From patchwork Fri May 21 20:26:02 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29495 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 AC7BF27BC81; Fri, 21 May 2021 21:33:26 +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 36C8227BC78 for ; Fri, 21 May 2021 21:33:26 +0100 (BST) Received: from localhost ([::1]:46564 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBpl-00042t-EU for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:33:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52548) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBki-0004rK-RI for guix-patches@gnu.org; Fri, 21 May 2021 16:28:12 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54507) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBki-00030e-Jl for guix-patches@gnu.org; Fri, 21 May 2021 16:28:12 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBki-0000OL-G5 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:12 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 30/50] gnu: r-vsn: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:12 +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=B48575.16216288521134 (code B ref 48575); Fri, 21 May 2021 20:28:12 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:32 +0000 Received: from localhost ([127.0.0.1]:37753 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk4-0000I8-2v for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:32 -0400 Received: from mail-wr1-f46.google.com ([209.85.221.46]:39709) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjS-0000An-DZ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:54 -0400 Received: by mail-wr1-f46.google.com with SMTP id v12so22200522wrq.6 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:54 -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=kE+FzhGHJKFbog33VGG5pEwrPhxNRKKdEb1FwbBz0Co=; b=FJXahakvG8Ko9RyhAByK0AA+oDo5Rm9Pvpxis0KZ1jGPOn8pSSYXz0YF38DLTpcWk8 80mO8glAqj4Vu+5JGOVBfPBMbSLBYqKaQrvbnTlI+kk8XNk/OddPIZzRqIU1noFua8CC KYQl+atfrx1axHD2VIVab6hB7cgxVjW7qQ7QybuFszeXZArqNS9rcdohYvVsZI4SJfT6 8DF7Z9emAnXtGtuOcbloycaSD0TUvugwPi2tJgkysZEFd/EtMtAs27IJ+PIXF0Z7Vp41 ZmXzJAGJBHMWJmq7ItZ0ssHhzOrSpiKG3UeWgGMJE2Gi/mQLyn5Svsr5qz9TGzaK9ozY 6D9w== 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=kE+FzhGHJKFbog33VGG5pEwrPhxNRKKdEb1FwbBz0Co=; b=DYyw7xe70YhoQUqRctZryGxCC4V1tSjrncG5k836RNvhUA9HRJfzbM3jV2vaap0mBM f3n/JwoTOzAzqERlg6hXstIWVLcxyQJpz6XQMm5kgTVP8Mu35l4cxukAOB13oBM286qh pxJsaVnOpmVfePVI4qMbL89ve9QLUsyVF6dtGOKTlZuS3qdIgfG7bSW8ad50zGTRaiuT j8Hzaf5p3PjMCAhq6VNLmBQiPILrTXgm1zr2w0rpXrIPYPPfSaJuOmrzyXVMjXuSuwH9 8QEYIxkvgAX9IttR6IQ3mwF/oQ1kuVnbNYUibfEY+DM7RVjNuP/dyK1vdqtLitBM0bn/ 7R+w== X-Gm-Message-State: AOAM533u5HvJfYhFZUn/o6g3Lyq0iIfqHyHMX06LOMZrtP+KMg6MItmt SomD0klhY7F2A4TYc6IFepoaD8infec= X-Google-Smtp-Source: ABdhPJwzJXlZKED7bY0Ec6/SOv7wrb32r6o/pA6mVEd+O4XLwaiq/WWncftRDN7ViengscFfFefofQ== X-Received: by 2002:adf:cd0b:: with SMTP id w11mr10828714wrm.178.1621628808817; Fri, 21 May 2021 13:26:48 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:48 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:02 +0200 Message-Id: <20210521202622.26591-30-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-vsn): Move from here... * gnu/packages/bioconductor.scm (r-vsn): ...to here. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 --------------------------------- 2 files changed, 36 insertions(+), 36 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d0ebcf8481..05c4896276 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3480,6 +3480,42 @@ dependencies between GO terms can be implemented and applied.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn + (package + (name "r-vsn") + (version "3.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +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-xvector (package (name "r-xvector") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7256df3f83..600c2ca81e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8934,42 +8934,6 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-vsn - (package - (name "r-vsn") - (version "3.58.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "vsn" version)) - (sha256 - (base32 - "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") - (synopsis "Variance stabilization and calibration for microarray data") - (description - "The package implements a method for normalising microarray intensities, -and works for single- and multiple-color arrays. It can also be used for data -from other technologies, as long as they have similar format. The method uses -a robust variant of the maximum-likelihood estimator for an -additive-multiplicative error model and affine calibration. The model -incorporates data calibration step (a.k.a. normalization), a model for the -dependence of the variance on the mean intensity and a variance stabilizing -data transformation. Differences between transformed intensities are -analogous to \"normalized log-ratios\". However, in contrast to the latter, -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-ensembldb (package (name "r-ensembldb")