From patchwork Wed Jul 24 18:21:54 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14758 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 E833817270; Wed, 24 Jul 2019 19:23:07 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id A914F1726E for ; Wed, 24 Jul 2019 19:23:07 +0100 (BST) Received: from localhost ([::1]:54006 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLut-0003Qm-BA for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41339) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuq-0003Ma-1K for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuo-0008Nr-V4 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57415) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuo-0008Nb-S7 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuo-0005OD-NQ for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36790] [PATCH 01/11] gnu: Add r-umap. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36790@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399254420510 (code B ref -1); Wed, 24 Jul 2019 18:23:02 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:24 +0000 Received: from localhost ([127.0.0.1]:37971 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Kd-9C for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:35128) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuB-0005KS-CP for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41025) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuA-0003G6-Cy for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLu9-0007AV-AO for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: from mail-wr1-x436.google.com ([2a00:1450:4864:20::436]:39719) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLu9-00079M-4g for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:21 -0400 Received: by mail-wr1-x436.google.com with SMTP id x4so47968393wrt.6 for ; Wed, 24 Jul 2019 11:22:21 -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=wljyQX5T4Om4XmkiAWJsFHRSb3sTgG1+ANXwr1zpL+c=; b=NBFlpPpdptTzZRANsARv64zUWUJQvkHDh5R7eMVGR0W+0CabPRCcsiijdwPzh/xSPL CfZVUAsgbpVYHoC3iTC4IJplyE9te4fCjBBNDi7i5+eAMIccSVCk3gCxfwZIaUSCnj9R HG7qKXzJqz6V6p/lR236TxlRVaqkhKuRjQeNISR+ciZvz0JY17rn2pbw8pkkTCS0jfg5 FpD1MS1urPuo1iMFg63btjJwcEX5R5K/fWpElm2U/in/Nb7FFL/SX+vrpPOl7aYEdJDE 1uliZRz/jmUOCbBF3eIvHH2SOXnpzLJ1NXJGTUC6D+SDFJFVo/ZHdk4gT2e/EdgGh6Dc O8Qg== 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=wljyQX5T4Om4XmkiAWJsFHRSb3sTgG1+ANXwr1zpL+c=; b=coOPOw/ysEU+NRSaK/IsS8ILMkwxDXHvo/0sfWimNoU/Z41EymDJr/5s6dN2SpTmc+ 2WscNOaP0sY6nbSA+PB6/ntzTSV5pgFf7Gfg0q5BuE48uRb/UrNrFTUgozbx2rnUZ0kD 4zmMDNJS+SLTd7MGnPBReFXk+cYAy5DkH3M+25/VHb8Rb0GFWx1CAX8Y0sLagjmny2uL oHoikU0QXa+EquU7GUu0O1ac7p2pYv7pDBOnJlwVi6wJv+nmNXI+jW75Y7IpVN84Jd1s L13suhZQsYk0b3gkx6IQLHBDS56ObvUpvv8VTEt6rfGNkJFqFpWO4Tx6JGlBIjf3ZwsQ xMAA== X-Gm-Message-State: APjAAAVxP+VVshVunQ1PtQdh1FOS9/nNQx49TNH12DW4U+usUdiogJI5 E/z+O8f+UTvUVF1AdlP2KIqSo0qr X-Google-Smtp-Source: APXvYqx5+SQgoc0ZEl+FaovThgL7Cx0g06EtlJckwNwlmk3d+NE4bAtrL7H5H88BbSI4XZ/4k3OQrw== X-Received: by 2002:a5d:51c1:: with SMTP id n1mr84349538wrv.254.1563992539918; Wed, 24 Jul 2019 11:22:19 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.19 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:19 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:21:54 +0200 Message-Id: <20190724182204.6818-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/cran.scm (r-umap): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3f0d819df7..768a7d09c5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14530,3 +14530,30 @@ including regression, classification and ranking. The package is made to be extensible, so that users are also allowed to define their own objectives easily.") (license license:asl2.0))) + +(define-public r-umap + (package + (name "r-umap") + (version "0.2.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "umap" version)) + (sha256 + (base32 + "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-reticulate" ,r-reticulate) + ("r-rspectra" ,r-rspectra))) + (home-page "https://github.com/tkonopka/umap") + (synopsis + "Uniform Manifold Approximation and Projection") + (description + "Uniform manifold approximation and projection is a technique for +dimension reduction. The algorithm was described by McInnes and Healy (2018) +in . This package provides an interface to the UMAP +algorithm in R, including a translation of the original algorithm into R with +minimal dependencies.") + (license license:expat))) From patchwork Wed Jul 24 18:21:55 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14759 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 4598417270; Wed, 24 Jul 2019 19:23:09 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 014F71726E for ; Wed, 24 Jul 2019 19:23:09 +0100 (BST) Received: from localhost ([::1]:54008 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuu-0003Tv-GH for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41357) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLur-0003Mb-2z for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLup-0008Ox-U6 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57417) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLup-0008Oa-Oz for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLup-0005OR-J1 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36791] [PATCH 02/11] gnu: Add r-kableextra. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36791 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36791@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255120571 (code B ref -1); Wed, 24 Jul 2019 18:23:03 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:31 +0000 Received: from localhost ([127.0.0.1]:37981 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuI-0005Lh-OM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from lists.gnu.org ([209.51.188.17]:56560) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Ke-AP for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41043) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuB-0003Hc-6q for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuA-0007BV-28 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from mail-wr1-x42f.google.com ([2a00:1450:4864:20::42f]:43436) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLu9-0007AL-Sg for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: by mail-wr1-x42f.google.com with SMTP id p13so47974634wru.10 for ; Wed, 24 Jul 2019 11:22:21 -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=7sQ4hMMewGNK1ZUfxvELsM3vEj41+txaX373UyUZUqs=; b=XYdgAYJY5iu+br3qnF+QyDWO/FlQiEh6fNqIPwb2Cq4F4krqYaX3vF7cu4GznNMpFP