From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Jul 28 13:10:20 2003 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 BEE2A37B401 for ; Mon, 28 Jul 2003 13:10:19 -0700 (PDT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 0608743FE3 for ; Mon, 28 Jul 2003 13:10:10 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.12.9/8.12.9) with ESMTP id h6SKAAUp006146 for ; Mon, 28 Jul 2003 13:10:10 -0700 (PDT) (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.9/8.12.9/Submit) id h6SKAAAk006145; Mon, 28 Jul 2003 13:10:10 -0700 (PDT) Resent-Date: Mon, 28 Jul 2003 13:10:10 -0700 (PDT) Resent-Message-Id: <200307282010.h6SKAAAk006145@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, Mark Linimon Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id B143D37B407 for ; Mon, 28 Jul 2003 13:09:22 -0700 (PDT) Received: from mail.soaustin.net (mail.soaustin.net [207.200.4.66]) by mx1.FreeBSD.org (Postfix) with ESMTP id 8270043FD7 for ; Mon, 28 Jul 2003 13:09:20 -0700 (PDT) (envelope-from linimon@lonesome.com) Received: from lonesome.lonesome.com (cs242746-11.austin.rr.com [24.27.46.11]) (using TLSv1 with cipher EDH-RSA-DES-CBC3-SHA (168/168 bits)) (No client certificate requested) by mail.soaustin.net (Postfix) with ESMTP id A935914397 for ; Mon, 28 Jul 2003 15:09:19 -0500 (CDT) Received: from lonesome.lonesome.com (localhost.lonesome.com [127.0.0.1]) by lonesome.lonesome.com (8.12.9/8.12.9) with ESMTP id h6RJeiWZ026846; Sun, 27 Jul 2003 14:40:44 -0500 (CDT) (envelope-from linimon@lonesome.lonesome.com) Received: (from linimon@localhost) by lonesome.lonesome.com (8.12.9/8.12.9/Submit) id h6RJegQc026845; Sun, 27 Jul 2003 14:40:42 -0500 (CDT) Message-Id: <200307271940.h6RJegQc026845@lonesome.lonesome.com> Date: Sun, 27 Jul 2003 14:40:42 -0500 (CDT) From: Mark Linimon To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113.1 cc: bdodson@scms.utmb.edu Subject: ports/54990: [patch][non-maintainer] fix fetch and plist for biology/nab X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 28 Jul 2003 20:10:20 -0000 >Number: 54990 >Category: ports >Synopsis: [patch][non-maintainer] fix fetch and plist for biology/nab >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: Mon Jul 28 13:10:10 PDT 2003 >Closed-Date: >Last-Modified: >Originator: Mark Linimon >Release: FreeBSD- >Organization: FreeBSD >Environment: System: FreeBSD lonesome.lonesome.com 4.8-STABLE FreeBSD 4.8-STABLE #1: Sun Jul 13 23:03:01 CDT 2003 root@lonesome.lonesome.com:/usr/src/sys/compile/MULTIMEDIA i386 >Description: Per the mastersite, the distfile has been upgraded: "Version 4.5.2 has some fix-ups to the manual and a faster implementation of the generalized Born algorithm." Also, the plist was incomplete >How-To-Repeat: per bento logs >Fix: The following fixes everything except one file in plist that clearly should not be installed, "/usr/local/share/nab/leap/?????". I'll leave that to the port maintainer to fix and send to the original authors. (There are other questionable files that are installed as well: *.dat~, *.exe). --- nab/Makefile.dist Tue Jul 8 06:50:36 2003 +++ nab/Makefile Sun Jul 27 14:07:44 2003 @@ -6,7 +6,7 @@ # PORTNAME= nab -PORTVERSION= 