From patchwork Fri Nov 3 14:55:56 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: 55888 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 9C1A727BBE2; Fri, 3 Nov 2023 14:57:49 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 4D5EB27BBEA for ; Fri, 3 Nov 2023 14:57:48 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qyvcB-0005an-O9; Fri, 03 Nov 2023 10:57:39 -0400 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 1qyvc1-0005a1-Px for guix-patches@gnu.org; Fri, 03 Nov 2023 10:57:32 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qyvbz-0004aN-LI for guix-patches@gnu.org; Fri, 03 Nov 2023 10:57:28 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qyvcZ-0005DD-5Q; Fri, 03 Nov 2023 10:58:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66917] [PATCH 1/2] gnu: Add r-mblm. 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: Fri, 03 Nov 2023 14:58:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66917 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <66917@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66917-submit@debbugs.gnu.org id=B66917.169902344819978 (code B ref 66917); Fri, 03 Nov 2023 14:58:03 +0000 Received: (at 66917) by debbugs.gnu.org; 3 Nov 2023 14:57:28 +0000 Received: from localhost ([127.0.0.1]:59524 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyvbz-0005C5-Vi for submit@debbugs.gnu.org; Fri, 03 Nov 2023 10:57:28 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:47659) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyvbx-0005Bb-2e for 66917@debbugs.gnu.org; Fri, 03 Nov 2023 10:57:26 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1699023399; x=1700837800; bh=5GZR8xQYymzTgyf +WC8qmJQqYx/g1JsF8vqD6LD2A9E=; b=ff3qdKZHP873nPOl9I2TRuHVucfxqO5 kSH17s58VQFTzoxdOV/OryQY7UdJnQrl/OgOTyiXvp71c8CjafTMmmoy0YSmcqiF fPAlNCH+oxFvHWxF7s6yu37HDJULkJxXIb4rMINbyCdObYAG07Cj3fIIl79NxC50 QX1YUbXsKEtQ= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 2B36EA0174 for <66917@debbugs.gnu.org>; Fri, 3 Nov 2023 15:56:39 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 3 Nov 2023 15:56:38 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 3 Nov 2023 15:55:56 +0100 Message-ID: <395c833b4e654eb62fb10c892716422b634080e5.1699023357.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27976.000 X-TM-AS-Result: No-10--5.859400-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/Exmr5hqNL1say5jJvrxqMEb6 weOxZY457MSP7SLpuGM4KFbsCNnaKTQlifLY1rnkfZhFimVQHWwTHaede/M0j64sf0Egj7iqsqx rFSI3/KVslxAfd+6tXElOOOz3JPpijxYyRBa/qJXcsDK2xBHh7jaPj0W1qn0TKayT/BQTiGqqsy u4o7z+hUUR4XxxSjMC9I+JvMMVvI0elb8v+Ucr/j98szMMr5o0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.859400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27976.000 X-TM-SNTS-SMTP: 227C8D2FF3E373242D3C5DE8F3DF5B536A604E8A1529DE46D51C0862A71D569B2000: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-mblm): New variable. Change-Id: Iddfa9bc03a4e5782623253cb70d1ae888545e2ec --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f2a035555b..ec7200749a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3149,6 +3149,27 @@ (define-public r-matrix-utils objects.") (license license:gpl3))) +(define-public r-mblm + (package + (name "r-mblm") + (version "0.12.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mblm" version)) + (sha256 + (base32 "1fipb3bryaimr30lcxsxrn0ymv24z39swca7s4z7p9xcfg3ban1b")))) + (properties `((upstream-name . "mblm"))) + (build-system r-build-system) + (home-page "https://www.r-project.org") + (synopsis "Median-based linear models") + (description + "This package provides linear models based on Theil-Sen single median and +Siegel repeated medians. They are very robust (29 or 50 percent breakdown point, +respectively), and if no outliers are present, the estimators are very similar +to OLS.") + (license license:gpl2+))) + (define-public r-mboost (package (name "r-mboost") From patchwork Fri Nov 3 14:55:57 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: 55887 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 EDAD627BBEC; Fri, 