-gw1.utmb.edu via csmap id 4aabff86_cb79_11d8_87b9_00304823f3bd_18600; Thu, 01 Jul 2004 11:11:21 -0500 (CDT) Received: from e500-gw1.utmb.edu (histidine.utmb.edu [129.109.65.24]) by utmb.edu (PMDF V6.1 #38124) with ESMTP id <0I06001OMKMOSS@utmb.edu> for FreeBSD-gnats-submit@freebsd.org; Thu, 01 Jul 2004 11:04:00 -0500 (CDT) Received: from histidine.utmb.edu(129.109.65.24) by e500-gw1.utmb.edu via csmap id 0c3754c6_cb79_11d8_83ce_00304823f3bd_18594; Thu, 01 Jul 2004 11:09:36 -0500 (CDT) Received: (from bdodson@localhost) by histidine.utmb.edu (8.12.11/8.12.11/Submit) id i61G3p3g084646; Thu, 01 Jul 2004 11:03:51 -0500 (CDT envelope-from bdodson) Message-Id: <200407011603.i61G3p3g084646@histidine.utmb.edu> Date: Thu, 01 Jul 2004 11:03:51 -0500 (CDT) From: "M. L. Dodson" To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Subject: ports/68561: maintainer update for biology/nab X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list Reply-To: "M. L. Dodson" List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 01 Jul 2004 16:11:41 -0000 >Number: 68561 >Category: ports >Synopsis: maintainer update for biology/nab >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Thu Jul 01 16:10:16 GMT 2004 >Closed-Date: >Last-Modified: >Originator: M. L. Dodson >Release: FreeBSD 5.2-CURRENT i386 >Organization: University of Texas Medical Branch >Environment: System: FreeBSD histidine.utmb.edu 5.2-CURRENT FreeBSD 5.2-CURRENT #0: Thu May 27 12:07:35 CDT 2004 bdodson@histidine.utmb.edu:/usr/src/sys/i386/compile/HISTIDINE i386 >Description: NA >How-To-Repeat: NA >Fix: file files/patch-atom.c should be deleted and is deleted by the diff file files/patch-src:molio.c is new and is created by the diff diff -ruN nab.bak/Makefile nab/Makefile --- nab.bak/Makefile Mon May 3 10:31:41 2004 +++ nab/Makefile Thu Jul 1 10:31:20 2004 @@ -2,11 +2,11 @@ # Date created: Sept. 10, 2000 # Whom: M. L. Dodson # -# $FreeBSD: ports/biology/nab/Makefile,v 1.14 2004/05/02 03:28:48 petef Exp $ +# $FreeBSD$ # PORTNAME= nab -PORTVERSION= 4.5.3 +PORTVERSION= 4.6 CATEGORIES= biology MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ \ http://www.scripps.edu/case/ \ @@ -60,7 +60,6 @@ pre-install: @cd ${WRKSRC}/src && \ ${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall - @${CP} ${WRKSRC}/config.h ${WRKSRC}/include/ do-install: @-${MKDIR} ${PREFIX}/share/nab @@ -79,8 +78,12 @@ ${CHMOD} -R ugo+rX-w nab) @-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords) ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin - ${INSTALL_DATA} ${WRKSRC}/include/* ${PREFIX}/share/nab/include - ${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib +.for f in ${INCS} + ${INSTALL_DATA} ${WRKSRC}/include/${f} ${PREFIX}/include + @-(cd ${PREFIX}/share/nab/include && ${LN} -sf ${PREFIX}/include/${f} .) +.endfor + ${INSTALL_DATA} ${WRKSRC}/config.h ${PREFIX}/share/nab/include + ${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib @-cd ${WRKSRC}/doc && ${GZIP_CMD} ${MAN1} ${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz ${PREFIX}/man/man1 .for f in ${BINARIES} diff -ruN nab.bak/distinfo nab/distinfo --- nab.bak/distinfo Mon May 3 10:31:41 2004 +++ nab/distinfo Fri Jun 18 23:05:46 2004 @@ -1,2 +1,2 @@ -MD5 (nab-4.5.3.tar.gz) = 844cc6e4dad076edb4773bd06e1fe126 -SIZE (nab-4.5.3.tar.gz) = 4045456 +MD5 (nab-4.6.tar.gz) = ec1e51b8a9f6d5a46770b952f0e59d26 +SIZE (nab-4.6.tar.gz) = 3794078 diff -ruN nab.bak/files/patch-Makefile nab/files/patch-Makefile --- nab.bak/files/patch-Makefile Tue Oct 14 07:18:51 2003 +++ nab/files/patch-Makefile Thu Jul 1 09:03:52 2004 @@ -1,12 +1,13 @@ ---- Makefile.orig Tue Jul 15 21:11:15 2003 -+++ Makefile Sat Aug 9 13:50:34 2003 -@@ -1,15 +1,15 @@ +--- Makefile.orig Tue May 18 15:46:55 2004 ++++ Makefile Thu Jul 1 09:03:32 2004 +@@ -1,16 +1,15 @@ # top-level Makefile for the NAB suite of programs -+all: compiler test ++all: compiler test compiler: -mkdir bin lib include - (cd ucpp-1.3; make install ) +- (cd byacc; make install ) (cd cifparse; make install ) (cd src; make install ) (cd nss; make install ) @@ -20,18 +21,24 @@ # note: "make test" needs to follow "make", since it is very hard to # tell if the compiler is completely "made" or not. -@@ -18,14 +18,12 @@ +@@ -19,18 +18,15 @@ (cd nss; make test ) clean: - (cd ucpp-1.3; make clean ) +- (cd byacc; make clean ) (cd cifparse; make clean ) (cd src; make clean ) (cd nss; make clean ) (cd tleap; make clean ) - +- ++ uninstall: - (cd ucpp-1.3; make uninstall ) (cd cifparse; make uninstall ) (cd src; make uninstall ) (cd nss; make uninstall ) + (cd tleap; make uninstall ) + -/bin/rm config.h +- ++ diff -ruN nab.bak/files/patch-atom.c nab/files/patch-atom.c --- nab.bak/files/patch-atom.c Sat May 1 22:28:49 2004 +++ nab/files/patch-atom.c Wed Dec 31 18:00:00 1969 @@ -1,10 +0,0 @@ ---- tleap/atom.c.orig Sat Apr 20 22:35:09 2002 -+++ tleap/atom.c Sat Mar 6 08:02:25 2004 -@@ -908,6 +908,7 @@ - for ( i=0; i + #include +-#include ++#include + + #include "database.h" + diff -ruN nab.bak/files/patch-src:molio.c nab/files/patch-src:molio.c --- nab.bak/files/patch-src:molio.c Wed Dec 31 18:00:00 1969 +++ nab/files/patch-src:molio.c Fri Jun 18 23:28:08 2004 @@ -0,0 +1,10 @@ +--- src/molio.c.orig Mon May 10 16:53:34 2004 ++++ src/molio.c Fri Jun 18 23:26:01 2004 +@@ -1,7 +1,6 @@ + #include + #include + #include +-#include + #include + #include + #include diff -ruN nab.bak/pkg-plist nab/pkg-plist --- nab.bak/pkg-plist Mon May 3 10:31:42 2004 +++ nab/pkg-plist Thu Jul 1 10:05:20 2004 @@ -9,6 +9,10 @@ bin/tss_init bin/tss_main bin/tss_next +include/defreal.h +include/nab.h +include/nabcode.h +include/nabtypes.h lib/cifparse.a lib/libnab.a lib/libsym.a @@ -70,9 +74,6 @@ share/nab/dgdb/basepairs/ct.XVIII.pdb share/nab/dgdb/basepairs/cu.XVII.pdb share/nab/dgdb/basepairs/cu.XVIII.pdb -share/nab/dgdb/basepairs/CVS/Entries -share/nab/dgdb/basepairs/CVS/Repository -share/nab/dgdb/basepairs/CVS/Root share/nab/dgdb/basepairs/ga.IX.pdb share/nab/dgdb/basepairs/ga.VIII.pdb share/nab/dgdb/basepairs/ga.X.pdb @@ -142,9 +143,6 @@ share/nab/dgdb/stacking/ag.tdna.pdb share/nab/dgdb/stacking/at.adna.pdb share/nab/dgdb/stacking/at.bdna.pdb -share/nab/dgdb/stacking/CVS/Entries -share/nab/dgdb/stacking/CVS/Repository -share/nab/dgdb/stacking/CVS/Root share/nab/dgdb/stacking/at.cdna.pdb share/nab/dgdb/stacking/at.ddna.pdb share/nab/dgdb/stacking/at.tdna.pdb @@ -244,6 +242,7 @@ share/nab/examples/gcg10.pdb share/nab/examples/gcg10.pdb.save share/nab/examples/getbase.nab +share/nab/examples/mme_typical_calling_sequence.nab share/nab/examples/program_1.nab share/nab/examples/program_10.nab share/nab/examples/program_11.nab @@ -299,8 +298,6 @@ share/nab/reslib/bdna.std/bdna.std.pdb