L7178xI+hX1ci6g5aZEOLEzXhUUR3OsoToxHQ81KHerR6C5FT+Y1xeJEyxAeqFA3pbRy pKEtFuAOesifjCKzvv0rz+AoDLJyttPv92D6mAPD/nNhL5CbdPiy9qV626os3hgQBm3o 1RyZUiOD1+OLyXwvNXGzUT8WKvUQDVlEPoiiC1XUfXSq6/oq9aTabOBQWJM5fEfluGhG Z9oDMBaJjtGr9tF4sdXtHGEqsxj2phjzt/AZXbnhseUZDMQ04Ng36m6rPuxvvcr62exd sfsw== 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=7sQ4hMMewGNK1ZUfxvELsM3vEj41+txaX373UyUZUqs=; b=jSwS85TtTE5295PVRRmcrwQqhkD66CcGz897WoYndMVi6+HKlo7EcwdvvruMaoqACp SHRhc9GHOErr5bvshZtd/0yIONEZ06NAm7zhwMHZUn08k5mmkJ5sJOeJDTwbp22n1Pf/ zcrh2Wc7vMxtZfloP9dViI1a/mDm0dokcYAffyeKnU6xpXX+EMhhx2S2w1E6jsafr5Ms LhyI54hNb9c54Ttb/ti1k+NZAs+LJlfM1MKJhX47p6DFpB4ka5hAEmxq6wIH0JXINIUV +H2a9h4Cef5bb9iRonpqJj4T0kqSmlrICxT8heh91zF31AFaYj48QJXJ2cNop4w6gz5F InNw== X-Gm-Message-State: APjAAAUwaHfnAbDiqRJtRw7eg4YeJJb+Fw0Ly1GJb0SISqnSH6fxhyoe Bex4DBKRS14Nu80jmy/o23/wRpjn X-Google-Smtp-Source: APXvYqy9rS2iAxcsrW9VrdpwvwnYN3avi70ONFvF5PWzl8rkTGt7W0ZLCglayQdJH6KUBExaGmQAag== X-Received: by 2002:a5d:6408:: with SMTP id z8mr73352019wru.246.1563992540767; Wed, 24 Jul 2019 11:22:20 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.19 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:20 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:21:55 +0200 Message-Id: <20190724182204.6818-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/cran.scm (r-kableextra): New variable. --- gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 768a7d09c5..7349a9513e 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14557,3 +14557,43 @@ in . This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R with minimal dependencies.") (license license:expat))) + +(define-public r-kableextra + (package + (name "r-kableextra") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "kableExtra" version)) + (sha256 + (base32 + "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i")))) + (properties `((upstream-name . "kableExtra"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-glue" ,r-glue) + ("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-readr" ,r-readr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) + ("r-rvest" ,r-rvest) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-viridislite" ,r-viridislite) + ("r-webshot" ,r-webshot) + ("r-xml2" ,r-xml2))) + (home-page + "http://haozhu233.github.io/kableExtra/") + (synopsis + "Construct Complex Table with 'kable' and Pipe Syntax") + (description + "Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and +the piping syntax from 'magrittr'. Function 'kable()' is a light weight table +generator coming from 'knitr'. This package simplifies the way to manipulate +the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct +complex tables and customize styles using a readable syntax.") + (license license:expat))) From patchwork Wed Jul 24 18:21:56 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14760 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 AF61F17270; Wed, 24 Jul 2019 19:23:09 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 6DD411726E for ; Wed, 24 Jul 2019 19:23:09 +0100 (BST) Received: from localhost ([::1]:54010 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuu-0003WV-Vd for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41376) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLur-0003Ot-Qb for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuq-0008Q0-NR for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57419) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuq-0008Pm-Js for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuq-0005Og-FY for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36792] [PATCH 03/11] gnu: Add r-all. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36792 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36792@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255120586 (code B ref -1); Wed, 24 Jul 2019 18:23:04 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:31 +0000 Received: from localhost ([127.0.0.1]:37984 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Lk-2V for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:31 -0400 Received: from lists.gnu.org ([209.51.188.17]:36130) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuC-0005Kw-Un for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41054) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuB-0003Hg-Pm for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuA-0007CQ-ML for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: from mail-wr1-x42d.google.com ([2a00:1450:4864:20::42d]:46470) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuA-0007BH-GA for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:22 -0400 Received: by mail-wr1-x42d.google.com with SMTP id z1so47975081wru.13 for ; Wed, 24 Jul 2019 11:22:22 -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=EBGiqIJ6MqoHCF1xFEtWHJ1TQ7cJOOpwKR35oebI/2o=; b=DPDpblrdhpnvpvcjT+K7QEilzzelwPmzzIBsCzwrYw1bGYRCNRU9JPE3U+zDb3pFX7 MenSkp6C/5IJ+L/6azdKGT4Se++aiFOzef5+daafcPaGs0uJDSqKP8egdvMouhQKu/G9 lJj+/OXKE3zK2SoLTGqCiZxPOVrTf0hKLuDipq2paItNDWij43PC2X2gSUHts+wswkBD cxT5mO0yGZEzltWP+3E/pRKoF8sJ/APm8NpYDmTNCNlO82XJ9jNiCcCEXAVLLnCV3qQ/ uEoQf0ShTSKv0TsMY5s5fnYBWdC7cocQ7qQZMeFGTXZ+5AgnxPhtqJN76FqyT/VG/b2e 36xQ== 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=EBGiqIJ6MqoHCF1xFEtWHJ1TQ7cJOOpwKR35oebI/2o=; b=EXKKhcsxH8tC7jWwSIJD4BIgTevyoQB8h2vwaRgm5bt4ZPEFcdfYGu1rKauykeGEDj eZ3RWhn7C6bS3NZlO3QdpOzrAN+ob9kI/Bz+LwXquKRWfdzFrKw2MRHsqXIb8sJDs8tq OFoS4gMEakFgyRbmfxHS2IbEzmbGX8cAvJMAasaqM3BVFDi6fEf8fmoqxF38dKRDJAnw dx418MD+CoqEjm8lHYxVZ8+ju4RciigcT8US7ajK/578/vU5Bbl7AajjtRKaMM5diX4Y XZqK9o09msEMyLESymQ5x0dm0v6joO1eJrbKlCabfGeDVfZm8IiO0gm3ohi4ioHXLmB8 Zg1w== X-Gm-Message-State: APjAAAVwKefCmBI+4EqBMvsMG4rO1AuCysny0zYee7WdPyBKVJowxKFV UabghP0REqJWsSwHGIsIrNJGNA+a X-Google-Smtp-Source: APXvYqx30FcyPS2v/zaUpi8X7US4YuGoKBjpwGy+V25kGjDlzOHRaZ7e4KntlCNReAbTHjMxRkH5Ow== X-Received: by 2002:adf:e444:: with SMTP id t4mr84469995wrm.262.1563992541413; Wed, 24 Jul 2019 11:22:21 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.20 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:20 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:21:56 +0200 Message-Id: <20190724182204.6818-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-all): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5a2d66b2d..18b5711496 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -865,6 +865,36 @@ which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.") (license license:artistic2.0))) +(define-public r-all + (package + (name "r-all") + (version "1.26.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ALL_" version ".tar.gz")) + (sha256 + (base32 + "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) + (properties + `((upstream-name . "ConsensusClusterPlus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase))) + (home-page + "https://bioconductor.org/packages/ALL") + (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") + (description + "The data consist of microarrays from 128 different individuals with +acute lymphoblastic leukemia (ALL). A number of additional covariates are +available. The data have been normalized (using rma) and it is the jointly +normalized data that are available here. The data are presented in the form of +an exprSet object.") + (license license:artistic2.0))) + ;;; Packages From patchwork Wed Jul 24 18:21:57 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14762 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 A0CC517270; Wed, 24 Jul 2019 19:23:13 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id F3B6E1726F for ; Wed, 24 Jul 2019 19:23:11 +0100 (BST) Received: from localhost ([::1]:54012 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLux-0003e5-I5 for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41394) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLus-0003RB-Ml for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLur-0008R4-F5 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57421) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLur-0008Qp-Au for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLur-0005Ox-6d for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36793] [PATCH 04/11] gnu: Add r-flowcore. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36793 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36793@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255220600 (code B ref -1); Wed, 24 Jul 2019 18:23:05 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:32 +0000 Received: from localhost ([127.0.0.1]:37987 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Ly-Ky for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:46301) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuD-0005L2-LJ for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41070) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuC-0003Ho-Kr for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuB-0007Dt-JB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: from mail-wr1-x431.google.com ([2a00:1450:4864:20::431]:43438) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuB-0007Cf-DF for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:23 -0400 Received: by mail-wr1-x431.google.com with SMTP id p13so47974699wru.10 for ; Wed, 24 Jul 2019 11:22:23 -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=rx7LUQvIHcLh54Mlx4vy8OaM3guvdfNahu+L7Qf6kUw=; b=A5n8zr5XDapjfpVzDCP8mYd8loT2PvPW6fbEIeXtGPhXeFfLZ1SiVMXzx83h9VIkO1 qfX0dWpJLS1w3pjqLaevfq6OWGNR6aOlgwaYokYijvC13oWJj9BcTua+DErbsVl1jZT7 iq3M6h2wAjvFReeuAHDb+BBkPS/9zzXodELyiMy+053IUgiccKEQstAcj6W9FKU/X52T SPoCfLG0aTxO34zsRbVP2r2ZcUjbPUFuZgCN/3D5ndOafPM052UDlYA+u1phIoWN/cMQ AMS1gQUxFWX8OKcMityO/yZYS497/YDKgR1zfkTdJDQXVkp7iJoDdf56Yto+nfgcJ4XA qGDg== 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=rx7LUQvIHcLh54Mlx4vy8OaM3guvdfNahu+L7Qf6kUw=; b=qpjlcH7FpSzrwji2etpz/4/cTVzFI4mFR2hPlSQXLEP37rCbqD+pkI3YHaV4jO9mjS cWk5rCSQJT3eWTQGU8ve2ZpYogYqhBHbVwLTW8dGCyB8dB3BVrZkD7HLTnMDbPlrL29D 5RgYAQKoiA/7OE4gcoHyOU8MlFFAXu7kqoKpwS7zv9MD2ZVFtyPmdHFDtdIFeuMvOCtS 9nxHuLyRacbthrKxXQBGpxZBFAw802Z682P/eqBBQXX0fILHOmz/jXRBdoI7514WAyZb QnuNneTP59+i5F4/+fyqVcrB3IwLxu18x7rhJiIuELSmiDouQQSx6KzDgU2zPSCWkbpp Z86w== X-Gm-Message-State: APjAAAW73DPJ79W2j+zs80qecTckXwblFfYboMgiER+4LB1Jnp6aoMAd pSAs26jZhustj1n0FCpm68kFgapO X-Google-Smtp-Source: APXvYqzFM1KPSMixiABfbX8e2HxGBDpvz061d663XnYDMnnTvhFY9LggOG04MgcQ92N7Odfpm+KNYQ== X-Received: by 2002:a5d:6a84:: with SMTP id s4mr12580003wru.125.1563992542287; Wed, 24 Jul 2019 11:22:22 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.21 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:21 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:21:57 +0200 Message-Id: <20190724182204.6818-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-flowcore): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 18b5711496..3a38042537 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4799,3 +4799,33 @@ read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) + +(define-public r-flowcore + (package + (name "r-flowcore") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowCore" version)) + (sha256 + (base32 + "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) + (properties `((upstream-name . "flowCore"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-corpcor" ,r-corpcor) + ("r-graph" ,r-graph) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rcpp" ,r-rcpp) + ("r-rrcov" ,r-rrcov))) + (home-page + "https://bioconductor.org/packages/flowCore") + (synopsis "Basic structures for flow cytometry data") + (description + "Provides S4 data structures and basic functions to deal with flow cytometry data.") + (license license:artistic2.0))) From patchwork Wed Jul 24 18:21:58 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14761 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 62BA617271; Wed, 24 Jul 2019 19:23:12 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id F365E1726E for ; Wed, 24 Jul 2019 19:23:11 +0100 (BST) Received: from localhost ([::1]:54014 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLux-0003eB-Eb for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41402) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLut-0003TE-5h for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLus-0008S2-4R for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57423) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLus-0008Rs-1S for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLur-0005PB-Tj for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36794] [PATCH 05/11] gnu: Add r-flowutils. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36794 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36794@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255220608 (code B ref -1); Wed, 24 Jul 2019 18:23:05 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:32 +0000 Received: from localhost ([127.0.0.1]:37989 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuK-0005MC-Fa for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:54749) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuE-0005L9-C3 for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41084) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuD-0003I5-8B for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuC-0007Ex-AZ for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: from mail-wr1-x42d.google.com ([2a00:1450:4864:20::42d]:33639) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuC-0007Do-3W for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:24 -0400 Received: by mail-wr1-x42d.google.com with SMTP id n9so48094453wru.0 for ; Wed, 24 Jul 2019 11:22:24 -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=OSpLDtjNGjfHmKRoGp1RTvE1NGPzUJ5XElI50Q6CEgw=; b=iegAibzrIREiO2fEUC8nsqr/ZpvTb4LNilB7sQXLjOV7c3LtbKvApSV20IiU0xQRk8 6Rltj5m7r1iwW2nLAO5227OcYLiOJtZ7kDY3to/1tQKMRJz9Grgo0gKz4mwRpG+jiJ2m tIokIp4HTZ+yZ1FJBzPe/hv9cywbLj0qoMSfecGfvxeJe4FWnYJMC/Rv6bj+1+JsMh0c exB64vzd7SbYzpEmx5NLgUHQO/qjCh0EpEFER9nNdNQNLtwwiNa0Pj5fJ52Ib3u+WbRz 4X2cYHvpD1qXQ2BMONNs1UOlcwEbaoIB6vLGJctLuflZ/DAnnCbAuodp6dkrONzqCGac rG5w== 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=OSpLDtjNGjfHmKRoGp1RTvE1NGPzUJ5XElI50Q6CEgw=; b=GgzU5p31ukxyJ40bTvhG7s4H5YDWTgOIDhoPTAlp6K2MMoxTrrmK2bD17Ru+D/yuTU MhpfVDjppGpNiztwKKHRgtbLDMi/PqI8hw5MgRPwhebLXC/Yg3LtK2lY1DNr90aBQeCv dbZpKuZYNMBTHZFEWhKyOanNBjuEyG9Aqj1zmUyaaS8Iea0k8nb4whSgcYuD7b69yZCj j2HObMAZ5PM9fbB4Fkgn6ZIpT2qhA8U6v9i7Kam60CzU189Pq7zSmUH97Tqp9xemujkb OLwX5NzO0/XT9CAUiYEGCbkwCrG4i0sIgznTOfhfOz0DPgQNFP7de/eWtZaVKbFMuxmq U0Tg== X-Gm-Message-State: APjAAAWiwiHI4fCHNVMeuXV3FUO8PeYZnYp0GJL2aCTwAQcggqrCha0h vMNYFunmlg4w5nQkdqo/nNXnq8+M X-Google-Smtp-Source: APXvYqzDEnKHSSGDJ2R+27497B6eZ63kVT1UTmRh53JrwGtXP6YT1Y0UQw6blGZ/M63N0NOOA7KPpg== X-Received: by 2002:adf:de10:: with SMTP id b16mr55952468wrm.296.1563992542948; Wed, 24 Jul 2019 11:22:22 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.22 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:22 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:21:58 +0200 Message-Id: <20190724182204.6818-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-flowutils): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3a38042537..d79ff729fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4800,6 +4800,33 @@ gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) +(define-public r-flowutils + (package + (name "r-flowutils") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowUtils" version)) + (sha256 + (base32 + "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) + (properties `((upstream-name . "flowUtils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-corpcor" ,r-corpcor) + ("r-flowcore" ,r-flowcore) + ("r-graph" ,r-graph) + ("r-runit" ,r-runit) + ("r-xml" ,r-xml))) + (home-page + "https://github.com/jspidlen/flowUtils") + (synopsis "Utilities for flow cytometry") + (description + "Provides utilities for flow cytometry data.") + (license license:artistic2.0))) + (define-public r-flowcore (package (name "r-flowcore") From patchwork Wed Jul 24 18:21:59 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14763 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 A5A1817270; Wed, 24 Jul 2019 19:23:14 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 68A8A1726E for ; Wed, 24 Jul 2019 19:23:14 +0100 (BST) Received: from localhost ([::1]:54018 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuz-0003nQ-SP for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41432) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuu-0003XK-18 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLus-0008T4-S6 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57425) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLus-0008Sn-OC for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLus-0005PQ-KP for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36795] [PATCH 06/11] gnu: Add r-consensusclusterplus. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36795 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36795@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255320617 (code B ref -1); Wed, 24 Jul 2019 18:23:06 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:33 +0000 Received: from localhost ([127.0.0.1]:37991 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuK-0005ML-QO for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:33 -0400 Received: from lists.gnu.org ([209.51.188.17]:42064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuF-0005LG-7A for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41096) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuE-0003Ix-6a for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuD-0007GU-4l for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from mail-wr1-x42e.google.com ([2a00:1450:4864:20::42e]:39999) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuC-0007Eu-Ut for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: by mail-wr1-x42e.google.com with SMTP id r1so47997542wrl.7 for ; Wed, 24 Jul 2019 11:22:24 -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=24W40LvZghPcbKV/H18xen7gsRhPS5H4z1oHo7bo37o=; b=rnqbXAjUbGifnfSO2GeQGZh0dc4in9l2FFDzbMa2r4+No3iWfFlW5kDSK6zMOmgtW3 2SMnZYV32ponjO/9S3WMrTgZZW3TKj4vKT4TA+OGqPVCsQ1Kg/CCrAgV51LJK+EL2pVb cl24I9l58S9hW8+IEZdFFQpSsJBtn4bLc2hnYKPB7QwnLTbuHGXvcXIRuSnwsn6wg0xw CKaCaxReizbyFrqw+dZBWZlq7BHHAEUibamWkZ+gsjagf9A9YRWbwwaoKCFu2Mz/vNMO 2ILflRcwss1a3vBgqXZOJRwqeeQP6EK/MvHX/VMjFqxFDsTVNvuDJG3/uJOprycZTT9w vTbQ== 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=24W40LvZghPcbKV/H18xen7gsRhPS5H4z1oHo7bo37o=; b=SIN8y4AD5vmwGOSqg6BYKYwOO3Bat+E6o7eBKJ0ikn4zdU3Jmj11ZqlmS/vkLTXlc7 CZFhqzi/V+vj0RzPAAzwf4mSFwLj2AlCumAIucL/vzR+yQF+oIk3+/1xk9A/Wcd4qjUm 0PMwv9ppAz1eIl4igDEPm9dRvEi0571rA/08p13G89s3ERE8fYbAn0qas1lSkc1ZJzXb gfcq4YDbwbB/xUYaUq14h96eG+L9qxdwp1Y9Zu23Jf1lY9wxAm6MM10NgumSP9llRH+w F86v+QC/uJJpCLUuyk2ICKqeSMgzax+I44cgwh/1mz681GFFHcgnMftPc/Msoi7SYwvi KdcA== X-Gm-Message-State: APjAAAXTDYOX7U62k1YMrKv+k/n+FLIJscrU9reWMjLutN92HPDg3f0Q aDAKjFMkKQFHSwy2hCdzY/qtD6mh X-Google-Smtp-Source: APXvYqwCXWThIC3B+SGJ91uJCfiUoKLOXuqkMDur6pAOubKmN3dlEbtcvfcg0Cj8OD6alf5bvtf3oQ== X-Received: by 2002:a5d:618d:: with SMTP id j13mr88213012wru.195.1563992543841; Wed, 24 Jul 2019 11:22:23 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.22 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:23 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:21:59 +0200 Message-Id: <20190724182204.6818-7-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-consensusclusterplus): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79ff729fc..d5bd512972 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4827,6 +4827,31 @@ and to both short and long sequence reads.") "Provides utilities for flow cytometry data.") (license license:artistic2.0))) +(define-public r-consensusclusterplus + (package + (name "r-consensusclusterplus") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ConsensusClusterPlus" version)) + (sha256 + (base32 + "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) + (properties + `((upstream-name . "ConsensusClusterPlus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-all" ,r-all) + ("r-biobase" ,r-biobase) + ("r-cluster" ,r-cluster))) + (home-page + "https://bioconductor.org/packages/ConsensusClusterPlus") + (synopsis "Clustering algorithm") + (description + "Algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") + (license license:gpl2))) + (define-public r-flowcore (package (name "r-flowcore") From patchwork Wed Jul 24 18:22:00 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14764 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 4CCB317271; Wed, 24 Jul 2019 19:23:15 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id E7ED81726E for ; Wed, 24 Jul 2019 19:23:14 +0100 (BST) Received: from localhost ([::1]:54020 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLv0-0003oF-6D for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41455) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuu-0003c1-Vp for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:10 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLut-0008UO-MT for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57427) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLut-0008UD-JA for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLut-0005Pf-Bp for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36796] [PATCH 07/11] gnu: Add r-flowmeans. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36796 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36796@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255320625 (code B ref -1); Wed, 24 Jul 2019 18:23:07 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:33 +0000 Received: from localhost ([127.0.0.1]:37993 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuL-0005MU-Cc for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:33 -0400 Received: from lists.gnu.org ([209.51.188.17]:48146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuG-0005LM-1R for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41112) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuF-0003J1-0q for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuD-0007Hc-Ui for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: from mail-wr1-x433.google.com ([2a00:1450:4864:20::433]:33645) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuD-0007GY-Oh for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:25 -0400 Received: by mail-wr1-x433.google.com with SMTP id n9so48094525wru.0 for ; Wed, 24 Jul 2019 11:22:25 -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=0foQD19vAMQrvcRH4ETjIMv5JzK13UlFkevMaKX88ck=; b=Yt14iPtbAHIlIr2twiukipiepKskFRoRYJ/6HzWUFW5fvCsTXeBOpSZz7CZUsYrrlm ZFD7kF9lgOsUKspSIF1OI1oAgZhZgv75HxtW7EbEWGN8iKVMDv3qV90DaOUEH+wzqd9D kx38SdkCvN/OKI7ysV186CWXTl7GDm0EeTLtVx5l7d2rQm/1MUh57dIXHXPI9yy38328 ko5VqPXzudjbBlwQz4DcvBywjknBddDDHpqvGxAFQz5Kl6f83HqEWCGFuJbkei9AK3/a iMBFvlj9CRerYSWVFyvHnAQDdycwiAYLoEODX8amswODkWOC99CmLHTvjJFjSkT4p0MX GTBA== 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=0foQD19vAMQrvcRH4ETjIMv5JzK13UlFkevMaKX88ck=; b=iR9UAloC+ZMj/NVRecf34BLin0gQsUX2qzezTmF6aQ/Lc5jmRZu+haAyzJ4iE2vQmZ fqZ/EHwUsPs1rPasgalXPgHESRtl5tNLNM6QNFFbglih09gDMFxREMoIpJIFXJk+CJFC /aPKi0jzefN4M1EbawsrKqUH+iqVY6qrQ23Tq8EKLr6gWHSCWNdT1JNJwSJTP9urhe59 sXendYIJiHK5aMW5eZiMHOozx61D+h6qnVcBDL1mJ8lOKeFUT462eKGjEwfYM7YZxwgK EPzNXBVUDIVrb3+7MfcURv2CgmJgx8uTd2y9dZTTd2APWnF/1YuTW1D6q8T7JQO4X1// fWww== X-Gm-Message-State: APjAAAXDFAs784XTgUyXz5UZGIUgjF5Cm2h2f+uxcl/jVtFFy7rdCLiN rcYAzQnxtDPHhd4GRnpIebc++rNO X-Google-Smtp-Source: APXvYqwYq0dfkdXt1gxoLntVS7kilXWftZ8hRBQZHMCpQ13GcBfbe/RIAbN0UZldoS/eSElsqWN9Aw== X-Received: by 2002:a5d:51c8:: with SMTP id n8mr78520379wrv.46.1563992544648; Wed, 24 Jul 2019 11:22:24 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.23 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:24 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:00 +0200 Message-Id: <20190724182204.6818-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-flowmeans): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d5bd512972..0f023665c2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4881,3 +4881,29 @@ and to both short and long sequence reads.") (description "Provides S4 data structures and basic functions to deal with flow cytometry data.") (license license:artistic2.0))) + +(define-public r-flowmeans + (package + (name "r-flowmeans") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowMeans" version)) + (sha256 + (base32 + "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) + (properties `((upstream-name . "flowMeans"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-feature" ,r-feature) + ("r-flowcore" ,r-flowcore) + ("r-rrcov" ,r-rrcov))) + (home-page + "https://bioconductor.org/packages/flowMeans") + (synopsis + "Non-parametric Flow Cytometry Data Gating") + (description + "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.") + (license license:artistic2.0))) From patchwork Wed Jul 24 18:22:01 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14765 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 67D6B17271; Wed, 24 Jul 2019 19:23:15 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 00C691726F for ; Wed, 24 Jul 2019 19:23:15 +0100 (BST) Received: from localhost ([::1]:54022 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLv0-0003pb-FI for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41473) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuv-0003dz-LE for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:10 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuu-0008Vk-GQ for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57429) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuu-0008VU-DB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:08 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuu-0005Pu-8k for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36797] [PATCH 08/11] gnu: Add r-flowpeaks. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36797 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36797@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255420632 (code B ref -1); Wed, 24 Jul 2019 18:23:08 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:34 +0000 Received: from localhost ([127.0.0.1]:37995 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuL-0005Mc-PM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:34 -0400 Received: from lists.gnu.org ([209.51.188.17]:46513) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuG-0005LT-OL for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41121) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuF-0003J5-Hb for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuE-0007IU-Gy for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: from mail-wr1-x436.google.com ([2a00:1450:4864:20::436]:44509) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuE-0007HO-B6 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:26 -0400 Received: by mail-wr1-x436.google.com with SMTP id p17so47980433wrf.11 for ; Wed, 24 Jul 2019 11:22:26 -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=4S+Veqfm6npZSUj8Yx0luhGHLFkIFmWE+cqCRUN3qhs=; b=iDV2GYp7W51EI4bxEMsoW6UwQkUSpzQUAQVK/aRGqgsvSwg2wpmZthZAX7oR8KsmGl z4AT0inmfNoky032YuXIdWTPtN1+pPWFmYQ45t2wwgLNM1zRvgHyxpZDPS2e9ZZXcI6g 3c/U6t+ibWfcElrnLIWjbi4Nbdv8bMtJQDQTO4L+qanSMRYw3Ws6Kj3AepdrqJPk9gSG cy8TR2wFcsWUBNHwNzFd1/Ahy4sKdrVM2s3gMONKaGhDAeAbQfUZXE1xI6nb8wyI/dQb PPshM1//9hH0wuHCz+GaTgqcHRNOJuAipKg651xOmpZQ50EPCX4n8D64VhB3uoZmqbZD 0y9A== 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=4S+Veqfm6npZSUj8Yx0luhGHLFkIFmWE+cqCRUN3qhs=; b=HfJ+GGSef49HFIs51BbECV6+Uj4DJDpA7rpYIMLv71+bqY8n/ZCHLsVpOwn6pjOano 0SSpDb85/hDHxV1AuV+WvmwNsJz8gHMLFjzveXT81tky2/yOp9R54YAQFPC7C7GfiBvl +4GLfB/JGBnCXRDfZHAp/M9foXccaV/038BTNwSUj8nP7lOk0mZmEliNgNbaHV3jJZJT 3A0FMrDl23l+8iWNali6+mqeuCZuGKVhT8l2u8QJckSEh5+9g6DJPGP035OYFWZcKno8 BnmYnnZz3Tu0Jo98pa97H9gAvqWbJSNtsMdcgy0Wu60Crk3hTMWmu8Q0KKGE5nPfSlEP bOEw== X-Gm-Message-State: APjAAAV6hjK2MtKmMx2YHzDN3N5qJtEj4ffR9+M/Fz5BsJw/cJ27Y8r6 0i0GeT9TSniUxM/uIpLGqj7rtFgy X-Google-Smtp-Source: APXvYqwd+3sdFWK0fNREs4/OvU/T3Ar2hlq3Wx+JFBQIIu/56Bg8qBuTO2LAKV9l8PNSMiKx20e6Zw== X-Received: by 2002:adf:ea88:: with SMTP id s8mr82370761wrm.68.1563992545301; Wed, 24 Jul 2019 11:22:25 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.24 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:24 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:01 +0200 Message-Id: <20190724182204.6818-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-flowpeaks): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0f023665c2..ab4d9f4075 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4907,3 +4907,26 @@ and to both short and long sequence reads.") (description "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.") (license license:artistic2.0))) + +(define-public r-flowpeaks + (package + (name "r-flowpeaks") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowPeaks" version)) + (sha256 + (base32 + "1ncz7n6n39svi444yy29ip53398392s3m6z0h2a77rhcnzg456wy")))) + (properties `((upstream-name . "flowPeaks"))) + (build-system r-build-system) + (inputs `(("gsl" ,gsl))) + (home-page + "https://bioconductor.org/packages/flowPeaks") + (synopsis + "An R package for flow data clustering") + (description + "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.") + (license license:artistic2.0))) ;TODO: artistic1.0 does not exist + From patchwork Wed Jul 24 18:22:02 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14766 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 71B6B17270; Wed, 24 Jul 2019 19:23:16 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 321BB1726E for ; Wed, 24 Jul 2019 19:23:16 +0100 (BST) Received: from localhost ([::1]:54026 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLv1-000407-QP for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41486) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuw-0003fJ-De for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:11 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuv-00005O-9g for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:10 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57431) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuv-000055-4o for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuv-0005Q8-07 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36798] [PATCH 09/11] gnu: Add r-flowsom. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36798 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36798@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399255420638 (code B ref -1); Wed, 24 Jul 2019 18:23:08 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:34 +0000 Received: from localhost ([127.0.0.1]:37997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuM-0005Mk-8b for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:34 -0400 Received: from lists.gnu.org ([209.51.188.17]:46489) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuH-0005La-TM for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41139) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuG-0003JC-Sm for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuF-0007Jz-H0 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: from mail-wm1-x336.google.com ([2a00:1450:4864:20::336]:37215) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuF-0007If-Af for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:27 -0400 Received: by mail-wm1-x336.google.com with SMTP id f17so42458535wme.2 for ; Wed, 24 Jul 2019 11:22:27 -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=Jy5PfItzZJVOlLqCCQqbG/YxP5343aRlpYkP9syQYug=; b=m9lGmm/xWzn683krnhDieT9FvrdJYmEBju8anez8FZ/2JOpnPj4p42R6iImYPFgd7v 6l/rf2nl61VccRcdlztzzLoF7BU/geVAjnb64ORTQrEeIOyvpCY7Kr2R7LKeG9+jMHIe j1XrDb1kM2wYAixlWDYnoZfWTglxcj7tcpXuSyosToNHaT2lo7NjBdUjVRHiXeLYIk3o lSg9i5ujx4qqZkW15G7dArVS5hoj8Ont/Pm73ow7MQP9kJ5Bjr4rVIsc0UXY72ROhXCl /rffSQ7x0UTrZzrwvqfXuT5wIetHrsNFnmM2jy+tPZCLyiHeO3tiZfWTU8oZclJLYrkJ alew== 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=Jy5PfItzZJVOlLqCCQqbG/YxP5343aRlpYkP9syQYug=; b=tT1vLR4rrw9bLRvAvj2chFkxVUR9j78fV+9lnphSOD84vnZEQbwgUgc2uxnSvZ6LHC t3iQRwaEnvlI+zk5J+UKDfzV3RHEMnLwIcczkhgmPFR8pFbgH+g3zFiDtST/H8xL4jrG rIcjbfSYF6+0xq2ayoyDWXjlsBjI/di2nOGWHn7yl2fBOo/5b8LK7IbEBMW6q+wf9Oen LNkBd6tc7i4GMkzMJWACfhQdGi7vWQ50tm/FWGuAfDXvo0XbtQ2jQXwh8cIPq2nYfeYf GFJDWywDKZQ8mjsOiN3+sHxTUDhdbsPCEL59bNayxxwNOLsEmDxfZu/nuRz4wfHg3p5W NiuA== X-Gm-Message-State: APjAAAWMIBKvy4oBfdymMeYkLFpuDz54PP3ksO3mv8lywqBDHiXGbTUR FM1oDAI05vgeptIn8GK80QvTn+pG X-Google-Smtp-Source: APXvYqwQ48qRtiK2RON5XQId43FA96hyYW6rs0IfMgkQVI5V0LkDH3RyjFCcTNu8yUaNx7w3GtjLWQ== X-Received: by 2002:a05:600c:2199:: with SMTP id e25mr72471457wme.72.1563992546181; Wed, 24 Jul 2019 11:22:26 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.25 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:25 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:02 +0200 Message-Id: <20190724182204.6818-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-flowsom): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ab4d9f4075..dd6570ed17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4930,3 +4930,32 @@ and to both short and long sequence reads.") "This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.") (license license:artistic2.0))) ;TODO: artistic1.0 does not exist +(define-public r-flowsom + (package + (name "r-flowsom") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FlowSOM" version)) + (sha256 + (base32 + "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) + (properties `((upstream-name . "FlowSOM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-consensusclusterplus" + ,r-consensusclusterplus) + ("r-flowcore" ,r-flowcore) + ("r-flowutils" ,r-flowutils) + ("r-igraph" ,r-igraph) + ("r-tsne" ,r-tsne) + ("r-xml" ,r-xml))) + (home-page "http://www.r-project.org") + (synopsis + "Using self-organizing maps for visualization and interpretation of cytometry data") + (description + "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.") + (license license:gpl2+))) + From patchwork Wed Jul 24 18:22:03 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14768 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 2416A17270; Wed, 24 Jul 2019 19:23:18 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id D4F2A1726E for ; Wed, 24 Jul 2019 19:23:17 +0100 (BST) Received: from localhost ([::1]:54034 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLv3-00046O-IL for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41510) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLux-0003kA-Bg for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuw-00006D-1K for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:11 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57433) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuv-00005z-SU for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuv-0005QO-NU for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36799] [PATCH 10/11] gnu: Add r-mixomics. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36799 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36799@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399257020664 (code B ref -1); Wed, 24 Jul 2019 18:23:09 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:50 +0000 Received: from localhost ([127.0.0.1]:37999 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLub-0005NC-Os for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:53309) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuI-0005Li-U9 for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:31 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41156) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JD-NB for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:30 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuG-0007LN-E5 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x444.google.com ([2a00:1450:4864:20::444]:37543) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007KG-7w for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x444.google.com with SMTP id n9so22935346wrr.4 for ; Wed, 24 Jul 2019 11:22:28 -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=OSVrzdIYMqZK1JmBVmn3id+dsxL+4LAG2m5E4h3cW3M=; b=sha95n4lGaGvY2bGThdgOf385qekX03bv61eBfpv2LEvAVZRVjU63K52ANguH9HtTz 04XNqFy8KXEQX+hDGGtS8ua4fn6ISFhGcSag6a0gUB1k2Lb3BM7oIFshmokDRh7cjiIO 6MVRaWwz/kNYDrDhuABoFnTHbei4fzV8ZRGfEXCsy+QHfmj9xzRfoJ5VzzRn3KZD9BHW Qbci9qgUSjY72Gqp2GxX73Rn+oqAS4bRrwNdUf1jxORL4nqh+2gW8JKKeIvr1JrCjkQX 2yaxMYuWcMc0uTHWVAw97UEKDg5ZxaPGwdIORcK3eU9jrW8UVjh4A3//Vu+i0ywKufQ1 lKpQ== 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=OSVrzdIYMqZK1JmBVmn3id+dsxL+4LAG2m5E4h3cW3M=; b=NYjBxCF1GICvMFMKa1ZbaSVZqFtFj9hfBXAX5CfTPUYf7cAFMmLkVfwxkYXnM7Xwxq XW7bwhuxaaN7IRgMlutbKFRRLlLhIc9kL0GN2r60hz+SlmbIkzyu705NRl56TCb7Pyct xHzi3MvRoG8j/yQXxM5zUCIqq0hs8SPVh6RkdEPbySU8f75OCh8pa9u99Q/2s50Rc3p3 J3pJhPpoIELMqb0fIHontAAjwMnPzc9horqZeHZrWAI4MtK9Vi16jeo/qAo9Q077B29j QessCVsxH8KbsCUmTjUuzVmrsSzYLbZtFk+vARDF0er86HhogxVgLHz5tI31VYufYvpM U/Fg== X-Gm-Message-State: APjAAAWSKC6b8Y5X4Sv3PJV8B8coepefU4Jc9S0QOePuT8oK244TXUSO hle41XYFNndUCmqG9ZUnDCVfa641 X-Google-Smtp-Source: APXvYqzyl11IBqOyaqgmhhrD+fF562RdIWpPtMnE28DsPNfTMy9rUwVULK1zqzOsXyGJRCib3fIPHg== X-Received: by 2002:adf:ec0f:: with SMTP id x15mr54221988wrn.165.1563992546975; Wed, 24 Jul 2019 11:22:26 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.26 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:26 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:03 +0200 Message-Id: <20190724182204.6818-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-mixomics): New variable. --- gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dd6570ed17..64625aedd4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4959,3 +4959,57 @@ and to both short and long sequence reads.") "FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.") (license license:gpl2+))) +(define-public r-mixomics + (package + (name "r-mixomics") + (version "6.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mixOmics" version)) + (sha256 + (base32 + "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk")))) + (properties `((upstream-name . "mixOmics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-dplyr" ,r-dplyr) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rarpack" ,r-rarpack) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.mixOmics.org") + (synopsis "Omics Data Integration Project") + (description + "Multivariate methods are well suited to large omics data sets where the +number of variables (e.g. genes, proteins, metabolites) is much larger than +the number of samples (patients, cells, mice). They have the appealing +properties of reducing the dimension of the data by using instrumental +variables (components), which are defined as combinations of all variables. +Those components are then used to produce useful graphical outputs that enable +better understanding of the relationships and correlation structures between +the different data sets that are integrated. mixOmics offers a wide range of +multivariate methods for the exploration and integration of biological +datasets with a particular focus on variable selection. The package proposes +several sparse multivariate models we have developed to identify the key +variables that are