From patchwork Tue Jan 17 12:25:35 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: 46219 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 37CA527BBED; Tue, 17 Jan 2023 12:26:20 +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 4C13827BBE9 for ; Tue, 17 Jan 2023 12:26:19 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHl2S-0005cx-UG; Tue, 17 Jan 2023 07:26:04 -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 1pHl2R-0005bn-Ts for guix-patches@gnu.org; Tue, 17 Jan 2023 07:26:03 -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 1pHl2Q-0006pl-48 for guix-patches@gnu.org; Tue, 17 Jan 2023 07:26:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pHl2P-0007cL-UV; Tue, 17 Jan 2023 07:26:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60877] [PATCH 1/4] gnu: Add r-baseline. References: In-Reply-To: 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 12:26:01 +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=B60877.167395836129272 (code B ref 60877); Tue, 17 Jan 2023 12:26:01 +0000 Received: (at 60877) by debbugs.gnu.org; 17 Jan 2023 12:26:01 +0000 Received: from localhost ([127.0.0.1]:36009 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2O-0007bz-VA for submit@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:01 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:49301) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2N-0007bd-Iv for 60877@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:00 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1673958352; x=1675772753; bh=jPhKZOnB7v5g2uS cg8q7n9Z4uVtJ/2u9IzUuS0bt4ds=; b=WGjeAPg6ra+qdtXbOqtHTTeUXBgk53G F7SNeLEuhfL10+sMZGl1aOb3zjfjS9hpgvSNXsst91GK+hzXOtHzGr6IxDx5b8MQ YadIDDmx12R3XfYZvhRI/dEAXSNMdBOBDtDUBjrqshmUhJMC4IqeeX97KkwnC/SQ 9WidR9pLdF28= 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 66487A00E5 for <60877@debbugs.gnu.org>; Tue, 17 Jan 2023 13:25:49 +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 13:25:35 +0100 Message-ID: <20230117122538.41537-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 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--1.974800-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6VPaJqbGA1Msgrcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbagsijoFeI56b5/AwQXCNXriq+GZ9ZHxIhuW77/y896siFzNNPDc6umOCbuVI7hVbL1xv NmiS10Z5PPWZgdfJwagiPMvT9S9ITjHFMyUt7B901PRCuPh/FNSFzI8m33tit64sf0Egj7iqsqx rFSI3/KRfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJUl4W8WVUOR/9xS3mVzWUuAojN1lLei7Rd3nc zcp/KcLnW9NaizqVjIvqu7tIGUCL3JH1HgsPLBilONd7CdPSF8GPh5kfmkP8pgm74Cy7Tbm5C52 2OQzs3ZSxie1FGcVp1koJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.974800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-SNTS-SMTP: 339189A1A980D9CA9596311D172152C02FC1F97E840F8E270E3871F8ABF952B42002: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/cran.scm (r-baseline): New variable. --- gnu/packages/cran.scm | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) base-commit: 789d73234d5b6bbd83bb054146d5bbd1d374d51a diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3fcbd3b9f6..53f3ebbcf5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2018 Sandeep Subramanian ;;; Copyright © 2018 Charlie Ritter ;;; Copyright © 2018 Konrad Hinsen -;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2020-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2018 Laura Lazzati ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2018 Marius Bakke @@ -9241,6 +9241,31 @@ (define-public r-base64url systems.") (license license:gpl3))) +(define-public r-baseline + (package + (name "r-baseline") + (version "1.3-4") + (source (origin + (method url-fetch) + (uri (cran-uri "baseline" version)) + (sha256 + (base32 + "1kl68zvyi2zd73jy3axrvrymwn4y6l4pd62nz0fciwbgkjhz3yyx")))) + (properties `((upstream-name . "baseline"))) + (build-system r-build-system) + (propagated-inputs (list r-limsolve r-sparsem)) + (home-page "https://github.com/khliland/baseline/") + (synopsis "Baseline correction of spectra") + (description + "This package is a collection of baseline correction algorithms. Beside +those it provides a framework and a Tcl/Tk enabled GUI for optimizing baseline +algorithm parameters. Typical use is the removal of the background effects from +spectra, which are originating from various types of spectroscopy