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Reply-To: bug#71341 <71341@debbugs.gnu.org> Date: Sat, 21 Jun 2025 17:40:56 +0000 retitle 71341 [PATCH] gnu: Add r-topdom. reassign 71341 guix-patches submitter 71341 "Afkhami, Navid" severity 71341 normal tag 71341 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Jun 03 10:49:23 2024 Received: (at submit) by debbugs.gnu.org; 3 Jun 2024 14:49:23 +0000 Received: from localhost ([127.0.0.1]:42181 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sE8zz-0006JW-Br for submit@debbugs.gnu.org; Mon, 03 Jun 2024 10:49:23 -0400 Received: from lists.gnu.org ([209.51.188.17]:39404) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sE8zv-0006JK-W9 for submit@debbugs.gnu.org; Mon, 03 Jun 2024 10:49:22 -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 1sE8zi-0007QH-Ok for guix-patches@gnu.org; Mon, 03 Jun 2024 10:49:06 -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 1sE8ze-0000Ap-VI for guix-patches@gnu.org; Mon, 03 Jun 2024 10:49:06 -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=1717426132; x=1719240533; bh=jocAZeE7oHUGeZc 3ifizofVKxdyMLy/8uKtWTghh8BU=; b=d6sB4DPQn4EX0AQ2NXuqNT4Kg1+WDYQ f+yoQJ5nO6OXlTtGdFSPViTx2epoDRRbC9g/8P2vnv+TkLd6FSCXZ7nBMnh4X6HE boNHfFRskcVyPXav5REGv+hT7yJ50ZM2P6YAISikq4fY+IizbdxLSxcFLLI6840Z mAyxFvsIKmp4= 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 04F3B30016F for ; Mon, 3 Jun 2024 16:48:51 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.2.1544.11; Mon, 3 Jun 2024 16:48:51 +0200 From: "Afkhami, Navid" To: Subject: [PATCH] gnu: Add r-topdom. Date: Mon, 3 Jun 2024 14:47:35 +0000 Message-ID: <264adf3424ada808c111117a9adec5fe93b36d33.1717426055.git.Navid.Afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] 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-14.0.0.3152-9.1.2019-28430.000 X-TM-AS-Result: No-10--10.517800-5.000000 X-TMASE-MatchedRID: HRm6PbbemxcEZ1mm50iAbnOjEKYddvv63O2+pOfl+vcwLJ9PZUBQhboC GrShPd9QjKW8K3tQE81SGsbcdf+3HIdGq5XlvEmXUrLQDoO1CVfumP3eaxnnYaFRWC8HCKx2+3D GARmE5RD2FNHpYWnkM/Uq+uCsoxv00DEbrM4yUgIyYhVjrk9k7w2LmwHT7i+nBK4oo7tJnZH+OG D8fImu3AObIzLs3GAWEgg3cwDHl/1Oj13VCsVwItZBcBEGL4iHcilEE+Pje887nRP0DvgcK8oxR 0nqileq4FPP+wnXR3zFPoVV+WRinAL0L3My7prcmq/rZ8xK4TUfqWBYKqQeM5hjbkoEU+3E X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--10.517800-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28430.000 X-TM-SNTS-SMTP: 9DE78FBA9EA1C4EE7AE54177122530876D4F5F29DF131C0321B9C5DCEC37ABF72000: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, 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 Cc: "Afkhami, Navid" 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 (--) * gnu/packages/cran.scm (r-topdom): New variable. Change-Id: I63d265470499affc8f0de94f88739c6631281a0d --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 16a864be93..b0ccee37bb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31108,6 +31108,30 @@ (define-public r-tolerance Visualizations are also available for most of these settings.") (license license:gpl2+))) +(define-public r-topdom + (package + (name "r-topdom") + (version "0.10.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "TopDom" version)) + (sha256 + (base32 "1rryfnwvdlpdrjgs6sciy91cxfp4jykll0swclasydjvj4n642i6")))) + (properties `((upstream-name . "TopDom"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-matrixstats r-reshape2 r-tibble)) + (home-page "https://github.com/HenrikBengtsson/TopDom") + (synopsis "Efficient method for Identifying genomic topological domains") + (description + "This method identifies topological domains in genomes from Hi-C sequence data. +The authors published an implementation of their method as an R script. This package +originates from those original @code{TopDom} R scripts and provides help pages adopted +from the original @code{TopDom} PDF documentation. It also provides a small number of +bug fixes to the original code.") + ;; Either version of the GPL + (license (list license:gpl2 license:gpl3)))) + ;; Keep this in sync with the liblantern package. (define-public r-torch (package base-commit: 1615084a9a4115d48b75b3db048761e7534efc87 prerequisite-patch-id: 191a8394dbe6f865a9dc55bfc1b62e9dffc2180d prerequisite-patch-id: 3ddb7b281335b1bb4ced1e60a1f243a12a5cba2b -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 28 05:59:19 2024 Received: (at 71341-done) by debbugs.gnu.org; 28 Jun 2024 09:59:19 +0000 Received: from localhost ([127.0.0.1]:44708 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sN8Nz-0000gh-IT for submit@debbugs.gnu.org; Fri, 28 Jun 2024 05:59:19 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21176) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sN8Nw-0000gW-TS for 71341-done@debbugs.gnu.org; Fri, 28 Jun 2024 05:59:18 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1719567848; cv=none; d=zohomail.com; s=zohoarc; b=RI+RiIMW8BAf7IKpAd4A4uxdDWQLZQwsF63vv3Z/Tmc1+uzy6NrYx7GPu9VlouCqun6pPGIGyLnletx9BhYBjvuq8sp1xo1/bJbT7VS/P52weg6ef8D54kOFsiw5efH6ac3Zb0LimwXaNOJr0V0bsPuBgQi+2MJk8dkErmsDY28= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1719567848; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=qZWeNUH/waPl+vc7Qy/PpGq+sq/w0Ex0YjtuTUVi/5A=; b=gFal9uzIke/upEra4b90gwBmW47GSQ9zCckoVhDhvhRMqaZ2ufHNv3yh7VctJgCW3SF5/j5qa1YfDcB0gYWJENxf8j5bAAkMCSsoXUWWA+NdUwexjqFCjfd6cPvpHeze4XONcfdJOYQ5Uulqhr5bUPE4f5srseMxJc8Q/iWB7ZQ= 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=1719567848; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=qZWeNUH/waPl+vc7Qy/PpGq+sq/w0Ex0YjtuTUVi/5A=; b=LWrkUNQmyDDFw7RS2JyZA8vsprGxFB7ITxWbeiOTjp5hHv/cainrw9HADCo1F1/l Da1595912gioM4xC9QUZ0Yxs5hrQ68j8UmlmXAnqpF0VxOjnSCTnn8obgbZ3Vo3zRPL 9sdMlEtO1RQlQwou7X0woH99TEpNH653BgdIM/FE= Received: by mx.zohomail.com with SMTPS id 1719567845513895.0285237635572; Fri, 28 Jun 2024 02:44:05 -0700 (PDT) From: Ricardo Wurmus To: 71341-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-topdom. Date: Fri, 28 Jun 2024 11:44:01 +0200 Message-ID: <87pls1wgf2.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 71341-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 (-) I've applied it with minor formatting and spelling changes. Thanks! -- Ricardo From unknown Sat Jun 21 10:40:56 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, 26 Jul 2024 11:24:09 +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