From unknown Thu Jun 19 14:00:59 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#56034 <56034@debbugs.gnu.org> To: bug#56034 <56034@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-amaretto. Reply-To: bug#56034 <56034@debbugs.gnu.org> Date: Thu, 19 Jun 2025 21:00:59 +0000 retitle 56034 [PATCH] gnu: Add r-amaretto. reassign 56034 guix-patches submitter 56034 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 56034 normal tag 56034 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 17 05:29:52 2022 Received: (at submit) by debbugs.gnu.org; 17 Jun 2022 09:29:52 +0000 Received: from localhost ([127.0.0.1]:43744 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o28Ia-0008AM-Bi for submit@debbugs.gnu.org; Fri, 17 Jun 2022 05:29:52 -0400 Received: from lists.gnu.org ([209.51.188.17]:53386) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o28IW-0008AA-G8 for submit@debbugs.gnu.org; Fri, 17 Jun 2022 05:29:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36024) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o28IW-0005eD-7W for guix-patches@gnu.org; Fri, 17 Jun 2022 05:29:48 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:53113) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o28IT-0008W5-Bl for guix-patches@gnu.org; Fri, 17 Jun 2022 05:29:47 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 44040300370 for ; Fri, 17 Jun 2022 11:29:41 +0200 (CEST) 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=1655458180; x=1657272581; bh=dqVSR48DBza5Vg32CzbE+CFKY6UYYmhIOsYfse8k49Q=; b=qS2XbgYsRzeT 4f5L3wbv09sRcH7t/Wa2toWOYrxoKXi0cfVBsG7triSJTt63bl8tZXCdaH49PM6E UwBOABGtN1DtijmHB1/D9KnigJf+Uw/mCpgBorIlueBdL2Fx+KXAeD1sNB7090sc v91RCGNtOTlt61zUhlHnUoQ3ypqi48Y= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 8cihlrlp0_2s for ; Fri, 17 Jun 2022 11:29:40 +0200 (CEST) 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 for ; Fri, 17 Jun 2022 11:29:40 +0200 (CEST) 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_256_GCM_SHA384) id 15.1.2507.9; Fri, 17 Jun 2022 11:29:39 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-amaretto. Date: Fri, 17 Jun 2022 11:29:29 +0200 Message-ID: <20220617092929.353-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net 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-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26960.006 X-TM-AS-Result: No-10--6.897400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcMu0i9VlgrN6hF4zyLyne+ATJDl9FKHbrn7fZJfDdCIXPo1 c6H9DbojwkwY92nLGuXj0Sbso8/33pXlm91Fv1IpvL/Dm1nUPdkXjfR3d0weRtodkNYFbOrOe9Q KgtmmT7F8FOHDsv49Nz2FT75yDfBlWi8Qip68NgfdCok3ibXlQeuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWxfIVs4QjZ1xabmiIVZgQ7uFYSnIZ/Eam3jcWFjLbXS3r7RTBZjMGZg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.897400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.006 X-TM-SNTS-SMTP: 1C2317CBFE9EBE87A04C23F8DA116A706D554359E424D3994B22F93186DE92982002: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: -1.4 (-) 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: -2.4 (--) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..a78ceb2de5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,58 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-amaretto + (package + (name "r-amaretto") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AMARETTO" version)) + (sha256 + (base32 + "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + (properties `((upstream-name . "AMARETTO"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocfilecache + r-callr + r-circlize + r-complexheatmap + r-curatedtcgadata + r-doparallel + r-dplyr + r-dt + r-foreach + r-ggplot2 + r-glmnet + r-gridextra + r-httr + r-impute + r-knitr + r-limma + r-matrix + r-matrixstats + r-multiassayexperiment + r-rcpp + r-readr + r-reshape2 + r-rmarkdown + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AMARETTO") + (synopsis "Regulatory network inference and driver gene evaluation") + (description + "This package @code{AMARETTO} represents an algorithm that integrates copy +number, DNA methylation and gene expression data to identify a set of driver +genes by analyzing cancer samples and connects them to clusters of co-expressed +genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer +setting to identify cancer driver genes and their modules on multiple cancer +sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle +and EMT, and modules that accurately predict survival and molecular subtypes. +This allows @code{AMARETTO} to identify novel cancer driver genes directing +canonical cancer pathways.") + (license license:asl2.0))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 30 09:51:36 2022 Received: (at 56034-done) by debbugs.gnu.org; 30 Jun 2022 13:51:36 +0000 Received: from localhost ([127.0.0.1]:33728 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o6ua0-0007nR-Fi for submit@debbugs.gnu.org; Thu, 30 Jun 2022 09:51:36 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21084) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o6uZy-0007nI-3F for 56034-done@debbugs.gnu.org; Thu, 30 Jun 2022 09:51:35 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1656597091; cv=none; d=zohomail.com; s=zohoarc; b=glzFLQZQSIH7Nz5srdS5u1bN0awT9xNS5shfNDbphC5EkQGLD6F30gRGTXbJLyrcEClpwhu64sG4QBJXirX6QUSr0BH23uq/5HMk+UIvwNMUHS+83LkhFMhALQ4OqiI93n4aHCauNr+vuKWXyOyAvrMvjjXOaK99hq+Sm5FkOR0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1656597091; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=zQr8Ti5Sg5D0LfUNUP59vI8AhRQSYsqJT1upSAnfLvI=; b=hFIEoNy51hh6RQQvogVUSv9jUHNk9YnUL1IpcOqPhBj7tNl28bJ2k094fRew19eV6E7rIPXlSjews9cQ0P9NfSY29xGudZ7wbkP1om/DH1RpVKnFC9mHAMRRhIQUvIA2tDSUE3YnVs/r+cVGnnrHOyC1yHVTiUugMgpzJItkG4U= 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=1656597091; 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=zQr8Ti5Sg5D0LfUNUP59vI8AhRQSYsqJT1upSAnfLvI=; b=Nwpu1m37isC3tXWPZsf1lBEMLkDewOXYq+tpTLgsiOrRaafh2vFHlbjZgYq+d6AA dumAs2dfYUz8ITAFBFUx3reJgJBXz4wO7xd9ooK3tGHL8nK+5EoHNLLCTotQVnfV6Cg WGKFA1ly07POuDhYJMwiu8L+gYILqkGbfs7kY75c= Received: from localhost (72-109-142-46.pool.kielnet.net [46.142.109.72]) by mx.zohomail.com with SMTPS id 1656597088662850.6420618760003; Thu, 30 Jun 2022 06:51:28 -0700 (PDT) References: <20220617092929.353-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#56034] [PATCH] gnu: Add r-amaretto. Date: Thu, 30 Jun 2022 15:50:59 +0200 In-reply-to: <20220617092929.353-1-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 Message-ID: <87mtdu8dk1.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: 56034-done Cc: 56034-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: > diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm > index 1e87b190c2..a78ceb2de5 100644 > --- a/gnu/packages/bioconductor.scm > +++ b/gnu/packages/bioconductor.scm > @@ -1987,6 +1987,58 @@ (define-public r-agimicrorna > objects are used so that other packages could be used as well.") > (license license:gpl3))) >=20=20 > +(define-public r-amaretto Applied (with a new commit message). Thanks! --=20 Ricardo From unknown Thu Jun 19 14:00:59 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 29 Jul 2022 11:24:06 +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