From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id 2FrwE5C8W1/eGwAA0tVLHw (envelope-from ) for ; Fri, 11 Sep 2020 18:06:08 +0000 Received: from aspmx2.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id sB1CDpC8W18DJwAAbx9fmQ (envelope-from ) for ; Fri, 11 Sep 2020 18:06:08 +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 aspmx2.migadu.com (Postfix) with ESMTPS id C6366680214 for ; Fri, 11 Sep 2020 18:06:07 +0000 (UTC) Received: from localhost ([::1]:33940 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kGnR0-0001DO-JY for larch@yhetil.org; Fri, 11 Sep 2020 14:06:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53420) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kGnQw-0001D9-KW for guix-patches@gnu.org; Fri, 11 Sep 2020 14:06:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:33834) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kGnQw-0005l3-BE for guix-patches@gnu.org; Fri, 11 Sep 2020 14:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kGnQw-0005F9-57 for guix-patches@gnu.org; Fri, 11 Sep 2020 14:06:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#43345] [PATCH 00/12] Move some CRAN packages to (gnu packages cran). 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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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -2.3 (--) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 Authentication-Results: aspmx2.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=WSuUP8z1; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx2.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 4.09 X-TUID: NMlHC5F5Pkfq 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