From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id UIaWATB8eGHqLwEAgWs5BA (envelope-from ) for ; Wed, 27 Oct 2021 00:07:44 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id EAboOC98eGF7JAAAB5/wlQ (envelope-from ) for ; Tue, 26 Oct 2021 22:07:43 +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 7E5A815515 for ; Wed, 27 Oct 2021 00:07:43 +0200 (CEST) Received: from localhost ([::1]:45258 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mfUbe-0003dq-4e for larch@yhetil.org; Tue, 26 Oct 2021 18:07:42 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37734) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mfU8w-0005Xf-FT for guix-patches@gnu.org; Tue, 26 Oct 2021 17:38:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:36181) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mfU8w-0003B2-77 for guix-patches@gnu.org; Tue, 26 Oct 2021 17:38:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mfU8w-0007M0-51 for guix-patches@gnu.org; Tue, 26 Oct 2021 17:38:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#51422] [PATCH] gnu: Add r-phyloseq Resent-From: Nicolas Vallet Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Oct 2021 21:38:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 51422 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 51422@debbugs.gnu.org Cc: Nicolas Vallet X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.163528425328220 (code B ref -1); Tue, 26 Oct 2021 21:38:01 +0000 Received: (at submit) by debbugs.gnu.org; 26 Oct 2021 21:37:33 +0000 Received: from localhost ([127.0.0.1]:47727 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mfU8R-0007L5-U0 for submit@debbugs.gnu.org; Tue, 26 Oct 2021 17:37:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:37258) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mfTzJ-000738-GZ for submit@debbugs.gnu.org; Tue, 26 Oct 2021 17:28:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36134) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mfTzJ-0002YZ-B3 for guix-patches@gnu.org; Tue, 26 Oct 2021 17:28:05 -0400 Received: from mail-wr1-x42f.google.com ([2a00:1450:4864:20::42f]:44914) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mfTzH-0001oS-1G for guix-patches@gnu.org; Tue, 26 Oct 2021 17:28:05 -0400 Received: by mail-wr1-x42f.google.com with SMTP id d13so524973wrf.11 for ; Tue, 26 Oct 2021 14:28:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=wOFFY9YohQTxmwatc0+F0QxsvTctTn+Aui8juN0cG4I=; b=kVkHETczPgj/2xtHgYkyu8x9y2CDaV/z2wD/xnb4C6rlhgXOekzevGcgQ0skjc2ujM iVa2ZidEIrpst2ggDsYUUmUtmhXdw0Wb+Ao3pVhkG1VX4ZSpy3RCJM0Txc6WHBId4qBm eli32LgLvHegOxdUYi1LUgiswBfKX1ZkPNr58CrZ+mTGJBhY052yCu4bHdQ/mcnJlJ4Q PuWzTNuEQIYVd4aSdaTXumzNgQsu4RCINMB+bsk+zzcVXWlPA3CpHBR6dFQofiyglNOQ 3vbf1pssTdPxBcmdXkqZ8JM4ZkE+d1SxA719nL936CPSVLRyYOGeRUHFqlKc4DKvaffe fRxg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=wOFFY9YohQTxmwatc0+F0QxsvTctTn+Aui8juN0cG4I=; b=is/GVmtuv87LMhdUKfPBflgA14n4G1CcEsi4gImk3l2mCbPUGVomMuIut6VdeGzfqx /WBpDRE4izlxJFCeWa//Q0em8aubV2mk1fXatesYpudFo74EJ79mff6cZGg/ay1oOpYc s6ZgceWmv29p9BKKL3fxHQjj8aCaNx1JtUtz5yRZ7M9R8QMIr+D5ESl5bfhCKfp95MhI CkkVd0vbXvMpLi935RdE2pWmdg8iVHr6r+6VIe9eXLiTzAXM+QLQORyc+RnbnzQXqBGD 5gQI/adAuH8gIM4tILlTYE1zZWnyX5W5xys0Z8vpl5j//a/r/lgSIQ8qqtZTWjriOx4v KsIg== X-Gm-Message-State: AOAM532MroCQ1z1S2pQHenDxt/N4Z0F6ijNmDFAC8KvWPK+KJf3ILTc9 JWSZv7u6Rhcdkwugt/aY+2yeG2PqBuRCuAdk X-Google-Smtp-Source: ABdhPJyZC71ucfYmhVGIdyd3HZmj0rz2nRg1y0h3doD4S2tnP8+Fo6UqqJcCosBfO7xppKRRYXsRgg== X-Received: by 2002:a5d:4890:: with SMTP id g16mr28505590wrq.10.1635283680732; Tue, 26 Oct 2021 14:28:00 -0700 (PDT) Received: from localhost.localdomain (86.94.136.88.rev.sfr.net. [88.136.94.86]) by smtp.gmail.com with ESMTPSA id 13sm8425554wrz.38.2021.10.26.14.28.