From patchwork Fri May 21 20:21:36 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 122 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 69BC127BC81; Fri, 21 May 2021 21:30:10 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E490C27BC78 for ; Fri, 21 May 2021 21:30:09 +0100 (BST) Received: from localhost ([::1]:39498 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBma-0007Pm-Fl for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:30:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51266) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBfi-0004L3-Bn for guix-patches@gnu.org; Fri, 21 May 2021 16:23:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54325) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBfi-0002GT-4M for guix-patches@gnu.org; Fri, 21 May 2021 16:23:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBfh-0008US-S5; Fri, 21 May 2021 16:23:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:23:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun , Ricardo Wurmus X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by submit@debbugs.gnu.org id=B.162162852232561 (code B ref -1); Fri, 21 May 2021 20:23:01 +0000 Received: (at submit) by debbugs.gnu.org; 21 May 2021 20:22:02 +0000 Received: from localhost ([127.0.0.1]:37637 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBek-0008T6-3C for submit@debbugs.gnu.org; Fri, 21 May 2021 16:22:02 -0400 Received: from lists.gnu.org ([209.51.188.17]:36502) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBee-0008Se-Pk for submit@debbugs.gnu.org; Fri, 21 May 2021 16:22:00 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:51080) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBee-0002n8-K5 for guix-patches@gnu.org; Fri, 21 May 2021 16:21:56 -0400 Received: from mail-wm1-x332.google.com ([2a00:1450:4864:20::332]:53114) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBeZ-00021S-9Z for guix-patches@gnu.org; Fri, 21 May 2021 16:21:56 -0400 Received: by mail-wm1-x332.google.com with SMTP id z130so11749474wmg.2 for ; Fri, 21 May 2021 13:21:50 -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=ynWUtDLp3YTo3cs0Bau+BpzrlQkquNF+iWM9/0+w5N4=; b=ctN2zlcyUxRKw9/4oLC/aGFPAuNn+PfU61MqN7czG5qc7Et2bCbnehJuGRVTSosHjt JBJWpPeDV8NyAxyp/BAN+Xfhj+/AYp8rMY5oZDsHnwY0077S+IJqBNGnauQ+GCO3XTAI 0Zw6I759C6FQDPudn8XZaVwdTeYWL0apGLVX/LDKkVJrUSHySzaniZSdkyiVxhvVLDLD MwVnDphwJsdv04bbG2OMPOzgDfOjluBk+02ktH3XGHN9yOcYgJLVdq532kFZMHiq2HUD n6ZRtR1Hv4ZJBQC60n1/l2MVtRDgm5D6YHfOCBkgBjxERv1NOMPoJwlPuXf1BbNitshr 654A== 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=ynWUtDLp3YTo3cs0Bau+BpzrlQkquNF+iWM9/0+w5N4=; b=Qy+OcNC1V/C24NGMvW6b+98RV3FTmWMUC6Il2n+z2qdglZXsaY96JnWzo2Lh+YgDsl doS4p503wDuTq51SnPgiBiuM0TRef1/eoimEM3f4gypG/P2mBb0jz3rjW6VZ2TLe1DCb OhB/+ceUM5jKSElAI7XNFqL2bmbF2H5NGeDKXH41w8P7AEa/E2YDUrrUvxxU/7fluiIh 1SjXygNwRsdGApvVOMremro0dTApaCUdKjRuVMS1xJjWDuzbb8LTnQmVPyPOPVSGq+WZ v6bCKQAe4F0vdrFRj5988XCuShqFp7fK+b+pTP2pt4Ci92gXYQbcaY+8JsQEu8AuYSOu nVDg== X-Gm-Message-State: AOAM530a++9v571GTPX0zD/94ht30RnVc4/hP80XmUgkbqiaYfLqhsL7 SIqWe5lwNRCG6e0Qw1iRNLqcq+ChbAA= X-Google-Smtp-Source: ABdhPJykwCsHXSQATky+WUoDIHnFsCT1pf6yXs1R2WnGSxRoyRvOqGi8xRyJ21XfEns2NWboMJYDLA== X-Received: by 2002:a1c:5544:: with SMTP id j65mr10436699wmb.174.1621628509681; Fri, 21 May 2021 13:21:49 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id g10sm3227493wrq.12.2021.05.21.13.21.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:21:49 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:21:36 +0200 Message-Id: <20210521202136.26524-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 X-Debbug-CC: Ricardo Wurmus Received-SPF: pass client-ip=2a00:1450:4864:20::332; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x332.google.com 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: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches Hi, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- I did my best to preserve the copyright. But I do not guarantee it is error-free. Well, in doubt, I have been conservative. Then, I do: guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check