From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] gnu: Add hmmer Date: Sun, 21 Jun 2015 20:23:16 +0200 Message-ID: <87wpywhqej.fsf@elephly.net> References: <55867B39.3020207@uq.edu.au> <87zj3tgziz.fsf@elephly.net> <55868F4B.6060201@uq.edu.au> <87egl57zh0.fsf@netris.org> <20150621181131.GA17424@thebird.nl> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:43985) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6jtz-0000oV-ID for guix-devel@gnu.org; Sun, 21 Jun 2015 14:23:32 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z6jtw-0002Si-Bp for guix-devel@gnu.org; Sun, 21 Jun 2015 14:23:31 -0400 Received: from sender163-mail.zoho.com ([74.201.84.163]:25760) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z6jtw-0002SU-3w for guix-devel@gnu.org; Sun, 21 Jun 2015 14:23:28 -0400 In-reply-to: <20150621181131.GA17424@thebird.nl> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Pjotr Prins Cc: guix-devel@gnu.org Pjotr Prins writes: > It is quite common in bioinformatics tools to include foreign code. > One reason in favour of including the original setup that is it is > THAT what the authors and others test and run. Bringing in our own > dependencies is bound to open a can of worms - there often is a reason > they bring in that packaged code. One reason is that they depend on an older > version ;). With Guix we have no problem with packaging older versions. I have untangled a number of applications with bundled libraries before. It is doable, better for reproducibility, and better for security. I often submit bug reports upstream when I encounter bundling when attempting to package software and I encourage others to do the same. ~~ Ricardo