From owner-svn-ports-head@FreeBSD.ORG Sun Dec 28 18:18:26 2014 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 5AB747A2; Sun, 28 Dec 2014 18:18:26 +0000 (UTC) Received: from shepard.synsport.net (mail.synsport.com [208.69.230.148]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 2F2EF28BA; Sun, 28 Dec 2014 18:18:25 +0000 (UTC) Received: from [192.168.1.113] (c-174-61-88-207.hsd1.fl.comcast.net [174.61.88.207]) (using TLSv1 with cipher DHE-RSA-AES128-SHA (128/128 bits)) (No client certificate requested) by shepard.synsport.net (Postfix) with ESMTP id 37371435C7; Sun, 28 Dec 2014 12:18:13 -0600 (CST) Message-ID: <54A04955.3010601@marino.st> Date: Sun, 28 Dec 2014 19:17:57 +0100 From: John Marino Reply-To: marino@freebsd.org User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:24.0) Gecko/20100101 Thunderbird/24.5.0 MIME-Version: 1.0 To: =?UTF-8?B?RGFnLUVybGluZyBTbcO4cmdyYXY=?= , John Marino Subject: Re: svn commit: r370220 - in head/biology: . ncbi-blast References: <201410062016.s96KGZP8084850@svn.freebsd.org> <86r3vjg054.fsf@nine.des.no> In-Reply-To: <86r3vjg054.fsf@nine.des.no> Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Cc: svn-ports-head@freebsd.org, svn-ports-all@freebsd.org, jwbacon@tds.net, ports-committers@freebsd.org X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 28 Dec 2014 18:18:26 -0000 On 12/28/2014 18:22, Dag-Erling Smørgrav wrote: > John Marino writes: >> Log: >> Add new port biology/ncbi-blast >> >> PR: 190854 >> Submitted by: Jason Bacon >> >> 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. It's a brand new port with a unique name. Why is "bumping PORTEPOCH" considered necessary? Why is the existence of this port blocking the introduction of a new BLAST port? AFAIK, this port was not claiming to be a drop-in replacement for the blast port that was removed; no dependencies of other ports changed to this port. It seems that all that is needs is to update the pkg-descr file to specify it's the blast+ implementation. John