share/nab/reslib/bdna.std/dna.qr share/nab/reslib/bounds.db -share/nab/reslib/cdd.mol2 -share/nab/reslib/charlie.star.note share/nab/reslib/conf.lib share/nab/reslib/dna.amber94.3.rlb share/nab/reslib/dna.amber94.5.rlb @@ -346,7 +343,6 @@ share/nab/reslib/hetatm.amber94/hetatm.amber94.chi share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb share/nab/reslib/hetatm.amber94/hetatm.amber94.qr -share/nab/reslib/leap.log share/nab/reslib/leap/0README share/nab/reslib/leap/Notes share/nab/reslib/leap/all_amino91.lib @@ -361,12 +357,15 @@ share/nab/reslib/leap/dna.amberua.redch.lib share/nab/reslib/leap/ions91.lib share/nab/reslib/leap/ions94.lib -share/nab/reslib/leap/parm94.dat.istvan -share/nab/reslib/leap/leap.log share/nab/reslib/leap/leaprc.dna.amberua share/nab/reslib/leap/leaprc.dna.amberua.redch share/nab/reslib/leap/leaprc.nmr share/nab/reslib/leap/leaprc.protein.amberua +share/nab/reslib/leap/leaprc.ff03 +share/nab/reslib/leap/solvents.lib +share/nab/reslib/leap/frcmod.ff03 +share/nab/reslib/leap/all_amino03.lib +share/nab/reslib/leap/parm99.dat share/nab/reslib/leap/leaprc.rna share/nab/reslib/leap/leaprc.rna.amberua share/nab/reslib/leap/leaprc.std @@ -446,7 +445,6 @@ share/nab/reslib/rna.amberua/rna.amberua.chi share/nab/reslib/rna.amberua/rna.amberua.pdb share/nab/reslib/rna.amberua/rna.amberua.qr -share/nab/reslib/syblCDD.lib share/nab/suppose/Makefile share/nab/suppose/PCA_suppose.nab share/nab/suppose/ccmath.h @@ -463,8 +461,13 @@ share/nab/test/5pti.shifts.check share/nab/test/d01.lin.check share/nab/test/d01.pdb.check +share/nab/test/dhfrndpmtx.prmtop share/nab/test/dg_gyrate.nab share/nab/test/dg_gyrate.out.check +share/nab/test/dg_gyrate2.nab +share/nab/test/dhfrndpmtx.ambpdb +share/nab/test/dhfrndpmtx.nab +share/nab/test/dhfrndpmtx.out.check share/nab/test/dna.circle.nab share/nab/test/duplex.in share/nab/test/duplex.nab @@ -475,7 +478,6 @@ share/nab/test/gbrna.pdb share/nab/test/gbrna.prmtop share/nab/test/gbrna_long.nab -share/nab/test/gbrna_sa.nab share/nab/test/gbtrx.nab share/nab/test/gbtrx.out.check share/nab/test/get_pep_info.nab @@ -489,11 +491,11 @@ share/nab/test/ico.sym.out.check share/nab/test/ltest.nab share/nab/test/ltest.out.check -share/nab/test/msurf.nab +share/nab/test/mm_plus_dg.nab share/nab/test/pointplane.nab share/nab/test/prmtop share/nab/test/prmtop.gb2 -share/nab/test/prmtop.new +share/nab/test/pseudoknot.nab share/nab/test/rattle_md.nab share/nab/test/rattle_md.out.check share/nab/test/rattle_min.nab @@ -512,18 +514,6 @@ share/nab/test/trxox.2.4ns.pdb share/nab/test/trxox.2.4ns.x share/nab/test/write_sander_inp.nab -share/nab/test/lCmd -share/nab/test/1ubq/1ubq.pdb -share/nab/test/1ubq/5pti.pdb -share/nab/test/1ubq/leap.log -share/nab/test/1ubq/out.1 -share/nab/test/1ubq/prmtop -share/nab/test/1ubq/prmtop.1 -share/nab/test/1ubq/rattle_min.nab -share/nab/test/1ubq/runleap.nab -share/nab/test/2strand.nab -share/nab/test/2strand.pdb -@dirrm share/nab/test/1ubq @dirrm share/nab/test @dirrm share/nab/suppose @dirrm share/nab/reslib/rna.amberua @@ -546,9 +536,7 @@ @dirrm share/nab/include @dirrm share/nab/fd_data @dirrm share/nab/examples -@dirrm share/nab/dgdb/stacking/CVS @dirrm share/nab/dgdb/stacking -@dirrm share/nab/dgdb/basepairs/CVS @dirrm share/nab/dgdb/basepairs @dirrm share/nab/dgdb @dirrm share/nab/bin >Release-Note: >Audit-Trail: >Unformatted: