From patchwork Wed Oct 30 10:25:26 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15893 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 E9A3817685; Wed, 30 Oct 2019 10:26:14 +0000 (GMT) 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, RCVD_IN_MSPIKE_H2,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 A27FA17674 for ; Wed, 30 Oct 2019 10:26:14 +0000 (GMT) Received: from localhost ([::1]:38694 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB7-0007Qh-Ry for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40247) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlAy-0007QL-8y for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlAw-0002iT-UV for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40479) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlAw-0002iJ-R9 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlAw-0005Vg-FP for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 1/6] gnu: Add r-idpmisc. References: <20191030102324.12437-1-zimon.toutoune@gmail.com> In-Reply-To: <20191030102324.12437-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243115421129 (code B ref 37988); Wed, 30 Oct 2019 10:26:02 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:25:54 +0000 Received: from localhost ([127.0.0.1]:49286 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAh-0005UI-88 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: from mail-wr1-f50.google.com ([209.85.221.50]:34625) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAc-0005Tv-HK for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:45 -0400 Received: by mail-wr1-f50.google.com with SMTP id t16so1664710wrr.1 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:42 -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:mime-version :content-transfer-encoding; bh=9cMYqmaR/LIMgB3R2l2Dtxwtg+DR5wGOW5GznpttjNY=; b=seyLk6zlVOxAp07Xq7nMTncOW0ex+JUR+NM6slM2Op5UNLFmqquc2fRFZeeYDC+A0u Ceg/Q7PKKYHkZnLViyZm7B9N2X6bxollEZ+al5DmQljjYD/Nc2qOixEfX6FPIIPUKXRI 7dXYFGoXe7S7+mHkx0nNVljY2Q61FmNL/ASuttJ42QuyN97V3m6bSNnxE2x/N0YI9ofv pLNSLn3EXvPveco3bRiX9hHZJTHCwsVWqsFXE9b0DZwW3FZsjCfsQbYyrKgjOp0qxjP1 OTeK4b32fkzAuywpzzJ5xhUwvnzbPSE3zCn+zz6+sWpbkV/YNxRhd6M5cpm17opXCn2e 8Pow== 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:mime-version :content-transfer-encoding; bh=9cMYqmaR/LIMgB3R2l2Dtxwtg+DR5wGOW5GznpttjNY=; b=cu4pjXgVQFizBJ2R94jR79UA+CAxYuOaxt3qdVWa2CaC7Saq6rbh35Cg52F1jfNIU+ AL47b3ORt8ajkdVH+Yxfg7fgnAIv/Wk8y/5O4/d4QUXVHqN9EnX+M/F4/1mO65LtJitf jkUeCZN4i23gy/ycJ86ArSBjp6Tu+KwI/dZ7UnQUhy+ks8y7F/rfdPLJ5H+b9ek+qiWc J+nQJ8ushWRFyA3oD5lO+chlScDLzcbUfCRkfVVkH+uayuRkwxV+NHTnLrREJOnRZtJh tl/tIMAmzvkemnp55FHjEsFcf9YBV3QIuZknCFIkujx1MebgJhbxeHhHv0k9RiOXFl3R jptg== X-Gm-Message-State: APjAAAV4xJb58RBgsf16iJKypxp8KE0IycN5HUDvaEhRuwL53p8G4lPW pNYm91ZZzTPLUsLgUHzkvY0h2pFx X-Google-Smtp-Source: APXvYqx58Tx5JTTDExA/re1AIxH/nU1bqLgHAeX1k9TI6vB8v3XIpNw16LI2/LUrlN5vDY4Kt2mQaA== X-Received: by 2002:adf:c409:: with SMTP id v9mr23955652wrf.41.1572431136409; Wed, 30 Oct 2019 03:25:36 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.35 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:35 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:26 +0100 Message-Id: <20191030102531.12495-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 MIME-Version: 1.0 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-idpmisc): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b16b96dc77..f47eafc3bb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2018, 2019 Brett Gilio ;;; Copyright © 2019 Nicolò Balzarotti ;;; Copyright © 2019 Wiktor Żelazny +;;; Copyright © 2019 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -15653,3 +15654,32 @@ unique identifiers, and whether it is a certain length. In addition, files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) + +(define-public r-idpmisc + (package + (name "r-idpmisc") + (version "1.1.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "IDPmisc" version)) + (sha256 + (base32 + "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd")))) + (properties + `((upstream-name . "IDPmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "https://cran.r-project.org/web/packages/IDPmisc") + (synopsis "Miscellaneous tools of Institute of Data Analyses and Process Design") + (description "This package provides different high-level graphics +functions for displaying large datasets and circular data in a very flexible +way, finding local maxima, brewing color ramps, drawing nice arrows, zooming +2D-plots, creating figures with differently colored margin and plot region. +In addition, the package contains auxiliary functions for data manipulation +like omitting observations with irregular values or selecting data by logical +vectors, which include NAs. Other functions are especially useful in +spectroscopy and analyses of environmental data: robust baseline fitting, +finding peaks in spectra, converting humidity measures.") + (license license:gpl3+))) From patchwork Wed Oct 30 10:25:27 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15894 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 2C52C17685; Wed, 30 Oct 2019 10:26:16 +0000 (GMT) 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, RCVD_IN_MSPIKE_H2,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 E1DEE17674 for ; Wed, 30 Oct 2019 10:26:15 +0000 (GMT) Received: from localhost ([::1]:38696 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB8-0007RB-Kt for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40254) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlAy-0007QQ-Ud for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:06 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlAx-0002jF-Iz for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40480) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlAx-0002j4-Df for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlAx-0005Vu-7X for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 2/6] gnu: Add r-flowviz. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243116021151 (code B ref 37988); Wed, 30 Oct 2019 10:26:03 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:00 +0000 Received: from localhost ([127.0.0.1]:49292 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAp-0005V0-T7 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:56 -0400 Received: from mail-wm1-f65.google.com ([209.85.128.65]:52830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAg-0005U2-Or for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:47 -0400 Received: by mail-wm1-f65.google.com with SMTP id p21so1491399wmg.2 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:46 -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=nUws7C2qD+TDFt4SyqllH9cDNq7wx4R1DjuW4Rh2tFA=; b=u5k+aelhh9+Q6ZA5qOSdTIPNuRFG4RU3xAQ/e3HuBNKSaXFwlyZD7AFpzFhukkm2/O lSbx/0i9bcBZdgYeTF9WUoOz/MYvJOzCoHpXos7j4cTZjSWZBJPkREhLH5pmUxGXPNgj L8rVh9xi7bx3raCn+ywp348RafqWMXR/47NNG18BQTnQ2WLD2ZqIwMsyJ1Cauib7GLi4 wdrRyK3WhPX/RWFE64xj/sr2WJaySQcsple1uQutjJvFBg3xA23nhq20j/0lHmcLjoUE GTODQ4mGtNbYz4QlspuHKSi3MGjgbJztm5ZGApg2Uie9wZnbuzQD7p+HGpXhX0xaDfNW VqXw== 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=nUws7C2qD+TDFt4SyqllH9cDNq7wx4R1DjuW4Rh2tFA=; b=Mo3h/Q/RnpZPYMQRmIHnXMTV1p31JlO7cqdLweVHR8pKpPyvj5/hJc60RlPDWet85J J07WNU9AxPf57g8g+9d7JQppreMOdUnLYAPzraBs9OOME+LObcWgWvuNta0rcmnErLQH CE205fVXzhTEQZd6k1VTFufqU4MU1ehVfwAqOWjxfgKsDgSjOnm4Ru/NKZaGhJ9k7pTk rJpqa+AlX920891pK2R7YwhnnybQfTVO62BbCM8UxEXvwh4JUsovBdp3YTEov7IScyWL m4p+ZSwasYkd1I8REAIyhqxQXPzHj1Bf/yYd2eR+vzgerPf1txOJYarEn4LLsU2hK7c1 5/7g== X-Gm-Message-State: APjAAAU9hMBCgejnYWGQLTBmsgcF0XKMGdEqosDU6b3qAVmno0ajlOZg bmj5r7/IfcYXZ0aczkt9xsIwh/nc X-Google-Smtp-Source: APXvYqyaBbTmW0uzF2eqLBSVCoIeTEcfR14FsRPSiiF1H1GSnSE2mzeWEB9mhCL8sEkFuBZIYleoHA== X-Received: by 2002:a7b:c76d:: with SMTP id x13mr8375901wmk.155.1572431140703; Wed, 30 Oct 2019 03:25:40 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:40 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:27 +0100 Message-Id: <20191030102531.12495-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-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-flowviz): 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 6467fecb8c..92e5d3ec0b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6137,3 +6137,32 @@ features (e.g. genes, microRNAs).") data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) + +(define-public r-flowviz + (package + (name "r-flowviz") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowViz" version)) + (sha256 + (base32 + "00zwfzpdln62160h1ahcki5b96y06a1na7xjqs63b7571318xj20")))) + (properties + `((upstream-name . "flowViz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-flowcore" ,r-flowcore) + ("r-hexbin" ,r-hexbin) + ("r-idpmisc" ,r-idpmisc) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/flowViz") + (synopsis "Visualization for flow cytometry data") + (description "This package provides visualization tools for flow cytometry data.") + (license license:artistic2.0))) From patchwork Wed Oct 30 10:25:28 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15897 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 31D2417685; Wed, 30 Oct 2019 10:26:33 +0000 (GMT) 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, RCVD_IN_MSPIKE_H2,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 E68AD17674 for ; Wed, 30 Oct 2019 10:26:32 +0000 (GMT) Received: from localhost ([::1]:38706 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlBQ-0007kB-AX for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40290) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB0-0007Qg-GR for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlAz-0002ml-4S for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40482) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlAz-0002ma-0L for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlAy-0005W9-Rw for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243116121166 (code B ref 37988); Wed, 30 Oct 2019 10:26:04 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:01 +0000 Received: from localhost ([127.0.0.1]:49296 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAu-0005VD-NS for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:01 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:39867) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAh-0005U4-9D for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wr1-f68.google.com with SMTP id a11so1643415wra.6 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=IRQX+ltzgQQQCLJNrNgluNhY+yKeEN3wmYeHe2/L9Gc=; b=X4axORuWVXmRxnoXVcQdoZcvwOMLOS52xSOlBC0PH48QmPWP7Nnjx7myhw814kGOCq s/IgG1Rk8FJGIS4s+JWPOk09M3wD/5mCOZnbcs2yQdJngq+UR+wy8LtyFMxU9p28JG/U PR+iRIRfR46XFhnmJhm7h0bi/TxEIIMsareyDODoeK87bU/cbGth44NT2TJOy9DkAqPb T9BI0upSC391cC9zC8/F6YFiedrTKH/nFO7PKeud/2IGBjcfQpa98KVKFjXBBmBRyWcK Gg7Yzvg3/TdnFz0ohvnohawdo8KwMAV2vif6CL2YLdQInYOOjkufKTlTFMzSpHMivCC7 uWQA== 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=IRQX+ltzgQQQCLJNrNgluNhY+yKeEN3wmYeHe2/L9Gc=; b=Z2UFmiNU0x0DFLFij3lkR1ekZZLpwi9TT9RC31MQs6wRNzG+a8xWCLWI4O2jPCUcGR M1HNBDbKDV3iVge+qY+ded856J/x8pGsWfZ/RHv6amf4+otJO+nK0piW3VdnE3cTYWcN tY9L/QxIXQj0AYlCGJjikd535YR+Zp2BHtx+0jZFpGoAVMK2uD2bZRXfkrqr3733nB+7 AGhYgqS46B+Z4KMHoCEo4hUv3zLHb0wcePVji+xDt2RkN5bP3FT4Z+FWdzSCLqj8kRvn 55/PKzOu4O5nDkaKIdLkrveZwF/UfQgh4GC+mcp3Fe+cRpMcaSfyBhKx5gYuRUvI85R/ QYOQ== X-Gm-Message-State: APjAAAV86jMSuUdnwvaM+uEQP6HdiLz+pdRgPvXIAROJJHbb0BCf56XS znrUkHf9QGFy2EEJiw66ZW9X+2h+ X-Google-Smtp-Source: APXvYqyduEC57JABGmz9n6Z9134SIPlSSPsymLWu9z6tf7leY7U/gmyCsIfBvWUFUs8S7tlqOdtQvA== X-Received: by 2002:a5d:49c9:: with SMTP id t9mr24899332wrs.146.1572431141271; Wed, 30 Oct 2019 03:25:41 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:40 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:28 +0100 Message-Id: <20191030102531.12495-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-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-rprotobuflib): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92e5d3ec0b..7c1761852c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6166,3 +6166,42 @@ data.") (synopsis "Visualization for flow cytometry data") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) + +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg")))) + (properties + `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Contains unverified binaries: + ;; src/win/lib/{i386,x64}/libprotobuf.a + (add-after 'unpack 'remove-win-folder + (lambda _ + (delete-file-recursively "src/win") + #t)) + ;; Fix non-conventional packaging. + ;; The dependency to protobuf-2.6.0 is included as tgz and build + ;; by the R package itself. + (add-after 'unpack 'fix-wrong-hard-coded + (lambda _ + (with-directory-excursion "src" + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + (substitute* "src/protobuf-2.6.0/configure" + (("#! /bin/sh") (string-append "#!" (which "sh")))) + #t))))) + (home-page "https://bioconductor.org/packages/RProtoBufLib") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description "This package provides the headers and static library of +Protocol buffers 2.6.0 for other R packages to compile and link against.") + (license license:bsd-3))) From patchwork Wed Oct 30 10:25:29 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15896 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 75AC917685; Wed, 30 Oct 2019 10:26:25 +0000 (GMT) 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, RCVD_IN_MSPIKE_H2,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 3579417674 for ; Wed, 30 Oct 2019 10:26:25 +0000 (GMT) Received: from localhost ([::1]:38702 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlBI-0007dA-Ec for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:24 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40343) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB4-0007XW-U1 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlAz-0002p7-QC for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:10 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40483) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlAz-0002oA-LQ for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlAz-0005WH-DD for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 4/6] gnu: Add r-cytolib. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243116121177 (code B ref 37988); Wed, 30 Oct 2019 10:26:05 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:01 +0000 Received: from localhost ([127.0.0.1]:49298 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAv-0005VL-54 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:01 -0400 Received: from mail-wm1-f67.google.com ([209.85.128.67]:54928) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAi-0005U5-4e for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wm1-f67.google.com with SMTP id g7so1483210wmk.4 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:48 -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=FcZxrj0YZSeBRnqLcu/Ekvd3AWYSVWoCWNlHFphsfPs=; b=UvyrAbdwOYJWLwZMpq9nUhwAgit/UIsWJrNcO+QXXaESP5DBLVEakYYSZNCt10DYaW p049WElBzP2raCtk9ztl/Lm9zaf/LwTvOrI8g8YF9fgr5cezih4B9gw9udx5xneXd8V7 2VAw/YXw4tjh/63aF3KToEsbrufkNWBC71g3fvenC/xsVD8rWaEc4lRBYgtUHTDDl9+k 92gNA6JpnOFQfeCaiTVGN1FP6S/45M53WAsybZlKI3Ed1iA6pEWAzUf0rk7rkrjUS08o IUebQQJtw03V7xV+4tJjCDK6qv3zUXZhUgPzw3QxfCN4qtQ22MPTClgVcP5mqDdi6qBw xGhQ== 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=FcZxrj0YZSeBRnqLcu/Ekvd3AWYSVWoCWNlHFphsfPs=; b=AbQvN8MyzQB19Aw62SnifCOYzv19I7MnLeDGk37hfbf2ikNhqnQqLBRn+3k7bN25+N Nx4oVOEXjoZ9o/cV8oE+rg/FXN2bWIEsB51dnyodx3nDYv1MCuzT1LgoS4LggwWqcddw mgx1U0owqCFRCtIlMb3+v/hIWyZ3SZwLMi+B5hmUc3yFJjHF6lUkiP5skC+ccpmCjgQW hGp44PXTGfIkYAbhjRtdQzBPVwd7chIv1TTnr2rsovrNErY1eCGVXOoDJMTwem0dZte1 3mjaB0MRGkbti/Ymy8+PdxVDazkMfN3kt/ZhtNDGhJgAqdDCBYa0sgz2U78bxSi6kksJ qeEw== X-Gm-Message-State: APjAAAV/vN8FLnHwxBr5DJ8by9PXPARAoDBj3mZ412BSgQES1YEc7Qvc tLhQtZI7fH8fXKzp3cWhtFejPDp0 X-Google-Smtp-Source: APXvYqziPLoI9aw3UaSRs1kZqK6Xx7xP9wXTuK6/9RY2UhsCZOaKnwAv4kDErSb9I4lQqCnnP3dkjg== X-Received: by 2002:a1c:6308:: with SMTP id x8mr8402811wmb.140.1572431142301; Wed, 30 Oct 2019 03:25:42 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:41 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:29 +0100 Message-Id: <20191030102531.12495-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-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-cytolib): 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 7c1761852c..a5c6e1ed55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6205,3 +6205,26 @@ data.") (description "This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.") (license license:bsd-3))) + +(define-public r-cytolib + (package + (name "r-cytolib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cytolib" version)) + (sha256 + (base32 + "10sdkwrmzmp3sh59hl3x0zxwlw77v80jnv8gz1qrv66skjb764cq")))) + (properties + `((upstream-name . "cytolib"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rprotobuflib" ,r-rprotobuflib))) + (home-page "https://bioconductor.org/packages/cytolib") + (synopsis "C++ infrastructure for representing and interacting with the gated cytometry") + (description "This package provides the core data structure and API to +represent and interact with the gated cytometry data.") + (license license:artistic2.0))) From patchwork Wed Oct 30 10:25:30 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15898 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 EE00017685; Wed, 30 Oct 2019 10:26:38 +0000 (GMT) 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, RCVD_IN_MSPIKE_H2,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 AB9BE17674 for ; Wed, 30 Oct 2019 10:26:38 +0000 (GMT) Received: from localhost ([::1]:38710 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlBV-0007oT-R8 for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40326) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB3-0007Vh-Ic for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:11 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlB1-0002u7-Vh for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:09 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40484) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlB1-0002tG-RZ for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlB0-0005WQ-6A for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 5/6] gnu: Add r-ncdfflow. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243116221189 (code B ref 37988); Wed, 30 Oct 2019 10:26:06 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:02 +0000 Received: from localhost ([127.0.0.1]:49300 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAv-0005VV-LH for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:02 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:46939) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAi-0005U8-Ts for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:54 -0400 Received: by mail-wr1-f42.google.com with SMTP id n15so1609993wrw.13 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:48 -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=dr8HRKHlY7FqNgdC6GQexNyqk3uJt7l1BMmThsXxqlc=; b=gx+79W23Hvlzz1jBBHwaKZ3CyyPmP1v8AIEVIszOTIBst6tOIj512VbKF9tJwx59Hl YDyh3P6NeZZW9+rMziFKP8cZ5Q+PaEE5gJipUsEd9Lks/rFv132DjpUY44ORd9uelKso JvTZW1KZMsW6/e5FDJWbG1TJZs2gOG/t1w6uPFziWnzqWbfPUfrelyRARkeUZY7kJN79 QrmfYrmr1zT320Lm9f4doDpwPcze20WyEHHszXtIalmja5ZBaITHCRE2pyP6YZJop0Nq QmCjSD7uckRtHKex5O3HFNZuB+coyMVkFFrkzFqcXzFleD9n/DIJGrxxkRgBQc/EMxle iQyg== 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=dr8HRKHlY7FqNgdC6GQexNyqk3uJt7l1BMmThsXxqlc=; b=ieTL2jXGcxVx65D5DkyooQBOiu6X7+ZjJvfmwM/7QE86CfCsY2kU2ZWLYAQ2GdTly3 sxr/zyb8SvqDPgVnN99rMt2r36tgmY/MIOYR4jG8NTz5kyz4/e7kw+qb06gHaDLV5VKY 7F2vk1XbtrdnQDx/WO2B2pRjChrrlqFWkCl+U11qufSYJvci+lYrH9Y8BKY4JTyVh7f4 Nj1y5G3MQsXvL3j6LfFxlVPZvsDSvwS2yVCBJpZZseIVaVixZdqkiO3TO+N89dL8fZP2 Ygcl4QMEES6Xa7o6ZFwm1LB7ivfJ6UC7rI8/jMOQebW0h/MLmECB1Q1OFIziSB7xYs8b 6Yng== X-Gm-Message-State: APjAAAUSeRoi3OKcqIeHP/NQ7rpZlFHM5OHcVEjI2bgrqntMlXVIXq07 lwRcqkJVcs96y1c7vuj+gz67ZmHa X-Google-Smtp-Source: APXvYqxWNsEUqW273PK/4PpTjoLPBmP9ZxpjwM7tuITdJsmGIqZtXxBxx7RQuZS/0xd1adiDIZjD4Q== X-Received: by 2002:a5d:6b81:: with SMTP id n1mr23978369wrx.254.1572431143121; Wed, 30 Oct 2019 03:25:43 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:42 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:30 +0100 Message-Id: <20191030102531.12495-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-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-ncdfflow): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a5c6e1ed55..2636095e0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6228,3 +6228,35 @@ Protocol buffers 2.6.0 for other R packages to compile and link against.") (description "This package provides the core data structure and API to represent and interact with the gated cytometry data.") (license license:artistic2.0))) + +(define-public r-ncdfflow + (package + (name "r-ncdfflow") + (version "2.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ncdfFlow" version)) + (sha256 + (base32 + "02769pr4gipjdlknhk8adica7v37c9fviffv0qscrf9v5j26rxzw")))) + (properties + `((upstream-name . "ncdfFlow"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ncdfFlow") + (synopsis "Storage based on HDF5 for flow cytometry data") + (description + "This package provides HDF5 storage based methods and functions for +manipulation of flow cytometry data.") + (license license:artistic2.0))) From patchwork Wed Oct 30 10:25:31 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15895 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 5FBBC17685; Wed, 30 Oct 2019 10:26:18 +0000 (GMT) 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, RCVD_IN_MSPIKE_H2,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 18DDD17674 for ; Wed, 30 Oct 2019 10:26:18 +0000 (GMT) Received: from localhost ([::1]:38700 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlBB-0007Um-Cs for patchwork@mira.cbaines.net; Wed, 30 Oct 2019 06:26:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40274) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPlB0-0007QZ-0D for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:07 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPlAy-0002ld-KZ for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40481) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPlAy-0002lA-Fr for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPlAx-0005W1-PU for guix-patches@gnu.org; Wed, 30 Oct 2019 06:26:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH 6/6] gnu: Add r-flowworkspace. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Oct 2019 10:26:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157243116021158 (code B ref 37988); Wed, 30 Oct 2019 10:26:03 +0000 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:00 +0000 Received: from localhost ([127.0.0.1]:49294 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAu-0005V6-51 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:00 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:41219) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAj-0005UA-HR for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wr1-f68.google.com with SMTP id p4so1633895wrm.8 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:49 -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=M0rGms2nvbWS20tLFPIynEvDoGLaGhMxz3isshnakiA=; b=gjsSQyQjI7tclSqkDplypyrzcLqNY4GN2mtG+vDjZyuOZURF6LlFOP3FAeWoJdvqnt 60POUtQk7Vz/2Bkxo1jMxwHAEHGI7LFcaDXK3mMH2CNG3YgeCTEsJP8CDQ34fGOaCyYL gDCjxo4gLC4jtiSGHcN8BsCuJo9xhtsv9Ei9Io0F2SCL/ibwMFCzpE2kj/Uu1PPLG6U0 y5Mmv2c1xdJCUzclQUKjOl+HEPhF8BE1L5Rf12LfLkFXRrBNERhPzZdPHFH9vI0MJEH8 lEyFUJpEiwRIbqGkQ9DfW4n21Ocs3cf5+kNJiwGh8/nIpNkCpyuDAonT0CNg36avgPGO FU0Q== 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=M0rGms2nvbWS20tLFPIynEvDoGLaGhMxz3isshnakiA=; b=aB+zPXwe5IootGzGUsHh3NO92HXSfIkx7cYE4QY6NS51nSMaTrzgbm53Sf7xBepXeS mCyQ5EwiHPIheXc0Qi1tjWH8OWOrhLXN0mW5/Ig+tVYoNib3Kioh8h90yEZ4JOEXY5Lm z85Lur4JTQfRy+1uKa3VBfA/WPli9lqDZPMYJ9aA5Iv5FNuP2aMZZp2w68X9OvshrafB AY7ddId9ANEovgiEZTZTCXsHjbKjYyQVao4OPqFmQXqGzzH3AaYmYe4qKmqEqWf6Xzss 41B0jBpFqoEHGXf2l1gTjqH2G/d5xI9cPr5G3Z725KdNgMFRQF3GLenwBSu08Sznh16n qsIw== X-Gm-Message-State: APjAAAUU487F1tuHITxjB2yG8fJrmspq82bJUZP84sojXRQn/pyy10Mz KXBXSA+Lmu5lOj3z8NzAGeGJCFkK X-Google-Smtp-Source: APXvYqzEXQzBD6ORavqs/MGBtKWXqG/+HjoSEt61N12QO3Iz9yTqdn16lfEbsBX0VNcXrA5XOe2OmA== X-Received: by 2002:adf:f547:: with SMTP id j7mr5580227wrp.69.1572431143799; Wed, 30 Oct 2019 03:25:43 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:43 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:25:31 +0100 Message-Id: <20191030102531.12495-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-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-flowworkspace): New variable. --- gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2636095e0f..dabfcb2cb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6260,3 +6260,53 @@ represent and interact with the gated cytometry data.") "This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.") (license license:artistic2.0))) + +(define-public r-flowworkspace + (package + (name "r-flowworkspace") + (version "3.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspace" version)) + (sha256 + (base32 + "1r1xxqzlp2x2gf79f37ckninnyjkxcb7xz7rffg2nadmapl5shvw")))) + (properties + `((upstream-name . "flowWorkspace"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page + "https://bioconductor.org/packages/flowWorkspace") + (synopsis "Infrastructure for representing and interacting with cytometry data sets") + (description + "This package provides importer for basic workspaces from the proprietary +software FlowJo into the BioConductor package flowCore. It is designed to +facilitate comparison of automated gating methods against manual gating. +Gating hierarchies, groups of samples, compensation, and transformation are +performed so that the output matches the analysis from the proprietary +software FlowJo.") + (license license:artistic2.0)))