4.5.1 +PORTVERSION= 4.5.2 CATEGORIES= biology MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ \ http://www.scripps.edu/case/ --- nab/distinfo.dist Tue Jul 8 06:50:36 2003 +++ nab/distinfo Sun Jul 27 14:08:18 2003 @@ -1 +1 @@ -MD5 (nab-4.5.1.tar.gz) = 650be5581dfe5af1b7edb6da44a221d4 +MD5 (nab-4.5.2.tar.gz) = b5e9053e6ae97f36a55cc2a1317e9ba8 --- nab/pkg-plist.dist Tue Jul 8 06:50:36 2003 +++ nab/pkg-plist Sun Jul 27 14:27:40 2003 @@ -54,6 +54,8 @@ share/nab/examples/gcg10.pdb share/nab/examples/gcg10.pdb.save share/nab/examples/getbase.nab +share/nab/examples/program_1.c +share/nab/examples/program_1.exe share/nab/examples/program_1.nab share/nab/examples/program_10.nab share/nab/examples/program_11.nab @@ -186,6 +188,8 @@ share/nab/reslib/leap/parm91X.dat share/nab/reslib/leap/parm91X.ua.dat share/nab/reslib/leap/parm94.dat +share/nab/reslib/leap/parm94.dat.istvan +share/nab/reslib/leap/parm94.dat~ share/nab/reslib/leap/parm94X.dat share/nab/reslib/leap/pro-dna91.nmr.lib share/nab/reslib/leap/pro-dna91.nmr.prepin @@ -266,7 +270,21 @@ share/nab/suppose/suppose.1 share/nab/suppose/suppose.nab share/nab/suppose/trnm.c +share/nab/test/1ubq/1ubq.pdb +share/nab/test/1ubq/5pti.pdb +share/nab/test/1ubq/a.exe +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.c +share/nab/test/1ubq/rattle_min.nab +share/nab/test/1ubq/runleap.c +share/nab/test/1ubq/runleap.nab share/nab/test/2.pdb +share/nab/test/2strand.exe +share/nab/test/2strand.nab +share/nab/test/2strand.pdb share/nab/test/5pti.obs share/nab/test/5pti.pdb share/nab/test/5pti.shifts.check @@ -287,7 +305,7 @@ share/nab/test/gbrna.prmtop share/nab/test/gbrna_long.exe share/nab/test/gbrna_long.nab -share/nab/test/gbrna_long.out +share/nab/test/gbrna_sa.nab share/nab/test/gbtrx.nab share/nab/test/gbtrx.out.check share/nab/test/get_pep_info.nab @@ -299,11 +317,14 @@ share/nab/test/hash.out.check share/nab/test/ico.sym share/nab/test/ico.sym.out.check +share/nab/test/lCmd share/nab/test/ltest.nab share/nab/test/ltest.out.check +share/nab/test/msurf.nab share/nab/test/pointplane.nab share/nab/test/prmtop share/nab/test/prmtop.gb2 +share/nab/test/prmtop.new share/nab/test/rattle_md.nab share/nab/test/rattle_md.out.check share/nab/test/rattle_min.nab @@ -322,6 +343,7 @@ share/nab/test/trxox.2.4ns.pdb share/nab/test/trxox.2.4ns.x share/nab/test/write_sander_inp.nab +@dirrm share/nab/test/1ubq @dirrm share/nab/test @dirrm share/nab/suppose @dirrm share/nab/reslib/rna.amberua --- nab/files/patch-Makefile.dist Sun Jul 27 14:10:14 2003 +++ nab/files/patch-Makefile Sun Jul 27 14:15:24 2003 @@ -6,7 +6,7 @@ +all: compiler test compiler: -mkdir bin lib include -- (cd ucpp-0.7; make install ) +- (cd ucpp-1.3; make install ) (cd cifparse; make install ) (cd src; make install ) (cd nss; make install ) @@ -24,14 +24,14 @@ (cd nss; make test ) clean: -- (cd ucpp-0.7; make clean ) +- (cd ucpp-1.3; make clean ) (cd cifparse; make clean ) (cd src; make clean ) (cd nss; make clean ) (cd tleap; make clean ) uninstall: -- (cd ucpp-0.7; make uninstall ) +- (cd ucpp-1.3; make uninstall ) (cd cifparse; make uninstall ) (cd src; make uninstall ) (cd nss; make uninstall ) >Release-Note: >Audit-Trail: >Unformatted: