From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id nEApJqu9W1/hKwAA0tVLHw (envelope-from ) for ; Fri, 11 Sep 2020 18:10:51 +0000 Received: from aspmx2.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id kL1VIKu9W1+aPQAA1q6Kng (envelope-from ) for ; Fri, 11 Sep 2020 18:10:51 +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 aspmx2.migadu.com (Postfix) with ESMTPS id 221E66800E1 for ; Fri, 11 Sep 2020 18:10:51 +0000 (UTC) Received: from localhost ([::1]:45742 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kGnVZ-0006Cm-WE for larch@yhetil.org; Fri, 11 Sep 2020 14:10:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54268) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kGnUs-0005Nv-Fb for guix-patches@gnu.org; Fri, 11 Sep 2020 14:10:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:33879) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kGnUs-00068u-6E for guix-patches@gnu.org; Fri, 11 Sep 2020 14:10:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kGnUs-0005Oe-1e for guix-patches@gnu.org; Fri, 11 Sep 2020 14:10:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#43345] [PATCH 09/12] gnu: r-seurat: Move to (gnu packages cran). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 11 Sep 2020 18:10:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 43345 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 43345@debbugs.gnu.org Cc: zimoun Received: via spool by 43345-submit@debbugs.gnu.org id=B43345.159984775920606 (code B ref 43345); Fri, 11 Sep 2020 18:10:06 +0000 Received: (at 43345) by debbugs.gnu.org; 11 Sep 2020 18:09:19 +0000 Received: from localhost ([127.0.0.1]:45412 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kGnU7-0005MH-3Z for submit@debbugs.gnu.org; Fri, 11 Sep 2020 14:09:19 -0400 Received: from mail-wr1-f44.google.com ([209.85.221.44]:32778) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kGnTv-0005Jk-3b for 43345@debbugs.gnu.org; Fri, 11 Sep 2020 14:09:08 -0400 Received: by mail-wr1-f44.google.com with SMTP id m6so12380502wrn.0 for <43345@debbugs.gnu.org>; Fri, 11 Sep 2020 11:09:07 -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=YtNYVGa/XFn4b0F9PPHbXigftbO5WmHJ8etMVlQXHrM=; b=QXxmJI8HSNYj7VW93hfOtZ6LA3p4g8xvyHM6A+lzECydQRlU8Ttimv/I3ZAw4KIkT6 +MpN6O12f1HiPclvgV7BuXWUvpXXKqUtkCEqt1trMVI0KEgNajDgXnJoD31n/QzqAu6K NiX4t3hF7kQgBUyl1YeuNhy7dlzMYtDshnc1TkTHiYPqWQpd5x9Abx8TeSdBIXhCax92 aN5JwSu9YK+AMgTlrtvlNoMTo9c0cqo/H+OFvtcLiBgeJNf6dgPLDWpkrcGYuXNgx8ib cPHMmDxHFzNEa/WeuSGTPPn5Tcy23EVj+1g97hi6Ly4g0KeAOlEqFROly0mgxAJI9GOY JULg== 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=YtNYVGa/XFn4b0F9PPHbXigftbO5WmHJ8etMVlQXHrM=; b=G/i1VL+MtqCF5jcv8e9l/IzVOTuOtqzgnMCo4qC/wcAewKuY1I/OHvWnhwb+9dfGEL BSUXc96HnMdqFA52D9YoqsRtEBB3lg/uIbalBFCH88NEMhWsB/ktoEcNTEzKbm3u8Cpw VszK99p+FSixxg8jZ7PgftszXx6Z7YcQPmt30H75pfhfkteBkMlZmUNVqpBUUqRssxQR +rP+LoJB5POC3w0nFNZ9/1pbgprn89WP54T0CIZvnN+hEx14GfOxRzYXuzEizwGGwlTJ 2yZ3B76eFK40iKmxaBNFNF05GDCYCloQHx7SvhoHY4Iq0wcjAVIovcNogwhV3a5p8xYt +c9w== X-Gm-Message-State: AOAM532FZJ+bHj9NPe9VfqI6ZqNQYVXEmlW7PKthjx+VwZSpn1WZMFLW v3XOjUwMbXoVv89zErHUmlpVV0bBNf0= X-Google-Smtp-Source: ABdhPJyO0zg0ESeuz86swTwCM/FTWE0W3e81bmhm2w5+25HylEikCP2yIprplmvhb+53nYfyp6jALw== X-Received: by 2002:adf:8481:: with SMTP id 1mr3108643wrg.231.1599847741235; Fri, 11 Sep 2020 11:09:01 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id y1sm5914005wmd.22.2020.09.11.11.09.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 11 Sep 2020 11:09:00 -0700 (PDT) From: zimoun Date: Fri, 11 Sep 2020 20:08:46 +0200 Message-Id: <20200911180849.12582-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200911180849.12582-1-zimon.toutoune@gmail.com> References: <20200911180849.12582-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) 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-Scanner: scn0 Authentication-Results: aspmx2.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=QXxmJI8H; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx2.