From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Mar 20 17:00:42 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org 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 6AA3E16A425 for ; Mon, 20 Mar 2006 17:00:42 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 33C7243D70 for ; Mon, 20 Mar 2006 17:00:39 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k2KH0cwX011554 for ; Mon, 20 Mar 2006 17:00:38 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k2KH0cZg011553; Mon, 20 Mar 2006 17:00:38 GMT (envelope-from gnats) Resent-Date: Mon, 20 Mar 2006 17:00:38 GMT Resent-Message-Id: <200603201700.k2KH0cZg011553@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, Fernan Aguero Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 1AC8916A400 for ; Mon, 20 Mar 2006 16:50:08 +0000 (UTC) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: from omega.iib.unsam.edu.ar (omega.iib.unsam.edu.ar [170.210.49.14]) by mx1.FreeBSD.org (Postfix) with ESMTP id 0ECD643D48 for ; Mon, 20 Mar 2006 16:50:05 +0000 (GMT) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: from omega.iib.unsam.edu.ar (localhost [127.0.0.1]) by omega.iib.unsam.edu.ar (8.13.4/8.13.4) with ESMTP id k2KGn2Ua003814 for ; Mon, 20 Mar 2006 13:49:02 -0300 (ART) (envelope-from fernan@omega.iib.unsam.edu.ar) Received: (from fernan@localhost) by omega.iib.unsam.edu.ar (8.13.4/8.13.3/Submit) id k2KGn1WF003813; Mon, 20 Mar 2006 13:49:01 -0300 (ART) (envelope-from fernan) Message-Id: <200603201649.k2KGn1WF003813@omega.iib.unsam.edu.ar> Date: Mon, 20 Mar 2006 13:49:01 -0300 (ART) From: Fernan Aguero To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/94741: [ maintainer update ] update biology/fasta3 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Fernan Aguero List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 20 Mar 2006 17:00:42 -0000 >Number: 94741 >Category: ports >Synopsis: [ maintainer update ] update biology/fasta3 >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: Mon Mar 20 17:00:38 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 6.0-RELEASE-p4 i386 >Organization: IIB-UNSAM >Environment: System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386 >Description: A new version of the fasta distribution, fasta34t25d5.shar.Z, is available from: ftp://ftp.virginia.edu/pub/fasta/fasta34t25d5.shar.Z In general, the major changes in this version are internal; the functions producing alignments and alignment coordinates have been simplified. One of the consequences is that for the parallel versions, alignments are calculated only once, even if the alignment information is needed several times (e.g. in the list of best scores and as final alignments). The major new feature is the ability to work with asymmetric scoring matrices. Although the FASTA programs use the NxN scoring matrix format used by BLAST, only half of the matrix was actually read andthe rest inferred by symmetry. This has been changed, and asymmetric matrices can be used. In addition, the -V "*#" annotation option is now available in the parallel versions of the programs, and some minor bug fixes are included. Bill Pearson >How-To-Repeat: >Fix: --- fasta3.diff begins here --- diff -u /usr/ports/biology/fasta3/Makefile fasta3/Makefile --- /usr/ports/biology/fasta3/Makefile Wed Mar 1 20:11:41 2006 +++ fasta3/Makefile Mon Mar 20 13:38:06 2006 @@ -7,7 +7,7 @@ # PORTNAME= fasta3 -PORTVERSION= 34.t25.d4 +PORTVERSION= 34.t25.d5 CATEGORIES= biology MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/ DISTNAME= fasta${PORTVERSION:S/.//g} diff -u /usr/ports/biology/fasta3/distinfo fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo Wed Mar 1 20:11:41 2006 +++ fasta3/distinfo Mon Mar 20 13:38:09 2006 @@ -1,3 +1,3 @@ -MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7 -SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe -SIZE (fasta34t25d4.shar.Z) = 799416 +MD5 (fasta34t25d5.shar.Z) = 500a449fe3eeebbeb3e7f53f652505c7 +SHA256 (fasta34t25d5.shar.Z) = bcb7c25b6e3d883cc4c61c35b94b4dc42c49a158859cfefbf6a3f9357c0e7482 +SIZE (fasta34t25d5.shar.Z) = 795675 Common subdirectories: /usr/ports/biology/fasta3/files and fasta3/files --- fasta3.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted: