From patchwork Tue Jan 17 12:25:37 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 46222 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 23C0E27BBED; Tue, 17 Jan 2023 12:27:39 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 1B60827BBE9 for ; Tue, 17 Jan 2023 12:27:38 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHl3Q-0006VH-Aa; Tue, 17 Jan 2023 07:27:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pHl3O-0006TQ-BR for guix-patches@gnu.org; Tue, 17 Jan 2023 07:27:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pHl3O-00076R-34 for guix-patches@gnu.org; Tue, 17 Jan 2023 07:27:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pHl3N-0007eZ-U1; Tue, 17 Jan 2023 07:27:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60877] [PATCH 3/4] gnu: Add r-speaq. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 17 Jan 2023 12:27:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60877 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60877@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60877-submit@debbugs.gnu.org id=B60877.167395836529323 (code B ref 60877); Tue, 17 Jan 2023 12:27:01 +0000 Received: (at 60877) by debbugs.gnu.org; 17 Jan 2023 12:26:05 +0000 Received: from localhost ([127.0.0.1]:36016 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2S-0007cm-Ls for submit@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:05 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:39287) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2O-0007bg-DV for 60877@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:01 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1673958354; x=1675772755; bh=1vNR4dNNkSCu2gV046OoR5yjikXvypHxhPlQmn0FPkU=; b=gQYJo2ueYs6K YzlJM0yNemGmGVohZZrBsirHXbTRtSZ60P3336b0RMwpOGGl9dMMnMaA8k61P7HI 6Hqdpsy3GHjrXoTFO7MQHCsYfgjbjXCjE1Mb7RVIKqZo79y5v7HK9Ywx/qauAUdv vzEZznI4N2ediqb7VcG/okRLrnRy7M0= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 3067CA00FD for <60877@debbugs.gnu.org>; Tue, 17 Jan 2023 13:25:54 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.17; Tue, 17 Jan 2023 13:25:49 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 17 Jan 2023 13:25:37 +0100 Message-ID: <20230117122538.41537-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20230117122538.41537-1-madalinionel.patrascu@mdc-berlin.de> References: <20230117122538.41537-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-AS-Result: No-10-3.505400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOIqU frHU7PyNfobKmjcxu0juNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIMay5jJvrxqMP7f voZ2kxst7MSP7SLpuGIV8NIIr/0M2jizRBzpJMZQAPmNKDWsW0M9SJbNoRDCLU72YOAMDJjieAi CmPx4NwHJnzNw42kCxxEHRux+uk8jfhP1xgyx3DEo3+cKm5H/g9dfejfyi1eZUomt7lcw46xH2k HrccoiUnPMYA7ekg2IKopUj5E3sUuroEcouxJmhLZwp4+OENJgRL14a0dMOt9xSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-3.505400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-SNTS-SMTP: 6D9651B1C56761C7CD5928EF2BE3191A5ADAF3E3C7DBB7E5282C4365998998B32002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-speaq): New variable. --- gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2fa26cb59..7498c3a767 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier ;;; Copyright © 2020 Peter Lo -;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu +;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes @@ -7624,6 +7624,46 @@ (define-public r-slingshot graph construction.") (license license:artistic2.0))) +;; This is a CRAN package but it depends on a bionconductor package. +(define-public r-speaq + (package + (name "r-speaq") + (version "2.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "speaq" version)) + (sha256 + (base32 + "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk")))) + (properties `((upstream-name . "speaq"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-data-table + r-dosnow + r-foreach + r-ggplot2 + r-gridextra + r-impute + r-massspecwavelet + r-missforest + r-reshape2 + r-rfast + r-rvest + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=speaq") + (synopsis "Tools for nuclear magnetic resonance spectra alignment") + (description + "This package helps with @acronym{NMR, Nuclear Magnetic Resonance} spectroscopy +data analysis as easy as possible. It only requires a small set of functions to +perform an entire analysis. Speaq offers the possibility of raw spectra alignment +and quantitation but also an analysis based on features whereby the spectra are +converted to peaks which are then grouped and turned into features. These features +can be processed with any number of statistical tools either included in speaq +or available elsewhere on CRAN.") + (license license:asl2.0))) + (define-public r-stager (package (name "r-stager")