From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: [PATCH 2/3] gnu: Add python-pyxb. Date: Sat, 24 Sep 2016 10:23:10 +1000 Message-ID: <4cc91e33-1722-91e7-eda3-38b967fc1e73@uq.edu.au> 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> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40188) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bnakb-0003c7-2B for guix-devel@gnu.org; Fri, 23 Sep 2016 20:23:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bnakW-0008RI-TB for guix-devel@gnu.org; Fri, 23 Sep 2016 20:23:27 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:38825 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bnakW-0008O4-9e for guix-devel@gnu.org; Fri, 23 Sep 2016 20:23:24 -0400 In-Reply-To: <8737kqzk30.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 24/09/16 01:56, Marius Bakke wrote: > Ben Woodcroft writes: > >>>> Also, I notice that pysam bundles htslib, bcftools and samtools C code. >>>> Hopefully it should be straightforward enough to remove htslib as there >>>> are install instructions, I'm not sure about the other two. This >>>> shouldn't block the patch here, but would you mind taking a look? >>>> http://pysam.readthedocs.io/en/latest/installation.html#installation >>> I had a go at this, and also enabled tests since I was reading the build >>> system anyway. Samtools and bcftools does not seem possible to un-bundle >>> at this time, but htslib was straightforward. >> OK. I don't think it needs to be propagated though, right? Also, would >> you mind separating the change to modify-phases syntax and unbundling of >> htslib into two patches please? Other than that this whole series LGTM. > Modify-phases is now a separate patch. Thanks. > 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? ben