From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 29 08:23:42 2018 Received: (at submit) by debbugs.gnu.org; 29 Mar 2018 12:23:42 +0000 Received: from localhost ([127.0.0.1]:58092 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1Waf-0000Dp-MU for submit@debbugs.gnu.org; Thu, 29 Mar 2018 08:23:42 -0400 Received: from eggs.gnu.org ([208.118.235.92]:57470) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1Wae-0000De-Jv for submit@debbugs.gnu.org; Thu, 29 Mar 2018 08:23:36 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f1WaV-0006aU-BK for submit@debbugs.gnu.org; Thu, 29 Mar 2018 08:23:31 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:59442) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1f1WaV-0006aL-7O for submit@debbugs.gnu.org; Thu, 29 Mar 2018 08:23:27 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:48399) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f1WaT-0001z3-PN for guix-patches@gnu.org; Thu, 29 Mar 2018 08:23:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1f1WaQ-0006XW-7d for guix-patches@gnu.org; Thu, 29 Mar 2018 08:23:25 -0400 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:41517) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1f1WaQ-0006XM-2Z for guix-patches@gnu.org; Thu, 29 Mar 2018 08:23:22 -0400 Received: from ip-80-113-14-101.ip.prioritytelecom.net ([80.113.14.101]:57909 helo=yellowstone) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1f1WaP-00023v-J3 for guix-patches@gnu.org; Thu, 29 Mar 2018 08:23:21 -0400 User-agent: mu4e 1.0; emacs 25.3.1 From: Roel Janssen To: guix-patches Subject: [PATCH] gnu: Add r-regioner. Date: Thu, 29 Mar 2018 14:23:15 +0200 Message-ID: <871sg35avg.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) 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: -5.0 (-----) --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0001-gnu-Add-r-regioner.patch Content-Transfer-Encoding: 8bit >From b6b0a7900a3d8b87efe798ff65387838b7e2487c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 29 Mar 2018 14:20:20 +0200 Subject: [PATCH] gnu: Add r-regioner. * gnu/packages/bioconductor.scm (r-regioner): New variable. --- gnu/packages/bioconductor.scm | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f557dce8e..09581d9fd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Ricardo Wurmus +;;; Copyright © 2018 Roel Janssen ;;; ;;; This file is part of GNU Guix. ;;; @@ -21,7 +22,9 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system r) - #:use-module (gnu packages)) + #:use-module (gnu packages) + #:use-module (gnu packages statistics) + #:use-module (gnu packages bioinformatics)) (define-public r-hpar (package @@ -40,3 +43,30 @@ (description "This package provides a simple interface to and data from the Human Protein Atlas project.") (license license:artistic2.0))) + +(define-public r-regioner + (package + (name "r-regioner") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "regioneR" version)) + (sha256 + (base32 + "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp")))) + (properties `((upstream-name . "regioneR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-memoise" ,r-memoise) + ("r-genomicranges" ,r-genomicranges) + ("r-bsgenome" ,r-bsgenome) + ("r-rtracklayer" ,r-rtracklayer) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges))) + (home-page "https://bioconductor.org/packages/regioneR/") + (synopsis "Association analysis of genomic regions") + (description "This package offers a statistical framework based on +customizable permutation tests to assess the association between genomic +region sets and other genomic features.") + (license license:artistic2.0))) -- 2.16.2 --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Guix, I'd like to add “r-regioner”, which is a Bioconductor package. I noticed there is a “bioconductor.scm” module. Should I add it there, or should I add it to “bioinformatics.scm” instead? Kind regards, Roel Janssen --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 30 10:49:31 2018 Received: (at 30984-done) by debbugs.gnu.org; 30 Mar 2018 14:49:31 +0000 Received: from localhost ([127.0.0.1]:60335 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1vLM-0000y1-PJ for submit@debbugs.gnu.org; Fri, 30 Mar 2018 10:49:31 -0400 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:46323) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1f1vLK-0000xt-TL for 30984-done@debbugs.gnu.org; Fri, 30 Mar 2018 10:49:27 -0400 Received: from compute4.internal (compute4.nyi.internal [10.202.2.44]) by mailout.nyi.internal (Postfix) with ESMTP id 58F0A21161; Fri, 30 Mar 2018 10:49:26 -0400 (EDT) Received: from mailfrontend2 ([10.202.2.163]) by compute4.internal (MEProxy); Fri, 30 Mar 2018 10:49:26 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=cc:content-type:date:from:in-reply-to:message-id:mime-version :references:subject:to:x-me-sender:x-me-sender:x-sasl-enc; s= mesmtp; bh=6uBMzhxzYGb9+V/5GE+QBtDVepbSLYn0+26eWpvrEIU=; b=EztcR 3j/MCj7RGB9ghbEJ4xSpG3YHOjHUzY2+fzh1MJH6/Ij0XoBMY3VwXbDAseIoB/fU vr5ncTf+NkVMBni353xarppuQukvn/U7bmd2MnLPBrjQcOaZSTUbPqiGkM5KJOir OM0IfkQxWU5iTNwbkTsqeYelcSo0TodJkOZy2Y= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-sender :x-me-sender:x-sasl-enc; s=fm2; bh=6uBMzhxzYGb9+V/5GE+QBtDVepbSL Yn0+26eWpvrEIU=; b=fnANvYi7E+uje2giqd3JZZRdmKfmxDviJknoQmrstsHhE NfLEPee+iJC3habTigkkI98SM/56PSMWhAepx3fKsg53CspuIuL6Oc2E86cATRLs 9a2mGFdqhEyJCX0bnIZxF0+0CsSIz9rKqod2kQ0X/3okW5ghRsi3M4KeRyyqJe3P Z/PPYuhcpTVybO0I6oaATfcHFAguaTx2hidjoQ6SsK/XAhQgnAh29VjxmJnXyZfS O+UyYgkDWHfIG14FyYCWZdGt/pRgv9eneN0eVIW7oQZF0jU0au90IHIMiI6MaMFg q9pO0xG0/5Js4WO/NlfmrzUaTpFXgeq3KHUn6WTLg== X-ME-Sender: Received: from localhost (unknown [172.58.201.190]) by mail.messagingengine.com (Postfix) with ESMTPA id 1B42C10251; Fri, 30 Mar 2018 10:49:26 -0400 (EDT) Date: Fri, 30 Mar 2018 10:49:24 -0400 From: Leo Famulari To: Roel Janssen Subject: Re: [bug#30984] [PATCH] gnu: Add r-regioner. Message-ID: <20180330144924.GA21544@jasmine.lan> References: <871sg35avg.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="ikeVEW9yuYc//A+q" Content-Disposition: inline In-Reply-To: <871sg35avg.fsf@gnu.org> User-Agent: Mutt/1.9.3 (2018-01-21) X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 30984-done Cc: 30984-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: -0.7 (/) --ikeVEW9yuYc//A+q Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Thu, Mar 29, 2018 at 02:23:15PM +0200, Roel Janssen wrote: > From b6b0a7900a3d8b87efe798ff65387838b7e2487c Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Thu, 29 Mar 2018 14:20:20 +0200 > Subject: [PATCH] gnu: Add r-regioner. >=20 > * gnu/packages/bioconductor.scm (r-regioner): New variable. Thanks! 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