From patchwork Mon Feb 15 05:44:36 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Tim Howes X-Patchwork-Id: 27065 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 02F3F27BC45; Mon, 15 Feb 2021 09:36:28 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 8E26D27BC2E for ; Mon, 15 Feb 2021 09:36:27 +0000 (GMT) Received: from localhost ([::1]:48144 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lBaIs-0007Lz-OX for patchwork@mira.cbaines.net; Mon, 15 Feb 2021 04:36:26 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56730) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lBWgw-0000Wu-Hu for guix-patches@gnu.org; Mon, 15 Feb 2021 00:45:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:53851) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lBWgw-0008Qq-A7 for guix-patches@gnu.org; Mon, 15 Feb 2021 00:45:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lBWgw-0000kE-8n for guix-patches@gnu.org; Mon, 15 Feb 2021 00:45:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#46524] [PATCH 1/2] gnu: Add r-gsa. References: <20210215054029.47677-1-timhowes@lavabit.com> In-Reply-To: <20210215054029.47677-1-timhowes@lavabit.com> Resent-From: Tim Howes Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Feb 2021 05:45:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46524 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46524@debbugs.gnu.org Received: via spool by 46524-submit@debbugs.gnu.org id=B46524.16133678902826 (code B ref 46524); Mon, 15 Feb 2021 05:45:02 +0000 Received: (at 46524) by debbugs.gnu.org; 15 Feb 2021 05:44:50 +0000 Received: from localhost ([127.0.0.1]:37162 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgk-0000jV-CW for submit@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:50 -0500 Received: from lavabit.com ([38.147.122.66]:25308) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgj-0000jD-7Y for 46524@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:49 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id HIZPDQXN6WYY for <46524@debbugs.gnu.org>; Sun, 14 Feb 2021 23:44:43 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1613367883; bh=bgQ6LLKNBmxwA3n/uDLR348l0LueRjrte/FqngTlvTM=; h=From:To:Subject:Date:Message-Id:X-Mailer:MIME-Version: Content-Type:Content-Transfer-Encoding; b=NDSL58S1ixlA/dMUI5CS7w4FMsrJl85gZuzTmPwOwZRL/7BSsBpzrbAWs+ci/OKYd Bf3CMrUorMvz26TaLHW+n1cHuFWjYnFv1/7zekLmndLJ8Y84KGGbNp5D3+nDrFKtS7 l+bLj1qyVCigTW2Pb2hbMMZdsvVZArKCTUrByets95VSNN2IsgLggttZ2gzB4OojT0 KtXhH3YRD1vMf0X6WucHClYvsxOar4n1KnBi2GzHAC3bClN/TlsmpkLTuMpJ/7qPNh Epb7e9FRKoZDIXu5hquanItq2RY3IxCuUdWRcq8r0bUD5wYiYF4A2z1gCdZnm+/Kwf KDjOEFkqJyLrQ== Date: Sun, 14 Feb 2021 21:44:36 -0800 Message-Id: <20210215054437.47745-1-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Mon, 15 Feb 2021 04:36:19 -0500 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" Reply-to: Tim Howes X-ACL-Warn: , Tim Howes via Guix-patches X-Patchwork-Original-From: Tim Howes via Guix-patches via From: Tim Howes X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-gsa): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1fe90619cd..86b2df0a9f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,6 +33,7 @@ ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 Aniket Patil +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -26851,3 +26852,23 @@ from a source package. @code{pkgdown} converts your documentation, vignettes, README file, and more to HTML making it easy to share information about your package online.") (license license:expat))) + +(define-public r-gsa + (package + (name "r-gsa") + (version "1.03.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "GSA" version)) + (sha256 + (base32 + "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1")))) + (properties `((upstream-name . "GSA"))) + (build-system r-build-system) + (home-page + "https://statweb.stanford.edu/~tibs/GSA/") + (synopsis "Gene Set Analysis") + (description "Inference on gene sets in microarray studies.") + ;; Any version of the LGPL + (license license:lgpl3+))) From patchwork Mon Feb 15 05:44:37 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Tim Howes X-Patchwork-Id: 27066 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 5D54D27BC45; Mon, 15 Feb 2021 09:36:33 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 2706327BC2E for ; Mon, 15 Feb 2021 09:36:33 +0000 (GMT) Received: from localhost ([::1]:48566 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lBaIy-0007XS-CM for patchwork@mira.cbaines.net; Mon, 15 Feb 2021 04:36:32 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56732) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lBWgw-0000X1-TL for guix-patches@gnu.org; Mon, 15 Feb 2021 00:45:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:53852) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lBWgw-0008RT-M0 for guix-patches@gnu.org; Mon, 15 Feb 2021 00:45:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lBWgw-0000kn-L6 for guix-patches@gnu.org; Mon, 15 Feb 2021 00:45:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#46524] [PATCH 2/2] gnu: Add r-samr. Resent-From: Tim Howes Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Feb 2021 05:45:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46524 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46524@debbugs.gnu.org Received: via spool by 46524-submit@debbugs.gnu.org id=B46524.16133678922835 (code B ref 46524); Mon, 15 Feb 2021 05:45:02 +0000 Received: (at 46524) by debbugs.gnu.org; 15 Feb 2021 05:44:52 +0000 Received: from localhost ([127.0.0.1]:37164 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgm-0000jf-Kw for submit@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:52 -0500 Received: from lavabit.com ([38.147.122.66]:6440) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lBWgj-0000jE-M4 for 46524@debbugs.gnu.org; Mon, 15 Feb 2021 00:44:50 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id CQON08BU2Y86 for <46524@debbugs.gnu.org>; Sun, 14 Feb 2021 23:44:44 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1613367884; bh=tRtrFYvr3xZTAiItyf41/hMgBaJKE52eBaXg3a4+xII=; h=From:To:Subject:Date:Message-Id:X-Mailer:In-Reply-To:References: MIME-Version:Content-Transfer-Encoding; b=a3ZYYEcfMsZ7maYGvTmaPVvcKMzTU1PluB3Ba4W+v2BGf4rjWL0um0l3Sx2+TWKtx rF1YmXwIe5XPYMihGiN9Sa13LU7tHcpt972/e+a+Mwj3kTwysHCi5gLzxVFstwNO/V OQ4mt5ErH7ZHKSVyIyBzA5UxstQgqt1gNxSaoOjwJBM8B6z1NXAp2VXnb6/HqsOiXg N1x5e2O/ogYouKUFfK/D8WdR1gJ5mPUR3BqqcpL9TYBDpZyOT4sh36g6h4yY948wJK UmZn5XUygrCoQu1WLPZFM8j8WXg8KDBA/gg+IWsfM8D4nD47795eknHIzU6PENjBni ngKTVQWBBu0oQ== Date: Sun, 14 Feb 2021 21:44:37 -0800 Message-Id: <20210215054437.47745-2-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210215054437.47745-1-timhowes@lavabit.com> References: <20210215054437.47745-1-timhowes@lavabit.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Mon, 15 Feb 2021 04:36:19 -0500 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" Reply-to: Tim Howes X-ACL-Warn: , Tim Howes via Guix-patches X-Patchwork-Original-From: Tim Howes via Guix-patches via From: Tim Howes X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-samr): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 86b2df0a9f..d151f1cb50 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -26872,3 +26872,34 @@ package online.") (description "Inference on gene sets in microarray studies.") ;; Any version of the LGPL (license license:lgpl3+))) + +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page + "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis + "Significance Analysis of Microarrays") + (description + "Significance Analysis of Microarrays for differential expression +analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+)))