From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id iB2SGN5ysl/cZwAA0tVLHw (envelope-from ) for ; Mon, 16 Nov 2020 12:38:54 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id kNFwFN5ysl/PMQAA1q6Kng (envelope-from ) for ; Mon, 16 Nov 2020 12:38:54 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 734B6940416 for ; Mon, 16 Nov 2020 12:38:48 +0000 (UTC) Received: from localhost ([::1]:53722 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kedmR-0005vs-Fz for larch@yhetil.org; Mon, 16 Nov 2020 07:38:47 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:32966) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kedlo-0005vm-M8 for guix-devel@gnu.org; Mon, 16 Nov 2020 07:38:08 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:33041) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kedlo-0007yJ-D9; Mon, 16 Nov 2020 07:38:08 -0500 Received: from 2001-1c02-0b2a-aa00-93bf-7c8c-0fae-b738.cable.dynamic.v6.ziggo.nl ([2001:1c02:b2a:aa00:93bf:7c8c:fae:b738]:43126) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kedln-0001x5-5B; Mon, 16 Nov 2020 07:38:07 -0500 Message-ID: <5b6c661babc4fbda5cda5c72a654e79b14b0bf67.camel@gnu.org> Subject: Re: Updating to latest Bioconductor release From: Roel Janssen To: zimoun , guix-devel@gnu.org Date: Mon, 16 Nov 2020 13:38:01 +0100 In-Reply-To: <86k0ulscwv.fsf@gmail.com> References: <865z65tud5.fsf@gmail.com> <5bfaf0d22d0a4e9bd8b8d72edad6a3e0676e4989.camel@gnu.org> <86k0ulscwv.fsf@gmail.com> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.23 Precedence: list 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+larch=yhetil.org@gnu.org Sender: "Guix-devel" X-Scanner: ns3122888.ip-94-23-21.eu Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-devel-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-devel-bounces@gnu.org X-Spam-Score: -1.51 X-TUID: kDGlXDjHM7YF Hi Simon, On Mon, 2020-11-16 at 13:29 +0100, zimoun wrote: > Hi Roel, > > On Mon, 16 Nov 2020 at 13:10, Roel Janssen wrote: > > > Hehe. I'm building all R packages in the "wip-r" branch now to see > > what's left for me to fix. > > Cool!  I do not know if Ricardo fetched my branch to update ’wip-r’ > because an error about a missing symbol was there and then I > corrected > it in my branch.  Anyway. > > BTW, I would like to add the type ’workflow’ in addition to > ’annotation’ > and ’experiment’.  Because I need: > > > > > Well, I do not know if that should go to ’wip-r’ or directly to > ’master’.  WDYT? Well, I see we're getting R packages that fail to build because the source cannot be downloaded (anymore), due to the outdated Bioconductor version. So if we can do an upgrade to 3.12 soon, and add the 'workflow' type later, that'd be my preferred route. So to achieve that, I think we need to: 1. Update the Bioconductor version to 3.12 2. Update/build the Bioconductor packages that are already in Guix. 3. --> When all build failures have been resolved, push to master? 4. Add the bits for 'workflow' packages. 5. Add workflow packages / adjust the ones we have (do we have any?) and build/test them. 6. --> Push to master? WDYT? Kind regards, Roel Janssen