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Content preview: Content analysis details: (3.9 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -2.3 RCVD_IN_DNSWL_MED RBL: Sender listed at https://www.dnswl.org/, medium trust [209.51.188.17 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H4 RBL: Very Good reputation (+4) [209.51.188.17 listed in wl.mailspike.net] 0.9 SPF_FAIL SPF: sender does not match SPF record (fail) [SPF failed: Please see http://www.openspf.org/Why?s=mfrom;id=madalinionel.patrascu%40mdc-berlin.de;ip=209.51.188.17;r=debbugs.gnu.org] -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 2.3 EMPTY_MESSAGE Message appears to have no textual parts and no Subject: text 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager 2.0 BODY_EMPTY No body text in message From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 16 17:04:00 2020 Received: (at 45282) by debbugs.gnu.org; 16 Dec 2020 22:04:01 +0000 Received: from localhost ([127.0.0.1]:34125 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kpets-0007hR-JZ for submit@debbugs.gnu.org; Wed, 16 Dec 2020 17:04:00 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:45677) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kpetr-0007hJ-2F for 45282@debbugs.gnu.org; Wed, 16 Dec 2020 17:04:00 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 7EB631600D2; Wed, 16 Dec 2020 23:03:57 +0100 (CET) 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:received:received; s=mdc; t=1608156235; x=1609970636; bh=tmuLxEgj4jnfwV24cbMmpBTEn8uCWmKeTx+78MzO2LU=; b=M5Nitll78mWX uCmD1UC0fiboc78bnM/S1WHW6S+Joaui2fFqE1wtwaXNBUr2llaLcz9WawJINuW6 woyTP+faADoijoiPFzOlCpJUMbxDMy+eiViLfP+XQJUOMlf4PQwxzDhMUOZ7XYIf Z6DUVl93q3otem8UrQJtU4ywRnK6rM8= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id jfSI6EZhK4-l; Wed, 16 Dec 2020 23:03:55 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS; Wed, 16 Dec 2020 23:03:55 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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_128_GCM_SHA256) id 15.1.2106.2; Wed, 16 Dec 2020 23:03:55 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <45282@debbugs.gnu.org> Subject: [PATCH 1/2] gnu: Add r-kegggraph. Date: Wed, 16 Dec 2020 23:03:41 +0100 Message-ID: <20201216220342.3133-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-25854.003 X-TM-AS-Result: No-10--0.798400-8.000000 X-TMASE-MatchedRID: Z+/YWp2F+zUsaaYlMvaOHAPZZctd3P4BNwe5zfGEu3pe6bsL/Pg66vvM AqZVsxNriraWV2VugQxOjRzKJPqqS9WssQsVvEDfUYXhMajr0x53G1bsm5zfjMZygq/CPmro7pC UIx278DkwIlGOt0tC5gd2m1cUUwTvQ/iwA4k/JcKL6q5RsNhv5MLIFSKfPTIvcgfBE5DnP8M4c1 kfhp7b2wDHN+ym0W/W01CTCPwQxkmqivtKRvvg3HdrwHRqEx+DWuFm7TqL4eGpHpQYuqy67pgNM iEzDc45fS0Ip2eEHnyFh/DzryTTlvc8OJc7+0VJ9xS3mVzWUuBHZpq/WXaosmMgcFAOLXo1kHAQ alMRS7MANC6ObstCqY7sWcrGWq3sZbBqBHFZ0dBG1JkvfMb+bfelf69Q4VPZWPOnlRrrsda+iMO Th+UnSWuLCTjzz6qi2qQaz8sERlrwQVgIdVG4FE5aD4ZIh+0xjhMO3DAp+0s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.798400-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-25854.003 X-TM-SNTS-SMTP: 4026CEF4CCB32FC9DA7DCFC10F0ABCC51D6F83A573606E6F045C8FFE085135F02000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 45282 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-kegggraph): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4a1af4306..3026d1a496 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9247,3 +9247,29 @@ graph with the mapped data. In addition, @code{r-pathview} also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) + +(define-public r-kegggraph + (package + (name "r-kegggraph") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "KEGGgraph" version)) + (sha256 + (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) + (properties `((upstream-name . "KEGGgraph"))) + (build-system r-build-system) + (propagated-inputs + `(("r-graph" ,r-graph) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml))) + (home-page "http://www.nextbiomotif.com") ;;no https + (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") + (description + "@code{r-kegggraph} is an interface between Kegg Pathway database and graph +object as well as a collection of tools to analyze, dissect and visualize these +graphs. It parses the regularly updated kgml (Kegg xml) files into graph models +maintaining all essential pathway attributes. The package offers +functionalities including parsing, graph operation, visualization and etc.") + (license license:gpl2+))) -- 2.29.2 From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 16 17:16:33 2020 Received: (at 45282) by debbugs.gnu.org; 16 Dec 2020 22:16:33 +0000 Received: from localhost ([127.0.0.1]:34131 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kpf60-00080K-Qs for submit@debbugs.gnu.org; Wed, 16 Dec 2020 17:16:33 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:60063) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kpf5v-000807-C1 for 45282@debbugs.gnu.org; Wed, 16 Dec 2020 17:16:31 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id CC6111600E1; Wed, 16 Dec 2020 23:16:24 +0100 (CET) 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:received:received; s=mdc; t=1608156982; x=1609971383; bh=QrQlRdfDAduUo2zwfS1LA7R8HPAf3N4RJTWnGjDhYfE=; b=qomPKR6LBb3z fs9Jgg4okecnD1/ehWsV1hXgMEi8E18G5ZzyLhdKL9+sI74rbjqjo06NOWtzALE4 hxjhSi5cP8efaT7t1uuwqIP717gF0MHgd8PPQiNnHJtbwBguFq+MOy8I4QIRmcSq T8a7XxRTto/J78PTJ3cwHH9aGD3z1ug= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id BPuJE9ZgcvX4; Wed, 16 Dec 2020 23:16:22 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS; Wed, 16 Dec 2020 23:16:22 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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_128_GCM_SHA256) id 15.1.2106.2; Wed, 16 Dec 2020 23:16:22 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <45282@debbugs.gnu.org> Subject: [PATCH 2/2] gnu: Add r-pathview. Date: Wed, 16 Dec 2020 23:15:33 +0100 Message-ID: <20201216221533.3539-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-25854.003 X-TM-AS-Result: No-10--0.271800-8.000000 X-TMASE-MatchedRID: jKOZYMqOY08saaYlMvaOHAPZZctd3P4B/iHIRWzNKKPjW2KX8PkX4dxk cHrgwDdX6j33+BFSF5j5odUxplNHliN1dzbw87marKAvSPiudyH0IUHuSVWDh2myCG+JylaLZSk isg2H7q0wIlGOt0tC5jJw2KUmhkv8TLkTAzbQj8XKdqr1QlwmQbAUgNbbmVUmDfheddyhsqsuJa PbC+kbrGt9SSl+GQt64DHahalkaKVpDjo4VllSYB9CRIwXAbiiffXpER5TkJFe6bsL/Pg66vvMA qZVsxNriraWV2VugQzjD47KocCBC9Dew4wHcWTU4vM1YF6AJbbCCfuIMF6xLcK21zBg2KlfB00/ kkeBTwDs37Ik+pwXU07EofYQW/krZh6TU4GZDBnH0a/P9w0+XXOkBf8bKS45ME9Zw+UAsgpmgyI JK9lDN/3dE3QbPeOMXLdoIamwGEDGxtGzEkWA1hYZ6CluH+zH9XPESSHktUBZipn6czRzDQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.271800-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-25854.003 X-TM-SNTS-SMTP: 61E96FB6D6C5B0DFA5CB7B49B3E6B4C6CFA54454AA5BDB5153C15AAAEA6416D52000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 45282 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-pathview): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36274d0b39..b4a1af4306 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9213,3 +9213,37 @@ on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.") (license license:gpl2+))) + +(define-public r-pathview + (package + (name "r-pathview") + (version "1.