From patchwork Fri May 21 20:25:59 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29493 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 0DC8C27BC81; Fri, 21 May 2021 21:33:05 +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 93CFA27BC78 for ; Fri, 21 May 2021 21:33:04 +0100 (BST) Received: from localhost ([::1]:46098 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBpP-0003iw-Qk for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:33:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52540) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBki-0004nM-18 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:12 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54505) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkh-00030F-Oc for guix-patches@gnu.org; Fri, 21 May 2021 16:28:11 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkh-0000O6-LR for guix-patches@gnu.org; Fri, 21 May 2021 16:28:11 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 27/50] gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:11 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288511119 (code B ref 48575); Fri, 21 May 2021 20:28:11 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:31 +0000 Received: from localhost ([127.0.0.1]:37749 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk3-0000Ht-AE for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:31 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:33296) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjR-0000AJ-1X for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:53 -0400 Received: by mail-wr1-f51.google.com with SMTP id n2so22297933wrm.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:52 -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:in-reply-to:references :mime-version:content-transfer-encoding; bh=+/ohMXZD/XpdR6XwB+BhQJ/VD0IyC0iZqMenxEi1DYI=; b=HTKL7r8EVRER4YCQui4zIFYNGNX4PIRBOLCw+4+vtlWXrGv494IZj1wnzMfktXKSI/ dgVLviLCbGwt02E1hcuAtZ8jHPDSEllWi7rxIfvfcC9JX9d+LKyV1EEd9fy6gAqfnJ3U L0I/uLEjNnYcvbWcCM8rZwq9RDylMQhQpbFICDJl8Pg/uP7dlm4yW6PGt6CaeP7EXxL1 24qGLRZgzOR/9dJ4R9KHXIwmy5gimCd9gZuvOwwmXgun+JGKMD/nleTuXNyRnrl9e2Ux 4lJE7UMeZOyqOiFqMypUWz5y0gPd0aY8tsR1ckUjwUHQ+J7mlhI1Wuiff8Gz0XiaSezh SwEg== 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:in-reply-to :references:mime-version:content-transfer-encoding; bh=+/ohMXZD/XpdR6XwB+BhQJ/VD0IyC0iZqMenxEi1DYI=; b=ZTbrvnmxCI3Ke+Ls9z6xmovKpdkVkCoT8NslMtR8Rv/5b0leMGQIaEwvq4qVRtZ3EK HLHjf0lblDSlmrMd+pSVzWcufQwadw/CEAeguO4TjYj1YQ39JPkVPrxDLKV6qFHwXREy tfmxb1OjP7l/C/bln03ScbkWOBnElR+XzLU48qZSd7czibgjTUQb5LGD1tZWZxKVPESN c/+7CSyZRL4CYdTIgk/u4dE6MxT4XOHKvZ23qeNqoNmmtFPTzVb3V3fQrVkAys9Hes76 OYE/4UaNw8gD2PYcANAKmrLLHfPDcsG8+RUkBei5z+cxtJ8sKsC/KjLM7q0bMbyId4YY 2YCQ== X-Gm-Message-State: AOAM533Ef/62MUI91A2kQarrND1btC2fozP2c0tRD3er9Pukyul/tUQE qu5NEmjEddrtaLLVffQChHhDpmxZrk0= X-Google-Smtp-Source: ABdhPJwdFF2uIsct0widK3fA+DsZgAO1KJN6zMC0p4EnbkzRs+Crla66G0s+dNDBnL6Zd3OjxR3cSg== X-Received: by 2002:adf:fc91:: with SMTP id g17mr11360709wrr.191.1621628807491; Fri, 21 May 2021 13:26:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:47 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:59 +0200 Message-Id: <20210521202622.26591-27-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here... * gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e73e78f616..7717c821b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2235,6 +2235,35 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-dirichletmultinomial + (package + (name "r-dirichletmultinomial") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DirichletMultinomial" version)) + (sha256 + (base32 + "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) + (properties + `((upstream-name . "DirichletMultinomial"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/DirichletMultinomial") + (synopsis "Dirichlet-Multinomial mixture models for microbiome data") + (description + "Dirichlet-multinomial mixture models can be used to describe variability +in microbial metagenomic data. This package is an interface to code +originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): +1-15.") + (license license:lgpl3))) + (define-public r-edaseq (package (name "r-edaseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4836eee82c..0c7b3d602f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8994,35 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-dirichletmultinomial - (package - (name "r-dirichletmultinomial") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DirichletMultinomial" version)) - (sha256 - (base32 - "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) - (properties - `((upstream-name . "DirichletMultinomial"))) - (build-system r-build-system) - (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/DirichletMultinomial") - (synopsis "Dirichlet-Multinomial mixture models for microbiome data") - (description - "Dirichlet-multinomial mixture models can be used to describe variability -in microbial metagenomic data. This package is an interface to code -originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): -1-15.") - (license license:lgpl3))) - (define-public r-ensembldb (package (name "r-ensembldb")