From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [PATCH]: gnu: Add bedops. Date: Fri, 13 Feb 2015 14:40:18 +0100 Message-ID: <87bnkyylod.fsf@gnu.org> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41892) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YMGTo-00037n-2t for guix-devel@gnu.org; Fri, 13 Feb 2015 08:40:25 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YMGTk-0007aA-R4 for guix-devel@gnu.org; Fri, 13 Feb 2015 08:40:24 -0500 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:44576) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YMGTk-0007a6-Ny for guix-devel@gnu.org; Fri, 13 Feb 2015 08:40:20 -0500 In-Reply-To: (Ricardo Wurmus's message of "Wed, 11 Feb 2015 17:02:47 +0100") 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: Ricardo Wurmus Cc: Guix-devel Ricardo Wurmus skribis: > The build process for this application is a bit messy because the > sources include tarballs of modified upstream libraries (jansson, bzip2, > zlib), so we cannot just swap them out for system libraries. > > I'm in touch with the developers to see if we can get a build option to > link against system libraries instead of the bundled copies. To achieve > this, though, the patches have to be extracted first (already submitted > a patch upstream), and any feature that has been added by patching > upstream library sources would have to be implemented a different way. > Until then we can't do anything but go along with building these patched > library copies even though it isn't pretty. Uh, OK. I hope that=E2=80=99ll be resolved quickly because it=E2=80=99s re= ally unpleasant, notably for security reasons. > From 270b5a501c251e80a040342d4d39d4e236b90c97 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Wed, 11 Feb 2015 16:55:33 +0100 > Subject: [PATCH] gnu: Add bedops. > > * gnu/packages/bioinformatics.scm (bedops): New variable. [...] > + 'unpack 'unpack-tarballs > + (lambda _ > + ;; XXX Bedops includes tarballs of minimally patched upstream > + ;; libraries jansson, zlib, and bzip2. We cannot just use st= ock > + ;; libraries because at least one of the libraries (zlib) is > + ;; patched to add a C++ function definition (deflateInit2cpp). > + ;; Until the Bedops developers offer a way to link against sy= stem > + ;; libraries we have to build the in-tree copies of these thr= ee > + ;; libraries. Could you s/XXX/FIXME/ and add a link to the upstream discussion, if possible? > + (alist-delete 'check %standard-phases))))) Could you use #:tests? #f instead? I find it clearer. OK with these changes! Thanks, Ludo=E2=80=99.