From unknown Wed Jun 18 23:07:54 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#66915 <66915@debbugs.gnu.org> To: bug#66915 <66915@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-methylaid. Reply-To: bug#66915 <66915@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:07:54 +0000 retitle 66915 [PATCH] gnu: Add r-methylaid. reassign 66915 guix-patches submitter 66915 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 66915 normal tag 66915 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Nov 03 09:52:47 2023 Received: (at submit) by debbugs.gnu.org; 3 Nov 2023 13:52:47 +0000 Received: from localhost ([127.0.0.1]:57323 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyubO-0002uf-UL for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:52:47 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55584) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyub9-0002u9-UA for submit@debbugs.gnu.org; Fri, 03 Nov 2023 09:52:45 -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 1qyuaT-000544-M4 for guix-patches@gnu.org; Fri, 03 Nov 2023 09:51:49 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qyuaR-00023J-Fz for guix-patches@gnu.org; Fri, 03 Nov 2023 09:51:49 -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=1699019502; x=1700833903; bh=FQ0XlyJ0B5t8QPX 4L0jPAXqQHO1/L1BgOnAUZ7HCmqY=; b=G9h78OOVV1FUf8bWdX9N2EILin/53Uu EQRHrydfS69CetnjhHfRH0FDwgDr6ToQW4auhO2iqX6iDLv6G4RrrtgeZs1vai+k 80tRm0GeSu6iQmJGfMqP0Qr8lf6sXfFTAfjc4Get9/u5+t2Ttf8MtVV/qWkNns4+ Yrnvk49/TWyE= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 361F2300128 for ; Fri, 3 Nov 2023 14:51:42 +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 14:51:41 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-methylaid. Date: Fri, 3 Nov 2023 14:51:17 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net X-Debbugs-Cc: Ricardo Wurmus Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27974.007 X-TM-AS-Result: No-10--8.894500-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v//j4ZByyZz4qY5ZGw7wyeHiwO YVASrRstAL1jMXhSmSXB0/XJv5meXjQZr7vgT4dDjpxdo/JwVm7+a+v4FF31uD2veI3/hwm/izy 75l6H5qX0tCKdnhB58I/9UW5M5dRMpg5yOcdoVgvcUt5lc1lLgoGRyAacnhaYKbcF66oyyUhym2 Q9dtriIKNlyYP7A9J1dhNCLzQsIZ37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.894500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27974.007 X-TM-SNTS-SMTP: D6BE2C8EE135451365202E8BF5695B5653055F6F193220C95E4820A2D72958DA2000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioconductor.scm (r-methylaid): New variable. Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432 --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79236ea26..c60f440f3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8454,6 +8454,44 @@ (define-public r-metaneighbor profiles than cells of different types.") (license license:expat))) +(define-public r-methylaid + (package + (name "r-methylaid") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MethylAid" version)) + (sha256 + (base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d")))) + (properties `((upstream-name . "MethylAid"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-ggplot2 + r-gridbase + r-hexbin + r-matrixstats + r-minfi + r-rcolorbrewer + r-shiny + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://git.bioconductor.org/packages/MethylAid") + (synopsis + "Quality control of large Illumina DNA Methylation array data sets") + (description + "This package provides a visual and interactive web application using +RStudio's shiny package. Bad quality samples are detected using sample-dependent +and sample-independent controls present on the array and user adjustable +thresholds. In depth exploration of bad quality samples can be performed using +several interactive diagnostic plots of the quality control probes present on +the array. Furthermore, the impact of any batch effect provided by the user can +be explored.") + (license license:gpl2+))) + (define-public r-methylkit (package (name "r-methylkit") base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Sat Nov 04 11:15:43 2023 Received: (at 66915-done) by debbugs.gnu.org; 4 Nov 2023 15:15:43 +0000 Received: from localhost ([127.0.0.1]:35584 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzIND-0005fM-2s for submit@debbugs.gnu.org; Sat, 04 Nov 2023 11:15:43 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21796) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzIN8-0005fA-VP for 66915-done@debbugs.gnu.org; Sat, 04 Nov 2023 11:15:41 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1699110898; cv=none; d=zohomail.com; s=zohoarc; b=KQTFF3/hsgRQYUhXtwhVGo66mFa8v8RNo/jZr+RBdPaKfgmfo/MvKCNcyXe5Ocfy6LoZsf3yhaNF7imm3U1+3wDMM1B4T86g0UgTbCduBoawxqpbV/JQwX01yvdeLM71ZlXULKIl19La2zthtRaO4o3zP7I1lmAE1kHpKCeT6wI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1699110898; h=Content-Type:Content-Transfer-Encoding:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=8N+TgBcy8uJsZp0Bq9/7KndhllnfsfGqV5/0RhP2y54=; b=FjA/oISxNmbtrKtupkiyFdCe5GOHjgWawkOucK1N7mQ1xI9OK3BDItQBcblK/Y1u7+92EV+ZAARrK2IYdVpFEK+sS8LElbOkiLN1s+xRgxa3NNg7BF2eWz3PK+ZNhz5o9O6RIa9IBFQ2vbS0y5ZT9ncCIcVb+pyuyxnx93Z8Eko= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1699110898; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=8N+TgBcy8uJsZp0Bq9/7KndhllnfsfGqV5/0RhP2y54=; b=PNMe9rhXOmzyvesEbu6rc1ovnXwxnvEaT5NCbYe+k6Bkx9803tnJt0Plx2lJYjkG Uy9lVZRrh+H8BNMYEAP8tL433Q57lJeqTM4TGnyzJ8tPt/v9l/2pHwbp9O8KYATGX7K KveXR7db7S97/WPLV/su4ULLl15c3uJyC7H+QwiI= Received: from localhost (215-110-142-46.pool.kielnet.net [46.142.110.215]) by mx.zohomail.com with SMTPS id 1699110897210126.2448908480784; Sat, 4 Nov 2023 08:14:57 -0700 (PDT) References: User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#66915] [PATCH] gnu: Add r-methylaid. Date: Sat, 04 Nov 2023 16:14:43 +0100 In-reply-to: Message-ID: <87o7g9sg7m.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66915-done Cc: 66915-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioconductor.scm (r-methylaid): New variable. Applied, thanks! --=20 Ricardo From unknown Wed Jun 18 23:07:54 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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