3 Nov 2023 14:57:48 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 3F7AB27BBE2 for ; Fri, 3 Nov 2023 14:57:48 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qyvcB-0005b9-Vx; Fri, 03 Nov 2023 10:57:40 -0400 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 1qyvc1-0005a2-Qh for guix-patches@gnu.org; Fri, 03 Nov 2023 10:57:32 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qyvbz-0004aJ-KB for guix-patches@gnu.org; Fri, 03 Nov 2023 10:57:28 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qyvcY-0005D5-LD; Fri, 03 Nov 2023 10:58:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66917] [PATCH 2/2] gnu: Add r-ewastools. 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: Fri, 03 Nov 2023 14:58:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66917 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <66917@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 66917-submit@debbugs.gnu.org id=B66917.169902344819972 (code B ref 66917); Fri, 03 Nov 2023 14:58:02 +0000 Received: (at 66917) by debbugs.gnu.org; 3 Nov 2023 14:57:28 +0000 Received: from localhost ([127.0.0.1]:59522 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyvbz-0005C0-LX for submit@debbugs.gnu.org; Fri, 03 Nov 2023 10:57:27 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:32915) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyvbx-0005Be-2h for 66917@debbugs.gnu.org; Fri, 03 Nov 2023 10:57:25 -0400 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=1699023403; x=1700837804; bh=UIj8acHfuiEwYc/A20OA2XwWHz5ty4AZbtQQhN4vYuo=; b=JhUsQH9JiIoj RhJETK60dRs5D4Vr6MaQC+MqbLcXw8KebyMVbGBtbKzXSjmicxn20+wRN4fz/Gew 7suiaCoQXHqL+j21a2ofKuxuNBp1HGMjO5nJcxrJy7PJCcy0kGLMOaeQ8LZ0q6nV crgNeLxR/emKg5M0XWcxUhmhdUdyUh0= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 5F405A0184 for <66917@debbugs.gnu.org>; Fri, 3 Nov 2023 15:56:43 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 3 Nov 2023 15:56:39 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 3 Nov 2023 15:55:57 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <395c833b4e654eb62fb10c892716422b634080e5.1699023357.git.madalinionel.patrascu@mdc-berlin.de> References: <395c833b4e654eb62fb10c892716422b634080e5.1699023357.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27976.000 X-TM-AS-Result: No-10--7.533900-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/o5C9bTTxaUYue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbed/3m /AxvcR1HOlj6mOjC06LlABs5DhOfwL1vtt3X2p0VvTnqYKYXTRgseQVcTRnF2lwV2iaAfSWcURS Scn+QSXhhJCIHRlO51+gtHj7OwNO2BSJy8ngwKGVfS4agXUYUm6lOhIGtjBA81Ibl6b0n75fpxE Hm9BFf441dEf8COOO4= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.533900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27976.000 X-TM-SNTS-SMTP: 3D13EC6C45FDA897F22FE808F5980FE755C262769B8D2DC757E9F4B940A742122000: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/bioinformatics.scm (r-ewastools): New variable. Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a47e84bc33..11ca777fa2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -876,6 +876,38 @@ (define-public r-conqur simultaneously considered.") (license license:gpl3)))) +(define-public r-ewastools + (let ((commit "f7646cacd73266708479b3fea5d625054d179f95") + (revision "1")) + (package + (name "r-ewastools") + (version (git-version "1.7.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hhhh5/ewastools/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0irarlnxfnasa755adxsn67rxsy01zwhjhw18g4cag08cqiyyw41")))) + (properties `((upstream-name . "ewastools"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table + r-igraph + r-illuminaio + r-mblm + r-quadprog)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hhhh5/ewastools/") + (synopsis + "Quality control toolset for the Illumina Infinium DNA methylation") + (description + "Collection of useful functions for working with DNA methylation +micro-array data.") + (license license:unlicense)))) + (define-public r-numbat (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295") (revision "1"))