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pathview" version)) + (sha256 + (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) + (properties `((upstream-name . "pathview"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-graph" ,r-graph) + ("r-kegggraph" ,r-kegggraph) + ("r-keggrest" ,r-keggrest) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-png" ,r-png) + ("r-rgraphviz" ,r-rgraphviz) + ("r-xml" ,r-xml))) + (home-page "https://pathview.uncc.edu/") + (synopsis "Tool set for pathway based data integration and visualization") + (description + "@code{r-pathview} is a tool set for pathway based data integration and +visualization. It maps and renders a wide variety of biological data on +relevant pathway graphs. All users need is to supply their data and specify +the target pathway. This package automatically downloads the pathway graph +data, parses the data file, maps user data to the pathway, and render pathway +graph with the mapped data. In addition, @code{r-pathview} also seamlessly +integrates with pathway and gene set (enrichment) analysis tools for +large-scale and fully automated analysis.") + (license license:gpl3+))) -- 2.29.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 17 06:32:24 2020 Received: (at 45282-done) by debbugs.gnu.org; 17 Dec 2020 11:32:24 +0000 Received: from localhost ([127.0.0.1]:34865 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kprWB-0003EF-Mv for submit@debbugs.gnu.org; Thu, 17 Dec 2020 06:32:23 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21053) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kprWA-0003D2-HP for 45282-done@debbugs.gnu.org; Thu, 17 Dec 2020 06:32:23 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1608204741; cv=none; d=zohomail.com; s=zohoarc; b=nyuSZopY+FfAWDp9Um+zafck25sAWRDtEypUu9T9ELzkd6ypzJE/d5miAn/RxaebOA9IvjSL1+TgJefOrm0Nq3E/jMMdHmLRB2eBI6p5fxuAharoaB8C1lw3+ScQJiMyUxl9g6XAnvDeXG7khevffPLCc5jAmwlbx+GpzV+CXik= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1608204741; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=agQR4+fGJgB9aMdRUBpZb01X9RU4tXLtNGDDPw3SEtA=; b=Gcl2RXlS3bAMjumivK5+tOX9RFlMPHLMnFZZbUEWxXECJMUtHkzTwE4D2fj4shF7PDm4lPBs8qxpnCCp5INxPN2XuxaOJE9AqfuRAwp+VQGhpSlY3qob9PU4RQPm36ilL89HGyL82DvvVzDr4uaFol8Ng+Zv3zRj3z1Q/edMdKk= 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= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1608204741; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type; bh=agQR4+fGJgB9aMdRUBpZb01X9RU4tXLtNGDDPw3SEtA=; b=QOosWi0MZrfGf1VigGxYNF8GH8EB8X85NPHDFZkL7zo+DjZ+hjsbdI8bRLinqFQv p7Hrdea+eLQAbbzJscJc+f34fTlt4Rk9EzJWnSjbiV4dcsNlRKy+aOiPJoj0OWhycb2 J9yXMZQJWyNJtmRmY/xDDa+6bqmsZYGjAzMA2My4= Received: from localhost (p54ad49eb.dip0.t-ipconnect.de [84.173.73.235]) by mx.zohomail.com with SMTPS id 1608204739747767.1500860070266; Thu, 17 Dec 2020 03:32:19 -0800 (PST) References: <20201216220342.3133-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.13; emacs 27.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 1/2] gnu: Add r-kegggraph. In-reply-to: <20201216220342.3133-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 17 Dec 2020 12:32:15 +0100 Message-ID: <87lfdwoegw.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 45282-done Cc: 45282-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 (-) I applied these with a few changes (moved the packages around and reordered the commits). Thanks! -- Ricardo From unknown Sat Aug 16 11:11:37 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 14 Jan 2021 12:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator