From patchwork Fri May 21 20:26:07 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29473 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 DB51227BC83; Fri, 21 May 2021 21:30:41 +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 F3F6A27BC81 for ; Fri, 21 May 2021 21:30:39 +0100 (BST) Received: from localhost ([::1]:40988 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBn5-0008RU-4j for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:30:39 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52572) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkk-00050q-QN for guix-patches@gnu.org; Fri, 21 May 2021 16:28:14 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54512) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkk-00031f-Hl for guix-patches@gnu.org; Fri, 21 May 2021 16:28:14 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkk-0000Ow-Dp for guix-patches@gnu.org; Fri, 21 May 2021 16:28:14 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 35/50] gnu: r-sva: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:14 +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=B48575.16216288541171 (code B ref 48575); Fri, 21 May 2021 20:28:14 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:34 +0000 Received: from localhost ([127.0.0.1]:37763 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk6-0000Ii-6o for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:34 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:44793) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjU-0000BG-I3 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:57 -0400 Received: by mail-wm1-f44.google.com with SMTP id y184-20020a1ce1c10000b02901769b409001so7810109wmg.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:56 -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=AxB0i+TeHMRnPIZO77vQwEsAWsixThXNCMxsZu1rb8U=; b=KafGRQZs6UPxGalxGaX01wjWo4pjP1feW0e/eBE3dnbgyF0j/gx/WNNplYthb/+Alb C/aJJi9s8baXHsG7tecYDpMKJh/1A1RW3+fl6uLetjKtTdpwwQMYekcN2TRO0QeEevJ8 mpVAebhIb1U0y/N8+5to2RBYiIUJS3TrzPlby2p3FuSqKmAQWKuHcfcd4xhredExSSDR dCuPB8M8bAya15QTuG1dKJTFkW9xPSmHEJELsflPwAG7OAZpAiLxMCk0uUFfGDeNHavz SciwJxQ5rB4gPcoC9C6rGx0H9SDUMrPlsji5JDegq5LOgs10HYX/Jj99xASI4fPGM7rJ uyMQ== 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=AxB0i+TeHMRnPIZO77vQwEsAWsixThXNCMxsZu1rb8U=; b=gllbbcX/aNA8TuguaqIgYGW4mQ2G+Vaqc0etksaghNSVLyyLnEOr3yhZgPITGJe/r8 ueezBAi6g8/X5RUL9dlmheCn/iTfpqFWYOkYkuNE9/KuPZEfIZ9Uso7U6ozQIetJylNO kXoJ9bsdhvZEUHB/K7OIPdx4094Ylh4k0nSpAY9kFXvpRn/mlZCzx9K4kbpzi9etXqEh Ecw1GdS++/2MU68kq5XLDtnaTC6GkT4zVDiOH+weZ3uzZNV9ouRT6OT7dDiJ65mOylS6 AmgsRHkR8Uopmctyp5zhV7Vw44Wo/GWKdxdV4nn8L7gRdhz6pgR8qNuTXAjsEDz5LMp+ hYkA== X-Gm-Message-State: AOAM530Sw/4D6Ls9HidICPEqHnOViWZYx73blqTK8D3VTp39fgIF3dKZ eBnvfk3cfLv/NDNU6mjzxEPIe2QUSxg= X-Google-Smtp-Source: ABdhPJzNUPIRIKeNQhrZORAbZ4x6nhJihsNnQiO0mgv2emfORsufyzi5tPl3zLJ/T9pS/Al/UZa6pg== X-Received: by 2002:a7b:c5cd:: with SMTP id n13mr10317859wmk.97.1621628810951; Fri, 21 May 2021 13:26:50 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.50 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:50 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:07 +0200 Message-Id: <20210521202622.26591-35-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-sva): Move from here... * gnu/packages/bioconductor.scm (r-sva): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a9365a4018..a7b1c63b56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3524,6 +3524,37 @@ typically represent genomic ranges of interest and the columns represent samples.") (license license:artistic2.0))) +(define-public r-sva + (package + (name "r-sva") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha256 + (base32 + "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) + (home-page "https://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description + "This package contains functions for removing batch effects and other +unwanted variation in high-throughput experiment. It also contains functions +for identifying and building surrogate variables for high-dimensional data +sets. Surrogate variables are covariates constructed directly from +high-dimensional data like gene expression/RNA sequencing/methylation/brain +imaging data that can be used in subsequent analyses to adjust for unknown, +unmodeled, or latent sources of noise.") + (license license:artistic2.0))) + (define-public r-systempiper (package (name "r-systempiper") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6120cb6804..2cc41b7e98 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8790,37 +8790,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) -(define-public r-sva - (package - (name "r-sva") - (version "3.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "sva" version)) - (sha256 - (base32 - "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) - (build-system r-build-system) - (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) - (home-page "https://bioconductor.org/packages/sva") - (synopsis "Surrogate variable analysis") - (description - "This package contains functions for removing batch effects and other -unwanted variation in high-throughput experiment. It also contains functions -for identifying and building surrogate variables for high-dimensional data -sets. Surrogate variables are covariates constructed directly from -high-dimensional data like gene expression/RNA sequencing/methylation/brain -imaging data that can be used in subsequent analyses to adjust for unknown, -unmodeled, or latent sources of noise.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2")