From debbugs-submit-bounces@debbugs.gnu.org Fri Sep 11 14:05:49 2020 Received: (at submit) by debbugs.gnu.org; 11 Sep 2020 18:05:49 +0000 Received: from localhost ([127.0.0.1]:45380 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kGnQj-0005EV-AK for submit@debbugs.gnu.org; Fri, 11 Sep 2020 14:05:49 -0400 Received: from lists.gnu.org ([209.51.188.17]:56820) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kGnQf-0005EM-IC for submit@debbugs.gnu.org; Fri, 11 Sep 2020 14:05:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53344) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kGnQf-00017c-DT for guix-patches@gnu.org; Fri, 11 Sep 2020 14:05:45 -0400 Received: from mail-wm1-x32a.google.com ([2a00:1450:4864:20::32a]:34148) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kGnQd-0005gq-CD for guix-patches@gnu.org; Fri, 11 Sep 2020 14:05:45 -0400 Received: by mail-wm1-x32a.google.com with SMTP id l15so1593013wmh.1 for ; Fri, 11 Sep 2020 11:05:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Qz/cjGPvBPASZsMRyZ50WMYORQqp5eI7wWEz3Uno5tc=; b=WSuUP8z1LkABejQml8EZ3ivQ3/StKlsoy5fptffxDpl6HIelGWDQOcD58NqFmnuRyc 0dqvOqee16URdsW9cxD73RysSEdC8C0YfanQjYhgqj2qFbkWMYsqtWL/Cz8bLiDeSlFo b0kbry3XSQRU32meuEEn5tw2hl6B8j4XyLHqkRnl6IcGgtxtEXqX/l8c2NKgcPzQyzAz /w4G3kfu0JfzwbXFjj1u1rYU5r80w2FNzvM++xgdIE+hrMSjOB0VkimKOZUsGyFF8Y0Q SzJhdntmBt5zqWY3troYpy0eaYLvECYr63xceAntz2Hphc1Iw2pmn0sd5sHS02iTQotY UGgA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Qz/cjGPvBPASZsMRyZ50WMYORQqp5eI7wWEz3Uno5tc=; b=tchDMU+r6LMfHb6OCJ/a1eM8krI46d/TKIW+Q1jkQmk2urCBrzcWYhb3JO91oeQW/F tD5zxa4u00B/3TBTC62WyUKtiF53huSLXyRfgydSOYYXyHzlV4a6ApXchi3K3fO1e2yU EV98D5OOqexDQ07/4pgf68S49Ur1j5N10OjgaQpqitH8MUm7DuaQ+4QN2kGONkY67eLY wWbA4CDZFGoy+2rLKNM+zUu2S5BTQL0PTezHGK0VAV8MUqZZLu/f6BYu2Hq2r/6/BILL 3cT7xTKTugDx3sqQ/4aAKp9/hHvPchwlpKtz9ZP1XAig4bVEh2slHyjW8J42Wsuj/BPU 5Iyg== X-Gm-Message-State: AOAM532uv3v1YtQdXERxWirdd4x9BzuDLMwbzNe54+Yq/hBJhoOCHT7L Oyws5O3y6I3uToeXDGNK7nG2JWvFQx0= X-Google-Smtp-Source: ABdhPJwjaFnfAYd0jIgCaeXdBsSArri7bJcGSyLnzOX6hLxVBn7uCN6IHwoLLLk/UdbOOl0L1wng6Q== X-Received: by 2002:a1c:ba0b:: with SMTP id k11mr3349483wmf.20.1599847538581; Fri, 11 Sep 2020 11:05:38 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id i3sm5922068wrs.4.2020.09.11.11.05.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 11 Sep 2020 11:05:38 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/12] Move some CRAN packages to (gnu packages cran). Date: Fri, 11 Sep 2020 20:05:27 +0200 Message-Id: <20200911180527.11253-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::32a; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32a.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-Spam-Score: 0.7 (/) X-Debbugs-Envelope-To: submit Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Dear, Some clean up leading the recent discussion [1]. Now, the only remaining 'cran-uri' are from (gnu packages statistics). Modulo maybe some packages using "bad" uri, e.g., from r-qtl: --8<---------------cut here---------------start------------->8--- (uri (string-append "mirror://cran/src/contrib/qtl_" version ".tar.gz")) --8<---------------cut here---------------end--------------->8--- To ease the Copyright transfer between files, I used: git log --grep= git log --date=format:"%Y" --format="%ad %an" \ -- gnu/packages/.scm | sort | uniq -c After each move, I run: make ./pre-env-inst guix build ./pre-env-inst guix build --no-grafts --check to check that everything is fine. And at the end of all the move, I run: make as-derivation to verify that "guix pull" is not broken by something. (Well, I failed to use the regular ./pre-env-inst guix pull --branch=my-stuff --url=$PWD -p /tmp/new because of the "new" authentication, another story.) Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove 1 or 2 #:use-module (gnu packages ) from gnu/packages/bioinformatics.scm. [1] https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html All the best, simon zimoun (12): gnu: r-codedepends: Comment why is in bioconductor.scm. gnu: r-adaptivesparsity: Move to (gnu packages cran). gnu: r-diffusionmap: Move to (gnu packages cran). gnu: r-igraph: Move to (gnu packages cran). gnu: r-qtl: Move to (gnu packages cran). gnu: r-qtl2: Move to (gnu packages cran). gnu: r-seqminer: Move to (gnu packages cran). gnu: r-maldiquant: Move to (gnu packages cran). gnu: r-seurat: Move to (gnu packages cran). gnu: r-phangorn: Move to (gnu packages cran). gnu: r-diversitree: Move to (gnu packages cran). gnu: r-absfiltergsea: Move to (gnu packages cran). gnu/packages/bioconductor.scm | 1 + gnu/packages/bioinformatics.scm | 250 --------------------- gnu/packages/cran.scm | 346 ++++++++++++++++++++++++++++++ gnu/packages/graph.scm | 57 ----- gnu/packages/machine-learning.scm | 35 --- 5 files changed, 347 insertions(+), 342 deletions(-) base-commit: 24e37fbbc4d7a5a4792c57f97f1f280d3ed36e01 -- 2.28.0