From patchwork Fri May 21 20:25:46 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29482 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 B2FF327BC81; Fri, 21 May 2021 21:31:29 +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 4207B27BC78 for ; Fri, 21 May 2021 21:31:29 +0100 (BST) Received: from localhost ([::1]:43408 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBns-0001mq-ED for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:31:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52440) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkc-0004Tp-W2 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54492) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkc-0002wy-Md for guix-patches@gnu.org; Fri, 21 May 2021 16:28:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkc-0000MY-JD for guix-patches@gnu.org; Fri, 21 May 2021 16:28:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 14/50] gnu: r-pcamethods: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:06 +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=B48575.16216288461020 (code B ref 48575); Fri, 21 May 2021 20:28:06 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:26 +0000 Received: from localhost ([127.0.0.1]:37723 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjx-0000GI-Tz for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:26 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:35343) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjL-00008i-AO for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:48 -0400 Received: by mail-wm1-f47.google.com with SMTP id z19-20020a7bc7d30000b029017521c1fb75so8082942wmk.0 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:47 -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=vXPEXl3f2GvJD5MJv8Gt6hn4aM1kFQlLGP3n9BTq2YQ=; b=Bag2t7SQKW/ntUUgXmXBuw0U3O3PiMg3Zc/gCwNRc2xYqq25JMYxLjEt7hjdIZ/onM mvh6Um+Esjyd/QVFA0L+ybXHQyqciTXFGJxq+8Xp9tpL6RREv0QCCfI+B0zB8SfyfqxX uCseFY/Nk9u4KYE/JsnKspQUXlwe5Gcqj7KOYuk8y7nGKE/ElNhbTyJUjtQ+wh262Z4Q GRa5pZKsHCmQAGTdLrmfBJXEWKcqcIHWQEfmzPHqCnk5Y3p/XCUJlI9BtmGdIoIbhRMp Lm8r4440F/XY922BsfDpCCZxLUvUcG1hh7ZfOjgBKOOJrGSTFRxUZr6LLTT2tMza6knO ntbw== 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=vXPEXl3f2GvJD5MJv8Gt6hn4aM1kFQlLGP3n9BTq2YQ=; b=DQwhuszpU8CH5QrDAWQMDBnX9t3NZ8nKscz5fCWIGaGKEIPP/JY6Q1yb+fbC7DDBaD GrrSNMJomEYNR3bExnsChQy+Z9w9ZDXDjFx6G6E7n/4shMOfnIPycjJioi0C5x6W3SSH xlFCGgY1bA0PbrVgvk+zEXS2mDwjcP3LJ/ZzhsOj+tJS0Eu9mgZIqGKzMMBP2qVB6npA PvWddI5Mn143H1vNO0gqxFfrkz9W3tWA608Ls5hFslxl3DtmD6xqnWqg+e9PqanhO0Uf XQLOpx2bH6jcAHndUp5y43bahy5MymyE86xW4/hcm77BSEwQWEmKNL/9aQZkT/KIdTx0 Yxtw== X-Gm-Message-State: AOAM530uP9a1gHSjTQb78E/WzEAccK0jPGec6bD8k2LLSeshrwDE7446 oFKwpZQZFJB070dvsf67GwvEW4FaPf0= X-Google-Smtp-Source: ABdhPJzjbxwzSSMVALYDHXvN+jHBZpqgEJaMF/IQDGWZcTmoNG5wEut50BvtWlbgFG7AVjTOJph7Ag== X-Received: by 2002:a1c:c90f:: with SMTP id f15mr10710828wmb.142.1621628801843; Fri, 21 May 2021 13:26:41 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:41 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:46 +0200 Message-Id: <20210521202622.26591-14-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-pcamethods): Move from here... * gnu/packages/bioconductor.scm (r-pcamethods): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 22b5a6068e..1533e5b8f9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2526,6 +2526,36 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-pcamethods + (package + (name "r-pcamethods") + (version "1.82.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pcaMethods" version)) + (sha256 + (base32 + "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) + (properties `((upstream-name . "pcaMethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") + (description + "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, +Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method +for missing value estimation is included for comparison. BPCA, PPCA and +NipalsPCA may be used to perform PCA on incomplete data as well as for +accurate missing value estimation. A set of methods for printing and plotting +the results is also provided. All PCA methods make use of the same data +structure (pcaRes) to provide a common interface to the PCA results.") + (license license:gpl3+))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87254a9058..a98f3d5d8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9053,36 +9053,6 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) -(define-public r-pcamethods - (package - (name "r-pcamethods") - (version "1.82.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "pcaMethods" version)) - (sha256 - (base32 - "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) - (properties `((upstream-name . "pcaMethods"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/hredestig/pcamethods") - (synopsis "Collection of PCA methods") - (description - "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, -Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method -for missing value estimation is included for comparison. BPCA, PPCA and -NipalsPCA may be used to perform PCA on incomplete data as well as for -accurate missing value estimation. A set of methods for printing and plotting -the results is also provided. All PCA methods make use of the same data -structure (pcaRes) to provide a common interface to the PCA results.") - (license license:gpl3+))) - (define-public r-aroma-light (package (name "r-aroma-light")