highly correlated, and/or explain the biological outcome of +interest. The data that can be analysed with mixOmics may come from high +throughput sequencing technologies, such as omics data (transcriptomics, +metabolomics, proteomics, metagenomics etc) but also beyond the realm of +omics (e.g. spectral imaging). The methods implemented in mixOmics can also +handle missing values without having to delete entire rows with missing data. +A non exhaustive list of methods include variants of generalised Canonical +Correlation Analysis, sparse Partial Least Squares and sparse Discriminant +Analysis. Recently we implemented integrative methods to combine multiple +data sets: N-integration with variants of Generalised Canonical Correlation +Analysis and P-integration with variants of multi-group Partial Least +Squares.") + (license license:gpl2+))) From patchwork Wed Jul 24 18:22:04 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 14767 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 B0BD617270; Wed, 24 Jul 2019 19:23:17 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 6F3A41726E for ; Wed, 24 Jul 2019 19:23:17 +0100 (BST) Received: from localhost ([::1]:54032 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLv2-00043v-V8 for patchwork@mira.cbaines.net; Wed, 24 Jul 2019 14:23:16 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41536) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuy-0003oD-6H for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuw-00008z-Rz for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:12 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57435) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuw-00008Z-Mo for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:10 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1hqLuw-0005Qd-I4 for guix-patches@gnu.org; Wed, 24 Jul 2019 14:23:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#36800] [PATCH 11/11] gnu: Add r-depecher. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 24 Jul 2019 18:23:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 36800 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 36800@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.156399257120670 (code B ref -1); Wed, 24 Jul 2019 18:23:10 +0000 Received: (at submit) by debbugs.gnu.org; 24 Jul 2019 18:22:51 +0000 Received: from localhost ([127.0.0.1]:38001 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuc-0005NE-Ch for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:50 -0400 Received: from lists.gnu.org ([209.51.188.17]:57385) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hqLuJ-0005Lp-5J for submit@debbugs.gnu.org; Wed, 24 Jul 2019 14:22:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41160) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from ) id 1hqLuH-0003JI-VI for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1hqLuG-0007Ls-QE for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:29 -0400 Received: from mail-wr1-x42e.google.com ([2a00:1450:4864:20::42e]:46471) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1hqLuG-0007Kn-JF for guix-patches@gnu.org; Wed, 24 Jul 2019 14:22:28 -0400 Received: by mail-wr1-x42e.google.com with SMTP id z1so47975368wru.13 for ; Wed, 24 Jul 2019 11:22:28 -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=pgaMBeSPBUEIfWytGuX8ZLzsOG1AAzrXuronHOChjfQ=; b=arjY1DZIzQFyagrcaZBJyzZ2T2ROcRfcO6JCf37Y0fghwUjtnc7OdUi8mBBGcf8vOi ZGDuTAgOX2CvpF9UcTW284RetJLpHQ1zXiompK5fWQuW7PmuCatMG1lo9WpjywY/YV5Q EfPTDnZoyzcZkUluAxxn0SKMvzl0Aa5J0sGlMYz8KMKR83H+9HU8DFBRye5YybG6UW2G nzEUl5tfma6hqjPXAz3S6Ekb2A0nBwfOAI9ttyYtxkwh6y68FV7uB8tLmoVRNBI2Q8yb jHlocUl0Mz9XvnrHuFI6ra+sYTU9TbpNMl9LLLiq3DPfu4+f9SzX/cnACGdRTpKjZ2RE hcgw== 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=pgaMBeSPBUEIfWytGuX8ZLzsOG1AAzrXuronHOChjfQ=; b=Pwlk9A9Gu+hpb4t3Mn4826eHGjShPwrSED0X/aZVCIqSMY5jUHl3atnReblnYK+WKr VTaMic5wdkQ3Xtnxxiv4tXT2c/gSNH3+jV9i8MSeSYWwW3AGP85B965X26ZYkeTJT46t xdrgimk56G7blGSlXXhH937fT/Ciav+QtnONZcQvRM9CcJdbuuq18MZZcLiaWSHrOqT6 7WNM4PREytEV3rGT1gTXZZX2VNDmMahYtpEPWSINa9mXaDUfFC5KFzBLaB/stVo/bVZ/ R7EtXXZ91z8G3+t0poFeOG/Yd0XU6moO54uQ7/hGZc9HWtMZlx8Zudx08tV99tu2e2r2 HCjA== X-Gm-Message-State: APjAAAU1uMGMqkFXk0hGZEcKfoT41oRw8NYO9mICyBdhO1MifSsCqsQ6 WPfY5minMAVBRLzYS4LV8g/qgyvD X-Google-Smtp-Source: APXvYqzOY7O3H+91cgitdfrLSWMNn7eNp4gW4U+Wte0ELZHg89wmje+qFFkYGN0VOfFAZrqCrP8PQQ== X-Received: by 2002:adf:e444:: with SMTP id t4mr84470240wrm.262.1563992547529; Wed, 24 Jul 2019 11:22:27 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id g12sm66116616wrv.9.2019.07.24.11.22.26 (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 24 Jul 2019 11:22:27 -0700 (PDT) From: zimoun Date: Wed, 24 Jul 2019 20:22:04 +0200 Message-Id: <20190724182204.6818-12-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.22.0 In-Reply-To: <20190724182204.6818-1-zimon.toutoune@gmail.com> References: <20190724182204.6818-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-depecher): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 64625aedd4..7c9a3b7417 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5013,3 +5013,47 @@ data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.") (license license:gpl2+))) + +(define-public r-depecher + (package + (name "r-depecher") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DepecheR" version)) + (sha256 + (base32 + "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + (properties `((upstream-name . "DepecheR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beanplot" ,r-beanplot) + ("r-biocparallel" ,r-biocparallel) + ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-mixomics" ,r-mixomics) + ("r-moments" ,r-moments) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-reshape2" ,r-reshape2) + ("r-viridis" ,r-viridis))) + (home-page + "https://bioconductor.org/packages/DepecheR") + (synopsis + "Determination of essential phenotypic elements of clusters in high-dimensional entities") + (description + "The purpose of this package is to identify traits in a dataset that can +separate groups. This is done on two levels. First, clustering is performed, +using an implementation of sparse K-means. Secondly, the generated clusters +are used to predict outcomes of groups of individuals based on their +distribution of observations in the different clusters. As certain clusters +with separating information will be identified, and these clusters are defined +by a sparse number of variables, this method can reduce the complexity of +data, to only emphasize the data that actually matters.") + (license license:expat)))