and spectrometry. +Also, there is a possibility of optimizing this with regard to regression or +classification results. Correction methods include polynomial fitting, weighted +local smoothers and many more.") + (license license:gpl2))) + (define-public r-radiant-data (package (name "r-radiant-data") From patchwork Tue Jan 17 12:25:36 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 46220 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 185D427BBED; Tue, 17 Jan 2023 12:27:12 +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 7A05E27BBE9 for ; Tue, 17 Jan 2023 12:27:11 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHl3R-0006WB-Gq; Tue, 17 Jan 2023 07:27:05 -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-0006TM-LH 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-00076Q-0b 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-0007eQ-HX; Tue, 17 Jan 2023 07:27:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60877] [PATCH 2/4] gnu: Add r-missforest. 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=B60877.167395836429316 (code B ref 60877); Tue, 17 Jan 2023 12:27:01 +0000 Received: (at 60877) by debbugs.gnu.org; 17 Jan 2023 12:26:04 +0000 Received: from localhost ([127.0.0.1]:36014 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2S-0007ck-CW for submit@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:04 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:48273) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2N-0007be-Ix for 60877@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:00 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1673958353; x=1675772754; bh=g5vRy758EQrj/jGKaHqiQEoTBN2xY5QeTtuykCGun7k=; b=CRgI0Xe7w3ot px3LBpiJmh+qszOAOA1bo0QT1IHHluWagdzKaJoVoRA/2TWaAotuG6BiRpvw+0FA IU9jLDcZ3i3sA+2GdoqXj7c3CJZW0PBo8Qwkh92N22+S+4x3XcLeiuSz1is6kgAS nGQjOK0169+JHpK7FnFUnoL8IXFoHsI= 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 6C057A00FB for <60877@debbugs.gnu.org>; Tue, 17 Jan 2023 13:25:53 +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 13:25:36 +0100 Message-ID: <20230117122538.41537-2-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--4.422200-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOEKo /65yrX6peDD58ltWiLmBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRjIFcYKjRuw1zZe d9XvcyXod2kUAnaHjfmi/4EPlPQ60RYhdLOvDqAeQJOFc+qyqK515IJRl/rxKTPm/MsQarwONpx yS486Sbl7jTh0hLY36MCqIkhJgocDQ3sOMB3Fk1OLzNWBegCW29sZ0UX0EaOILbigRnpKlKTpcQ TtiHDgWUWA7He6cVsQxqs1MNg1DT7AgydGLD2d+g0oA8icLlixmMwE+j7bPWGNXf3GDBVihQfMX Dym+k6hpezr+W4Ri/Anq3zjdgSRO3yJq1ESN+kMTydv0PB1DgLaNtJpvWmDRSPEWnCfndI5+GPk JmSZLIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.422200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-SNTS-SMTP: 820C531D27B5FB2770CBBAF1ACB1A4A9BD9938C5B04A720B06E5C874E0DA252B2002: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/cran.scm (r-missforest): 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 53f3ebbcf5..6ae5b96eb2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -15227,6 +15227,36 @@ (define-public r-misc3d ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) +(define-public r-missforest + (package + (name "r-missforest") + (version "1.5") + (source (origin + (method url-fetch) + (uri (cran-uri "missForest" version)) + (sha256 + (base32 + "13c38hpl60ca1kwyv61cxsla6ccmsj4qzp0vrxcq7b827fh5aw21")))) + (properties `((upstream-name . "missForest"))) + (build-system r-build-system) + (propagated-inputs + (list r-dorng + r-foreach + r-iterators + r-itertools + r-randomforest)) + (home-page "https://github.com/stekhoven/missForest") + (synopsis "Nonparametric missing value imputation using Random Forest") + (description + "The function @code{missForest} in this package is used to impute missing +values, particularly in the case of mixed-type data. It uses a random forest +trained on the observed values of a data matrix to predict the missing values. +It can be used to impute continuous and/or categorical data, including complex +interactions and non-linear relations. It yields an @acronym{OOB, out-of-bag} +imputation error estimate without the need of a test set or elaborate cross- +validation. It can be run in parallel to save computation time.") + (license license:gpl2+))) + (define-public r-ks (package (name "r-ks") 