From patchwork Fri Nov 3 15:11:05 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: 55889 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 E235227BBEA; Fri, 3 Nov 2023 15:12:52 +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 1F78827BBE2 for ; Fri, 3 Nov 2023 15:12:52 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qyvqa-0001W8-Cx; Fri, 03 Nov 2023 11:12:32 -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 1qyvqW-0001Vs-TR for guix-patches@gnu.org; Fri, 03 Nov 2023 11:12:28 -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 1qyvqV-0000GZ-I0 for guix-patches@gnu.org; Fri, 03 Nov 2023 11:12:27 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qyvr4-0005fq-MD; Fri, 03 Nov 2023 11:13:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66918] [PATCH] gnu: Add r-rnbeads. 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 15:13:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 66918 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66918@debbugs.gnu.org Cc: Ricardo Wurmus X-Debbugs-Original-To: X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by submit@debbugs.gnu.org id=B.169902436821783 (code B ref -1); Fri, 03 Nov 2023 15:13:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 Nov 2023 15:12:48 +0000 Received: from localhost ([127.0.0.1]:59539 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyvqq-0005fG-B0 for submit@debbugs.gnu.org; Fri, 03 Nov 2023 11:12:48 -0400 Received: from lists.gnu.org ([2001:470:142::17]:48040) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qyvqn-0005ez-CO for submit@debbugs.gnu.org; Fri, 03 Nov 2023 11:12:46 -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 1qyvq8-0001SC-0E for guix-patches@gnu.org; Fri, 03 Nov 2023 11:12:04 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qyvq3-0000CD-74 for guix-patches@gnu.org; Fri, 03 Nov 2023 11:12:02 -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=1699024314; x=1700838715; bh=63lsag7LkJsoh9L KbyvLdPTe5HMoni8K8xyaSt3J4JE=; b=aqEH8lLXHVR0uRdzoXPWw54SmmRXa7G M6jQmzBjWA37hXSJtBalEw0s09i5n6WuY0d0614FLbg+BTqjSsVZL8K1t2GGL6Fp J1H8GySuiD7th0OxuL0kRnt1eIVQGAEP0lENzzHlNvqPNP4thdgGMjO+hKhd5pFh Gmj322rmFZck= 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 3C708A0174 for ; Fri, 3 Nov 2023 16:11:54 +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 16:11:53 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 3 Nov 2023 16:11:05 +0100 Message-ID: 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--5.700400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRjvzvGpLgmDXPNh MoIUJiCKGsZX0q3FpiOhAZQXEXXZurWL/xQJnm46rm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGo9VbVgm9IO5nVG5f7cXjVCfQA0cXsrAwHziS36W0SdEciM1dw5sE8w= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.700400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27976.000 X-TM-SNTS-SMTP: 59D652600BB2C3F7716820478EA75AD56BB9F0A6EF919C92427FABA4CCE90FB02000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.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-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-rnbeads): New variable. Change-Id: I78b248a449473fc37ac414295faa6e61269b8625 --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d79236ea26..bb51d389cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7976,6 +7976,42 @@ (define-public r-rhtslib of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+))) +(define-public r-rnbeads + (package + (name "r-rnbeads") + (version "2.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RnBeads" version)) + (sha256 + (base32 "15z7l4nmpy01xm19717l27nwf3rfsn6wjv211fn2y4ls40mz75qp")))) + (properties `((upstream-name . "RnBeads"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-cluster + r-ff + r-fields + r-genomicranges + r-ggplot2 + r-gplots + r-gridextra + r-illuminaio + r-iranges + r-limma + r-mass + r-matrixstats + r-methylumi + r-plyr + r-s4vectors)) + (home-page "https://bioconductor.org/packages/RnBeads") + (synopsis "RnBeads") + (description + "@code{RnBeads} facilitates comprehensive analysis of various types of DNA +methylation data at the genome scale.") + (license license:gpl3))) + (define-public r-impute (package (name "r-impute")