From owner-svn-ports-all@FreeBSD.ORG Sun Dec 28 17:22:34 2014 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id D7188A61; Sun, 28 Dec 2014 17:22:34 +0000 (UTC) Received: from smtp.des.no (smtp.des.no [194.63.250.102]) by mx1.freebsd.org (Postfix) with ESMTP id 993A666210; Sun, 28 Dec 2014 17:22:34 +0000 (UTC) Received: from nine.des.no (smtp.des.no [194.63.250.102]) by smtp-int.des.no (Postfix) with ESMTP id EFA359ECE; Sun, 28 Dec 2014 17:22:21 +0000 (UTC) Received: by nine.des.no (Postfix, from userid 1001) id 53F2812E34; Sun, 28 Dec 2014 18:22:16 +0100 (CET) From: =?utf-8?Q?Dag-Erling_Sm=C3=B8rgrav?= To: John Marino Subject: Re: svn commit: r370220 - in head/biology: . ncbi-blast References: <201410062016.s96KGZP8084850@svn.freebsd.org> Date: Sun, 28 Dec 2014 18:22:15 +0100 In-Reply-To: <201410062016.s96KGZP8084850@svn.freebsd.org> (John Marino's message of "Mon, 6 Oct 2014 20:16:35 +0000 (UTC)") Message-ID: <86r3vjg054.fsf@nine.des.no> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.4 (berkeley-unix) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Cc: svn-ports-head@freebsd.org, svn-ports-all@freebsd.org, jwbacon@tds.net, ports-committers@freebsd.org X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 28 Dec 2014 17:22:35 -0000 John Marino writes: > Log: > Add new port biology/ncbi-blast >=20=20=20 > PR: 190854 > Submitted by: Jason Bacon >=20=20=20 > The Basic Local Alignment Search Tool (BLAST) finds regions of local > similarity between sequences. The program compares nucleotide or protein > sequences to sequence databases and calculates the statistical > significance of matches. BLAST can be used to infer functional and > evolutionary relationships between sequences as well as help identify > members of gene families. I wish I had caught this in time. This is wrong. The port you committed installs BLAST+, not BLAST. These are two significantly different programs which implement the same algorithm. While the former is intended as a successor to the latter, they are not interchangeable. Many applications which use BLAST have not yet been, and may never be, ported to BLAST+, and this port stands in the way of a BLAST port. Since the authors, in their infinite stup^H^H^H^Hwisdom, decided to start numbering BLAST+ versions where BLAST left off, there is no way to fix this without either a) bumping PORTEPOCH or b) naming the BLAST port blast-legacy or something similar, while renaming this one to blast+ or blast-plus. DES --=20 Dag-Erling Sm=C3=B8rgrav - des@des.no