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") From patchwork Tue Jan 17 12:25:38 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 46221 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 4882327BBED; Tue, 17 Jan 2023 12:27:34 +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 873F227BBEB for ; Tue, 17 Jan 2023 12:27:33 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHl3R-0006WK-T3; Tue, 17 Jan 2023 07:27:05 -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-0006Tr-Pu for guix-patches@gnu.org; Tue, 17 Jan 2023 07:27:03 -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-00076c-FQ 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 1pHl3O-0007eh-AN; Tue, 17 Jan 2023 07:27:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60877] [PATCH 4/4] gnu: Add r-alpsnmr. 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 12:27:02 +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=B60877.167395836529329 (code B ref 60877); Tue, 17 Jan 2023 12:27:02 +0000 Received: (at 60877) by debbugs.gnu.org; 17 Jan 2023 12:26:05 +0000 Received: from localhost ([127.0.0.1]:36018 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2T-0007cu-4i for submit@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:05 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:37543) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHl2P-0007bj-CG for 60877@debbugs.gnu.org; Tue, 17 Jan 2023 07:26:02 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1673958355; x=1675772756; bh=5YVTqdFMF0Sc8IRrmNabLIHYx4YQq1/G3lO6kUjOSLE=; b=VYAfDtMddXry 4PuC7kFkPOv/cEs0AnB9SRXtOH4AgtO35Yc7EFlcxJ7/HskkIvRLk73V9YBRnuT+ 2v8pNoPwJio9vhz27+c3pBIqKPtb80lGrteQxcj9cG2g271FlSaAil/vbVmlNm6l quGukjRjjUb1nk3QxmNk1Y2l5AB0wnw= 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 24A69A0116 for <60877@debbugs.gnu.org>; Tue, 17 Jan 2023 13:25:55 +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 13:25:38 +0100 Message-ID: <20230117122538.41537-4-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--0.341900-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYknjvpTqmXN2tt5RGkMP+aywLYk+NSxc5oGAD6h6FZmEe88qtLWjN6Ygtp dYIvYnioS232z3nHFPNABuz7vZSu5OEt+E9fCvHuB381iZ59HqJ1Koz3Y/YrHY51XDO6Dn5g69K 4zHVFUDgx/sJ74sgV26a3flwysHKPQ3sOMB3Fk1OLzNWBegCW2wgn7iDBesS2sWV0bdkf4OXSm0 LYJYAIAsDQqn/EvP1ZTiG+aiMwbEW5/gLf2hWzlcU6vWnje8OtFpF827xwzbi5D4iH5KETID1ik DpaEHjF0wmQM6M5DiQcI4N0jMK86dAnzxkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68H qACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.341900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-SNTS-SMTP: 60F3800BC38BD2A62478B1230473CB1EA809856A3858935FC5B1A89181A2C8912002: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-alpsnmr): New variable. --- gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7498c3a767..118f218f4b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2598,6 +2598,59 @@ (define-public r-alpine data.") (license license:gpl2+))) +(define-public r-alpsnmr + (package + (name "r-alpsnmr") + (version "4.0.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlpsNMR" version)) + (sha256 + (base32 + "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl")))) + (properties `((upstream-name . "AlpsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-baseline + r-biocparallel + r-dplyr + r-fs + r-future + r-generics + r-ggplot2 + r-glue + r-htmltools + r-magrittr + r-matrixstats + r-mixomics + r-pcapp + r-purrr + r-readxl + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-signal + r-speaq + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://sipss.github.io/AlpsNMR/") + (synopsis "Automated spectral processing system for NMR") + (description + "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data +directories both zipped and unzipped. It provides automated and efficient signal +processing for untargeted NMR metabolomics. It is able to interpolate the samples, +detect outliers, exclude regions, normalize, detect peaks, align the spectra, +integrate peaks, manage metadata and visualize the spectra. After spectra +proccessing, it can apply multivariate analysis on extracted data. Efficient +plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported +JDX samples is also available.") + (license license:expat))) + (define-public r-altcdfenvs (package (name "r-altcdfenvs")