To avoid a break, I check with: for ci in $(git log --format="%H" -51 --reverse); do ./pre-inst-env guix pull --commit=$ci \ -p /tmp/test-${ci} \ --url=$(pwd) --branch=janitor --disable-authentication done and everyting seems fine. At least, "guix pull" should be checked at the end of the series. Last, I have checked the imported modules in gnu/packages/bioinformatics.scm. All should be fine. Now, I get: --8<---------------cut here---------------start------------->8--- $ ag 'bioconductor' gnu/packages/bioinformatics.scm 69: #:use-module (gnu packages bioconductor) 11550: (synopsis "Extra base functions for Bioconductor") 11553:provided by Bioconductor packages.") --8<---------------cut here---------------end--------------->8--- which ends the move, I guess. Except the package r-rcurl in gnu/packages/statistics.scm, let as an exercise for the reader. ;-) On a side note about the Copyright lines, I did: git blame --date=format:"%Y)" gnu/packages/bioinformatics.scm \ | cut -d')' -f1 | cut -d'(' -f2 | sed 's/ //g' \ | sort | uniq -c and it is possible that there is some "mistake", FWIW. All the best, simon zimoun (50): gnu: r-genomicalignments: Move to (gnu packages bioconductor). gnu: r-rtracklayer: Move to (gnu packages bioconductor). gnu: r-genomicfeatures: Move to (gnu packages bioconductor). gnu: r-topgo: Move to (gnu packages bioconductor). gnu: r-bsgenome: Move to (gnu packages bioconductor). gnu: r-msnid: Move to (gnu packages bioconductor). gnu: r-msnbase: Move to (gnu packages bioconductor). gnu: r-samr: Move to (gnu packages bioconductor). gnu: r-impute: Move to (gnu packages bioconductor). gnu: r-seqpattern: Move to (gnu packages bioconductor). gnu: r-go-db: Move to (gnu packages bioconductor). gnu: r-genomation: Move to (gnu packages bioconductor). gnu: r-genomationdata: Move to (gnu packages bioconductor). gnu: r-pcamethods: Move to (gnu packages bioconductor). gnu: r-mzid: Move to (gnu packages bioconductor). gnu: r-aroma-light: Move to (gnu packages bioconductor). gnu: r-deseq: Move to (gnu packages bioconductor). gnu: r-edaseq: Move to (gnu packages bioconductor). gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). gnu: r-annotationhub: Move to (gnu packages bioconductor). gnu: r-fastseg: Move to (gnu packages bioconductor). gnu: r-affy: Move to (gnu packages bioconductor). gnu: r-keggrest: Move to (gnu packages bioconductor). gnu: r-gage: Move to (gnu packages bioconductor). gnu: r-complexheatmap: Move to (gnu packages bioconductor). gnu: r-genomicfiles: Move to (gnu packages bioconductor). gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). gnu: r-organismdbi: Move to (gnu packages bioconductor). gnu: r-affyio: Move to (gnu packages bioconductor). gnu: r-vsn: Move to (gnu packages bioconductor). gnu: r-biovizbase: Move to (gnu packages bioconductor). gnu: r-ensembldb: Move to (gnu packages bioconductor). gnu: r-mzr: Move to (gnu packages bioconductor). gnu: r-protgenerics: Move to (gnu packages bioconductor). gnu: r-sva: Move to (gnu packages bioconductor). gnu: r-motifrg: Move to (gnu packages bioconductor). gnu: r-seqlogo: Move to (gnu packages bioconductor). gnu: r-zlibbioc: Move to (gnu packages bioconductor). gnu: r-rhtslib: Move to (gnu packages bioconductor). gnu: r-bamsignals: Move to (gnu packages bioconductor). gnu: r-rcas: Move to (gnu packages bioconductor). gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). gnu: r-tximport: Move to (gnu packages bioconductor). gnu: r-rhdf5filters: Move to (gnu packages bioconductor). gnu: r-annotationfilter: Move to (gnu packages bioconductor). gnu: r-rhdf5: Move to (gnu packages bioconductor). gnu: r-chipseq: Move to (gnu packages bioconductor). gnu: r-copyhelper: Move to (gnu packages bioconductor). gnu: r-copywriter: Move to (gnu packages bioconductor). gnu: r-methylkit: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 1826 +++++++++++++++++++++++++++++-- gnu/packages/bioinformatics.scm | 1645 ---------------------------- gnu/packages/cran.scm | 30 - 3 files changed, 1749 insertions(+), 1752 deletions(-) base-commit: bd382fae71d899e243e81688bf5baed26171f2ea