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-Spam-Score: 4.09 X-TUID: lZNhy36Gps5z * gnu/packages/bioinformatics.scm (r-seurat): Move from here ... * gnu/packages/cran.scm (r-seurat): ... to here. --- gnu/packages/bioinformatics.scm | 65 --------------------------------- gnu/packages/cran.scm | 65 +++++++++++++++++++++++++++++++++ 2 files changed, 65 insertions(+), 65 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fecb3c072d..a6505099fc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9735,71 +9735,6 @@ 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-seurat - (package - (name "r-seurat") - (version "3.2.0") - (source (origin - (method url-fetch) - (uri (cran-uri "Seurat" version)) - (sha256 - (base32 - "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2")))) - (properties `((upstream-name . "Seurat"))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-cluster" ,r-cluster) - ("r-cowplot" ,r-cowplot) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-httr" ,r-httr) - ("r-ica" ,r-ica) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-jsonlite" ,r-jsonlite) - ("r-kernsmooth" ,r-kernsmooth) - ("r-leiden" ,r-leiden) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-plotly" ,r-plotly) - ("r-png" ,r-png) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppprogress" ,r-rcppprogress) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rocr" ,r-rocr) - ("r-rsvd" ,r-rsvd) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-sctransform" ,r-sctransform) - ("r-shiny" ,r-shiny) - ("r-spatstat" ,r-spatstat) - ("r-tibble" ,r-tibble) - ("r-uwot" ,r-uwot))) - (home-page "http://www.satijalab.org/seurat") - (synopsis "Seurat is an R toolkit for single cell genomics") - (description - "This package is an R package designed for QC, analysis, and -exploration of single cell RNA-seq data. It easily enables widely-used -analytical techniques, including the identification of highly variable genes, -dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering -algorithms; density clustering, hierarchical clustering, k-means, and the -discovery of differentially expressed genes and markers.") - (license license:gpl3))) - (define-public r-aroma-light (package (name "r-aroma-light") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a6c2518978..8b2a5fc1dc 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23802,3 +23802,68 @@ statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.") (license license:gpl3+))) + +(define-public r-seurat + (package + (name "r-seurat") + (version "3.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "Seurat" version)) + (sha256 + (base32 + "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2")))) + (properties `((upstream-name . "Seurat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-cluster" ,r-cluster) + ("r-cowplot" ,r-cowplot) + ("r-fitdistrplus" ,r-fitdistrplus) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggridges" ,r-ggridges) + ("r-httr" ,r-httr) + ("r-ica" ,r-ica) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-jsonlite" ,r-jsonlite) + ("r-kernsmooth" ,r-kernsmooth) + ("r-leiden" ,r-leiden) + ("r-lmtest" ,r-lmtest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-miniui" ,r-miniui) + ("r-patchwork" ,r-patchwork) + ("r-pbapply" ,r-pbapply) + ("r-plotly" ,r-plotly) + ("r-png" ,r-png) + ("r-rann" ,r-rann) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppprogress" ,r-rcppprogress) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-rocr" ,r-rocr) + ("r-rsvd" ,r-rsvd) + ("r-rtsne" ,r-rtsne) + ("r-scales" ,r-scales) + ("r-sctransform" ,r-sctransform) + ("r-shiny" ,r-shiny) + ("r-spatstat" ,r-spatstat) + ("r-tibble" ,r-tibble) + ("r-uwot" ,r-uwot))) + (home-page "http://www.satijalab.org/seurat") + (synopsis "Seurat is an R toolkit for single cell genomics") + (description + "This package is an R package designed for QC, analysis, and +exploration of single cell RNA-seq data. It easily enables widely-used +analytical techniques, including the identification of highly variable genes, +dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering +algorithms; density clustering, hierarchical clustering, k-means, and the +discovery of differentially expressed genes and markers.") + (license license:gpl3))) -- 2.28.0