From debbugs-submit-bounces@debbugs.gnu.org Mon Jun 29 11:14:17 2020 Received: (at submit) by debbugs.gnu.org; 29 Jun 2020 15:14:17 +0000 Received: from localhost ([127.0.0.1]:49091 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jpvU8-0007K8-5v for submit@debbugs.gnu.org; Mon, 29 Jun 2020 11:14:17 -0400 Received: from lists.gnu.org ([209.51.188.17]:34636) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jpvQ4-0007Au-U9 for submit@debbugs.gnu.org; Mon, 29 Jun 2020 11:10:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:57120) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jpvQ4-0006Y9-DU for guix-patches@gnu.org; Mon, 29 Jun 2020 11:10:04 -0400 Received: from mout01.posteo.de ([185.67.36.65]:60678) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jpvQ2-0006i3-4Z for guix-patches@gnu.org; Mon, 29 Jun 2020 11:10:04 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id A27F5160060 for ; Mon, 29 Jun 2020 17:09:58 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1593443398; bh=I+kBV8H+M7xIwyBfDPgo+jpXwIXBgbgAXsPQ0UAZcRM=; h=From:To:Cc:Subject:Date:From; b=PAR1ZOtaWq8n8ZU6bJI1gVKQflGnuW0aUt7sXWiQJJSmnbBP3U9Pv0ineivjF/1cD 6FoiEEv/Zu6hmZ+VQC7uhdCrdvR6/2RgqxSmpDEuCoAKtNiaD0yUEm+voFQuWExiRB 8uXd/BTYlXTbDtwjH0U+fUuW0p3dbMqFoODhZ86SlhdGdDl8UJybf8teJPHZR2yQve ga4mSADUbvKGfazMhOx9mHLOHsKfPYWyozVq4iXclkyijd+achVxOkl9x0JyytrFG7 dzAf3RTm9HqmfBM5YAH1jkjNJcYsxWilefvSVfCvjsp5WNKyspTP1wl9XUywR8PzM3 HDjeT/NGEjYIA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 49wWBF4nB7z6tmW; Mon, 29 Jun 2020 17:09:57 +0200 (CEST) From: =?UTF-8?q?Antoine=20C=C3=B4t=C3=A9?= To: guix-patches@gnu.org Subject: [PATCH] gnu: Add r-transphylo Date: Mon, 29 Jun 2020 11:05:18 -0400 Message-Id: <20200629150517.28452-1-antoine.cote@posteo.net> X-Mailer: git-send-email 2.27.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=antoine.cote@posteo.net; helo=mout01.posteo.de X-detected-operating-system: by eggs.gnu.org: First seen = 2020/06/29 11:09:59 X-ACL-Warn: Detected OS = Linux 3.11 and newer 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, RCVD_IN_MSPIKE_H4=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=_AUTOLEARN X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Mon, 29 Jun 2020 11:14:14 -0400 Cc: =?UTF-8?q?Antoine=20C=C3=B4t=C3=A9?= 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: -2.3 (--) --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 70af2d30f0..749eee7856 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2020 Danjela Lura ;;; Copyright © 2020 Naga Malleswari ;;; Copyright © 2020 Eric Brown +;;; Copyright © 2020 Antoine Côté ;;; ;;; This file is part of GNU Guix. ;;; @@ -22372,3 +22373,27 @@ using @dfn{SHAP} (Shapley additive explanation) visualization plots for and force plot. It relies on the @code{XGBoost} package to produce SHAP values.") (license license:expat))) + +(define-public r-transphylo + (package + (name "r-transphylo") + (version "1.4.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "TransPhylo" version)) + (sha256 + (base32 + "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9")))) + (properties `((upstream-name . "TransPhylo"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) ("r-rcpp" ,r-rcpp))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/web/packages/TransPhylo/") + (synopsis + "Inference of Transmission Tree from a Dated Phylogeny") + (description + "Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) , Didelot et al. (2017) .") + (license license:gpl2+))) -- 2.27.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Sep 11 04:52:07 2020 Received: (at 42126-done) by debbugs.gnu.org; 11 Sep 2020 08:52:07 +0000 Received: from localhost ([127.0.0.1]:42277 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kGems-0002eO-Tv for submit@debbugs.gnu.org; Fri, 11 Sep 2020 04:52:07 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21127) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kGemq-0002eF-KN for 42126-done@debbugs.gnu.org; Fri, 11 Sep 2020 04:52:05 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1599814322; cv=none; d=zohomail.com; s=zohoarc; b=iGdmN0pjUkpFsUnXZEYLeafRI0/zrcrGfdo/tJ9tAfFwb+pq/X8bfNXGrOTe2a2qAwF34KZkJjzY5u2Kzwwc7GjTyCKuPNHHGAWwxy0obzxPSz3Gbz4ELk+K4EQ5ECjUrRzo1PNfwc4sTkMpu9+NxQ8YMxf3045usXbsmtYO9qY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1599814322; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=EczMvKpqgaW68h2LyYU2jF/TUNlmWZFPEH2MEuDixBo=; b=PMcz/ajsfMRGfyyE+wXC3TEhBZbX2+SWdPKECKaq4hThwCqGmF58BGGnkreXmHpKYThXi/S1j8CzcmB1/2R78H/t2gr4Rhtbms5zvZTl2yaGj1/8b0Hnj8EiMpYCArA02bqf15Bjn8qsHske/9IfuvdoF1sk/rKPiF6jJdEb+J4= 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=1599814322; 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:Content-Transfer-Encoding; bh=EczMvKpqgaW68h2LyYU2jF/TUNlmWZFPEH2MEuDixBo=; b=Va5EriNAqxtQ59c6NhZ+VUpTU+ZRSopqBoc4+MhKcajN1ozQs/CEs/X2Ts+qI7Uu g6gYcuRt3XpnLarCPF7YcIgkJiO5QUWfpiTm1VTGJ6wNRsl0qfYE+Gcdpjoein1Kibb NpGM/N4g8jUY8cqn1Ijbz+rnQRIUvFPLt7wFX7wo= Received: from localhost (p54ad420a.dip0.t-ipconnect.de [84.173.66.10]) by mx.zohomail.com with SMTPS id 159981432014064.25154899701045; Fri, 11 Sep 2020 01:52:00 -0700 (PDT) References: <20200629150517.28452-1-antoine.cote@posteo.net> User-agent: mu4e 1.4.13; emacs 27.1 From: Ricardo Wurmus To: Antoine =?utf-8?B?Q8O0dMOp?= Subject: Re: [bug#42126] [PATCH] gnu: Add r-transphylo In-reply-to: <20200629150517.28452-1-antoine.cote@posteo.net> 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: Fri, 11 Sep 2020 10:53:14 +0200 Message-ID: <87blic3dad.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: 42126-done Cc: 42126-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 (-) Hi Antoine, thank you for your patch! I have updated the description and synopsis, fixed the indentation, and pushed the patch to the =E2=80=9Cmaster=E2=80=9D branch with commit 5412b14= ba6. My apologies for the delay! --=20 Ricardo From unknown Sun Jun 22 08:07:13 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, 09 Oct 2020 11:24:07 +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