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 26 Oct 2021 14:28:00 -0700 (PDT) From: Nicolas Vallet Date: Tue, 26 Oct 2021 23:27:52 +0200 Message-Id: <20211026212752.21242-1-nls.vallet@gmail.com> X-Mailer: git-send-email 2.25.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::42f; envelope-from=nls.vallet@gmail.com; helo=mail-wr1-x42f.google.com X-Spam_score_int: 10 X-Spam_score: 1.0 X-Spam_bar: + X-Spam_report: (1.0 / 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, FUZZY_WALLET=3.099, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Tue, 26 Oct 2021 17:37:30 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Tue, 26 Oct 2021 18:07:26 -0400 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-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1635286063; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=wOFFY9YohQTxmwatc0+F0QxsvTctTn+Aui8juN0cG4I=; b=OsuiBzLA3DdLRlwLJM24Ym4p8Q2XD3y+1vox+nT1i1rdTUYecaXhsYd6af3UyQmLuPByAd gXQqPIgFOswqoIWPjlQKtMOclKpEwNM87chKYLLnxwDsyBfRV4I28W0xHC2JedpHG9WRJX 9Tfq/uzqUfBb1704rIt1vX2ICm8KD8LnXPFq/wzJHH1WVswoMklhq0m5qXU8u4EGVxr9bu 2wrzhRBVEd8PtFWISNxouxNK+5UQUS9Id5AA+9qkmFA+uOk1fBCu3HWKXroath0vqeaAgA TFGfqlYc2fsonrGtVr26wUVnWaR4Qpx8f2exiV6mJ0hzvmkMNw8G06sqITefdw== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1635286063; a=rsa-sha256; cv=none; b=tLONBGnI+LwyoBFhphX7kYaKiuQqU+FX/iN12d1iZdFbomIt4Ar/xkmmpETwcrw9UE838E h6+5KJjvPbbiA2tia65Qp8CrqmSgArEBX2xq0Ra9r9b+E5unB/ak/37AHnbvpUrQtxlGj3 rd0zUjhO8Y/5ABIrORDoiZS6nu7FZ9FGsV6iCZ4sAbQJxvW2/wWgQlmy2MEDTlLQoBKVLR 8/oA24bgiLaEaOJSiNJw/8XrKXnLE1eyivLTGKhgqUWRpjBU9sTJNqJ2dnLSalN35vAROI qjJM9mqVnPBhHZ/Ua2mQP1zsHMvUFNLsqLvkkEKzmkmUZ58hU44EDF7GCzMRrg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=kVkHETcz; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.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-Migadu-Spam-Score: 0.17 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=kVkHETcz; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.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-Migadu-Queue-Id: 7E5A815515 X-Spam-Score: 0.17 X-Migadu-Scanner: scn0.migadu.com X-TUID: ihyFP0BhQBCN From: Nicolas Vallet * gnu/packages/cran.scm (r-phyloseq): New variable --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..8dc875de69 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes +;;; Copyright © 2021 Nicolas Vallet ;;; ;;; This file is part of GNU Guix. ;;; @@ -14813,3 +14814,42 @@ and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.") (license license:gpl2))) + + +(define-public r-phyloseq + (package + (name "r-phyloseq") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "phyloseq" version)) + (sha256 + (base32 "192gv00xfnv9ljkgb0iw8sqzsay4f3vllyyc1slzsn15713fc4pi")))) + (properties `((upstream-name . "phyloseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-ape" ,r-ape) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomformat" ,r-biomformat) + ("r-biostrings" ,r-biostrings) + ("r-cluster" ,r-cluster) + ("r-data-table" ,r-data-table) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-multtest" ,r-multtest) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-vegan" ,r-vegan))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/joey711/phyloseq") + (synopsis "Handling and analysis of high-throughput microbiome census data") + (description + "Phyloseq provides a set of classes and +tools to facilitate the import, storage, analysis, +and graphical display of microbiome census data.") + (license license:agpl3+))) base-commit: c6adc0947396daa6d85ab08837f9cbc86f4d8722 -- 2.25.1