From unknown Tue Aug 19 23:13:47 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61252] [PATCH 3/3] gnu: Add r-dorothea. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Feb 2023 12:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61252 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61252@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16754267724986 (code B ref -1); Fri, 03 Feb 2023 12:20:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:32 +0000 Received: from localhost ([127.0.0.1]:36663 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2S-0001IM-Ax for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:32 -0500 Received: from lists.gnu.org ([209.51.188.17]:39742) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2Q-0001ID-7B for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:31 -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 1pNv2L-0005Xu-Uo for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:26 -0500 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 1pNv2I-0005pD-A6 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:25 -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=1675426751; x=1677241152; bh=8gMs13RjcFm7Ib7dhV+P1XLIuucG7EinnFOA2S1dWSY=; b=U6PSnHFsQO8d lSSCX//TM25JkGQT4gTFjfD8MVQalEksK4RKxEPhHl2vR0TcYxytubxoqg2rHpGF t/Jsp3HbFhuOazBrTPjtMeoV/u/3jZHqn4VQz7V59H4297xUoXYZKLByTV7RlQid 0nYJMqQ1KMldrnzjHG0mGBcLDNPPcsk= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 2D2DD300476 for ; Fri, 3 Feb 2023 13:19:11 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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; Fri, 3 Feb 2023 13:19:06 +0100 From: Navid Afkhami Date: Fri, 3 Feb 2023 13:18:54 +0100 Message-ID: <20230203121854.95308-3-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> References: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [10.84.128.45] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10--5.692400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6MKPrF7dK57MXjfR3d0weRpQOYBrXJCKAWFC ZbvPiXUWOpcUW0o8+sKD8el0BdzuolAEOTWU7+ZWrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGij+ffe3B1tiAu8sKJSXbINbwjHXliV4XMOSR1u+6Od8u1AJBZ5UxqA= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.692400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: 22E8D98D8E5D3F45818B6CDCE81E41EB190CE94F0116AEE689D110AC5F7CCD282002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) 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-dorothea): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 521d6c00be..0786160b5e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -466,6 +466,31 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10 in Biostrings objects.") (license license:artistic2.0))) +(define-public r-dorothea + (package + (name "r-dorothea") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dorothea" version + 'experiment)) + (sha256 + (base32 + "05vkb5mash2m8p6njk842sy5pz7vblrm8n9bphqbslm86kld5n92")))) + (properties `((upstream-name . "dorothea"))) + (build-system r-build-system) + (propagated-inputs (list r-bcellviper r-dplyr r-magrittr r-viper)) + (native-inputs (list r-knitr)) + (home-page "https://saezlab.github.io/dorothea/") + (synopsis "Collection of human and mouse TF regulons") + (description + "DoRothEA is a gene regulatory network containing signed transcription factor. +DoRothEA regulons, the collection of a TF andits transcriptional targets, +were curated and collected from different types ofevidence for both human +and mouse. A confidence level was assigned to each TF-target interaction +based on the number of supporting evidence.") + (license license:gpl3))) + (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") -- 2.34.1 From unknown Tue Aug 19 23:13:47 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Navid Afkhami Subject: bug#61252: closed ([PATCH 3/3] gnu: Add r-dorothea.) Message-ID: References: <87a61u929c.fsf@elephly.net> <20230203121854.95308-3-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 61252 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61252@debbugs.gnu.org Date: Fri, 03 Feb 2023 15:51:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1675439462-14521-1" This is a multi-part message in MIME format... ------------=_1675439462-14521-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61252: [PATCH 3/3] gnu: Add r-dorothea. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 61252@debbugs.gnu.org. --=20 61252: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61252 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1675439462-14521-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61252-done) by debbugs.gnu.org; 3 Feb 2023 15:50:48 +0000 Received: from localhost ([127.0.0.1]:39823 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNyKu-0003lm-8V for submit@debbugs.gnu.org; Fri, 03 Feb 2023 10:50:48 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21177) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNyKr-0003le-Rh for 61252-done@debbugs.gnu.org; Fri, 03 Feb 2023 10:50:46 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1675439444; cv=none; d=zohomail.com; s=zohoarc; b=ehO4ckdx05fwWAGRKjYvXJlsIp4scvl5O6cPwBGOEfb2rl2Shjw3gqho65ocDo5lBi2Q2RCOT4R+xG/0r0H0q2MEbXGtzVmSSs3NLhMzsqXiqvCz6Q/vZgfD2WBAGIqChtnwptWmY60ct2GXpBlZEQDCHSrlr2Uci2B7klOLUT0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1675439444; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To; bh=N78/0Ck54npSrREuJefTDByAY4lqhxx2SzyLYHZfPEg=; b=gqZitmGmkOPF7SQCrbWgqkqzi2VKuJXY6COtxZfXbfwWPodLjtouP8N3J8227cr/AT4OU7WVZLlaYIal60/8HrJmc3I9v2tFnT97hmOPLgI30JUyYAfm2CipJyskX+thEtljb+NfcUbvojrDh/2WKx3X9OwFSzoHqF4/+s/F9+o= 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=1675439444; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=N78/0Ck54npSrREuJefTDByAY4lqhxx2SzyLYHZfPEg=; b=c42mOm4NrhcpBkblQrZ0oGF24VsVw7n/Fpv0mP7iTINJiF/VUcuMlS0JrdNVUKjc Fv16WBWopOBl5OP0YK7rtgyjjGcPuazqTeHCIbrfqdt7irrRfg+SnY2umS+/JgKchGA 69AasArXMIYsOB474yp3qyYUMrahgNEUnosL91qI= Received: from localhost (i5E862D0C.versanet.de [94.134.45.12]) by mx.zohomail.com with SMTPS id 1675439442594216.60007723623232; Fri, 3 Feb 2023 07:50:42 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61252-done@debbugs.gnu.org Subject: [PATCH 3/3] gnu: Add r-dorothea. Date: Fri, 03 Feb 2023 16:49:38 +0100 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 Message-ID: <87a61u929c.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: 61252-done 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 (-) Thanks for the patch! Since this depends on r-viper, which is nonfree I cannot add this package to Guix. I have instead pushed it to the channel =E2=80=9Cguix-science-nonfree=E2=80=9D. --=20 Ricardo ------------=_1675439462-14521-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:32 +0000 Received: from localhost ([127.0.0.1]:36663 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2S-0001IM-Ax for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:32 -0500 Received: from lists.gnu.org ([209.51.188.17]:39742) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2Q-0001ID-7B for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:31 -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 1pNv2L-0005Xu-Uo for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:26 -0500 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 1pNv2I-0005pD-A6 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:25 -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=1675426751; x=1677241152; bh=8gMs13RjcFm7Ib7dhV+P1XLIuucG7EinnFOA2S1dWSY=; b=U6PSnHFsQO8d lSSCX//TM25JkGQT4gTFjfD8MVQalEksK4RKxEPhHl2vR0TcYxytubxoqg2rHpGF t/Jsp3HbFhuOazBrTPjtMeoV/u/3jZHqn4VQz7V59H4297xUoXYZKLByTV7RlQid 0nYJMqQ1KMldrnzjHG0mGBcLDNPPcsk= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 2D2DD300476 for ; Fri, 3 Feb 2023 13:19:11 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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; Fri, 3 Feb 2023 13:19:06 +0100 From: Navid Afkhami To: Subject: [PATCH 3/3] gnu: Add r-dorothea. Date: Fri, 3 Feb 2023 13:18:54 +0100 Message-ID: <20230203121854.95308-3-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> References: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [10.84.128.45] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10--5.692400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6MKPrF7dK57MXjfR3d0weRpQOYBrXJCKAWFC ZbvPiXUWOpcUW0o8+sKD8el0BdzuolAEOTWU7+ZWrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGij+ffe3B1tiAu8sKJSXbINbwjHXliV4XMOSR1u+6Od8u1AJBZ5UxqA= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.692400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: 22E8D98D8E5D3F45818B6CDCE81E41EB190CE94F0116AEE689D110AC5F7CCD282002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-dorothea): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 521d6c00be..0786160b5e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -466,6 +466,31 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10 in Biostrings objects.") (license license:artistic2.0))) +(define-public r-dorothea + (package + (name "r-dorothea") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dorothea" version + 'experiment)) + (sha256 + (base32 + "05vkb5mash2m8p6njk842sy5pz7vblrm8n9bphqbslm86kld5n92")))) + (properties `((upstream-name . "dorothea"))) + (build-system r-build-system) + (propagated-inputs (list r-bcellviper r-dplyr r-magrittr r-viper)) + (native-inputs (list r-knitr)) + (home-page "https://saezlab.github.io/dorothea/") + (synopsis "Collection of human and mouse TF regulons") + (description + "DoRothEA is a gene regulatory network containing signed transcription factor. +DoRothEA regulons, the collection of a TF andits transcriptional targets, +were curated and collected from different types ofevidence for both human +and mouse. A confidence level was assigned to each TF-target interaction +based on the number of supporting evidence.") + (license license:gpl3))) + (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") -- 2.34.1 ------------=_1675439462-14521-1--