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 GPHxE3Z4sl/xGgAA0tVLHw (envelope-from ) for ; Mon, 16 Nov 2020 13:02:46 +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 yCngD3Z4sl99RgAA1q6Kng (envelope-from ) for ; Mon, 16 Nov 2020 13:02:46 +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 17AA59402C8 for ; Mon, 16 Nov 2020 13:02:46 +0000 (UTC) Received: from localhost ([::1]:40790 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kee9d-0008K8-0T for larch@yhetil.org; Mon, 16 Nov 2020 08:02:45 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:38134) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kee9Q-0008Hi-Tw for guix-devel@gnu.org; Mon, 16 Nov 2020 08:02:32 -0500 Received: from mail-wr1-x436.google.com ([2a00:1450:4864:20::436]:35688) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kee9P-0008CB-3o; Mon, 16 Nov 2020 08:02:32 -0500 Received: by mail-wr1-x436.google.com with SMTP id k2so18643115wrx.2; Mon, 16 Nov 2020 05:02:30 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:in-reply-to:references:date:message-id:mime-version; bh=ZpgEkLFahLk38dQqcpGKm7yrQ+75Ieh1zGBnrc0tEVU=; b=pPJxlRCbA2ErtpyewbIFY3IOLphouJbYnAoKiAMGwIpMr3jEWLLEhoV3GfT+2uDR3c HlwoEPokPHypWpQDPOe5Yc/kmWc0lZBwQbAY2/9nXjTtYnFfmaqP4jzMB9qjUYhf5dBi cg67nJqj7GNWz58QrTA3g75YvCxq1rvplHva05witSvm0kDpeHkQBrX4bkz2e5HJhpLD zf8GLTCnepg7hx75NQTKFrpOd9PrAbHi6MdG1TMYt7TdCcj3Cp5VxNOIFS4ESKDso40c LZw92qAVeWfjUzRQYpntsaK3AiadsAshpOrLQGWxv0n+foZGw7sC97/ntj0fYwTAgH33 VmdA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:in-reply-to:references:date :message-id:mime-version; bh=ZpgEkLFahLk38dQqcpGKm7yrQ+75Ieh1zGBnrc0tEVU=; b=hgkbwf4yn9BzYG/Hz6jQkNwvC5zQM2wMysSzZPHcea4vGehxC9X7pdFkKu/o3tf7Jd MD+nLApzpS4pQWDnedc7A2Qfh7AAMxUhrH6UC/Hx+Dl9x+zcmqAjOnbE8Bcu8cr9gAk+ thKxepDps594HaUuktH6xnQC4ZU6q2ncMc+rxplujbKC3a2QHum1f17LWvd2lv8oD1q8 hahMI0ECR061TYBJudD4wgmZ6+LS2OIX/VYzkmwdg7MaXIuCzdNbKHc/6hi2VO8XGYzi jF4o2frsaMuvrhT0FAxU3TvmiMAORNc0YOOZJhHtTjrfMWYAMMlsD59ZFZMXxxNRS7nT ZIvw== X-Gm-Message-State: AOAM530jb8LF2ogCm1PG+FBDGzxHi53NaU42SUCftbtSE26BJ2YK5P9k 4Me8EPMcmtf8tp1QbZ8mU3+iC3zVSPK+OQ== X-Google-Smtp-Source: ABdhPJzvYiQtwDxwYart7MGHZeVCJC8jICsF9KnlY3yzdHDHE5tGrZhRWRdsbDEUas4Oo2vAKL58qQ== X-Received: by 2002:adf:ea03:: with SMTP id q3mr18220753wrm.141.1605531748873; Mon, 16 Nov 2020 05:02:28 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id i5sm24633413wrw.45.2020.11.16.05.02.28 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 16 Nov 2020 05:02:28 -0800 (PST) From: zimoun To: Roel Janssen , guix-devel@gnu.org Subject: Re: Updating to latest Bioconductor release In-Reply-To: <5b6c661babc4fbda5cda5c72a654e79b14b0bf67.camel@gnu.org> References: <865z65tud5.fsf@gmail.com> <5bfaf0d22d0a4e9bd8b8d72edad6a3e0676e4989.camel@gnu.org> <86k0ulscwv.fsf@gmail.com> <5b6c661babc4fbda5cda5c72a654e79b14b0bf67.camel@gnu.org> Date: Mon, 16 Nov 2020 13:59:25 +0100 Message-ID: <86eektsbiq.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2a00:1450:4864:20::436; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x436.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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=pass header.d=gmail.com header.s=20161025 header.b=pPJxlRCb; dmarc=pass (policy=none) header.from=gmail.com; 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: -1.71 X-TUID: WWrI1bR4TfYu Hi again, :-) On Mon, 16 Nov 2020 at 13:38, Roel Janssen wrote: > 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 Do you mean related to #39885? > 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? Ok. > 4. Add the bits for 'workflow' packages. > 5. Add workflow packages / adjust the ones we have (do we have any?) > and build/test them. I do not think we have any. But I have not checked everything neither. :-) All the best, simon