From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH 2/3] gnu: Add python-pyxb. Date: Tue, 27 Sep 2016 21:01:15 +1000 Message-ID: References: <20160917101047.4597-1-mbakke@fastmail.com> <20160917101047.4597-3-mbakke@fastmail.com> <3bd16b58-b3d1-d47c-2433-c3a721681463@uq.edu.au> <39d81c47-a96d-1f1c-ad1d-a80e7b7f109d@uq.edu.au> <1a9d61d6-0ee2-1161-25b4-9ffd32396039@uq.edu.au> <87h999ymzk.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> <679cc096-9eed-152f-0a01-f4a1d85c422e@uq.edu.au> <87eg4cyni4.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> <03badac9-3d2d-25ad-b0ed-3695d8a70bc7@uq.edu.au> <8737kqzk30.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> <4cc91e33-1722-91e7-eda3-38b967fc1e73@uq.edu.au> <87vaxmxa2z.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> <8760pio6l8.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> Mime-Version: 1.0 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37299) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1boq8l-0008N8-Dp for guix-devel@gnu.org; Tue, 27 Sep 2016 07:01:36 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1boq8h-0006R9-Kj for guix-devel@gnu.org; Tue, 27 Sep 2016 07:01:35 -0400 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:33952 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1boq8h-0006PV-2P for guix-devel@gnu.org; Tue, 27 Sep 2016 07:01:31 -0400 In-Reply-To: <8760pio6l8.fsf@ike.i-did-not-set--mail-host-address--so-tickle-me> 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" To: Marius Bakke , "guix-devel@gnu.org" On 27/09/16 04:32, Marius Bakke wrote: > Ben Woodcroft writes: > >> On 24/09/16 13:15, Marius Bakke wrote: >>> Ben Woodcroft writes: >>> >>>>> Htslib is propagated because it >>>>> is included by the installed samtools and bcftools headers; at least one >>>>> of pysams dependencies failed to build when it was a regular input. >>>> Ah, I see. Can this be avoided with patchelf? >>> I don't think so. The htslib headers need to be propagated for anything >>> that uses header files from pysam, since they contain contain code such >>> as "include ". Perhaps you can update the comment to make >>> it more clear? >>> >>> Patchelf is probably what made that work when htslib was bundled. >> Ah, ok I see, so the problem is that python-plastid requires the .h >> files during build. Given that this is the only package that has an >> issue, and perhaps pysam doesn't intend to provide these .h files as >> part of it's "interface", I think it might be best to simply put htslib >> as an input to python-plastid. > I'm not sure, we would have to do this with every package that uses > the pysam cython interface. Ah, you're right. I overlooked the cython interface. I pushed the series propagating htslib with pysam, ending in 99caa6f. Thanks for persevering. ben