From unknown Tue Jun 24 05:10:16 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#57340 <57340@debbugs.gnu.org> To: bug#57340 <57340@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-organism-dplyr. Reply-To: bug#57340 <57340@debbugs.gnu.org> Date: Tue, 24 Jun 2025 12:10:16 +0000 retitle 57340 [PATCH] gnu: Add r-organism-dplyr. reassign 57340 guix-patches submitter 57340 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 57340 normal tag 57340 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 22 07:26:51 2022 Received: (at submit) by debbugs.gnu.org; 22 Aug 2022 11:26:51 +0000 Received: from localhost ([127.0.0.1]:38137 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ5Zy-0002as-Ri for submit@debbugs.gnu.org; Mon, 22 Aug 2022 07:26:51 -0400 Received: from lists.gnu.org ([209.51.188.17]:53990) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ5Zv-0002ak-T0 for submit@debbugs.gnu.org; Mon, 22 Aug 2022 07:26:49 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60332) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ5Zv-0001iK-OD for guix-patches@gnu.org; Mon, 22 Aug 2022 07:26:47 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:37499) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ5Zs-0006GM-UR for guix-patches@gnu.org; Mon, 22 Aug 2022 07:26:47 -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=1661167600; x=1662982001; bh=lJ7nK7dGZ/yVXRS ywUpRxfGciZEdYJrYN/qgA00WAxg=; b=lSAhe08wrp8eQOd+iDsR0/OHfJYqrKS JeZvjMCB88e5T55PQyhsyuHAqD0dowa+ZO7HB8BaIPG8HYbLLNRTtwnbVFlKY+gb R9kTCRscJb7+vRSzqw1hsmY6OrtzAX+NBUe+dr9o0xTcEHBNeMQMfh2MWUjkr+iy 36m0liBGcUIA= 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 0DEAA300240 for ; Mon, 22 Aug 2022 13:26:39 +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 15.1.2507.12; Mon, 22 Aug 2022 13:26:39 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-organism-dplyr. Date: Mon, 22 Aug 2022 13:26:27 +0200 Message-ID: <20220822112627.32123-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.2 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-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-14.0.0.3092-9.0.1002-27092.007 X-TM-AS-Result: No-10--6.154400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcOj1LmhIerwYArcxrzwsv5uwTlc9CcHMZerwqxtE531VGb6 PphVtfZgftxOuKmFYcnuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIOfdksK3etFJ35r P8TLPXhR7MSP7SLpuGIek6stLzp1eWi8Qip68NgfdCok3ibXlQeuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgW9jOHvog8CCfFlJCWqTg5fS/eZJv7Trifxdem+NvTtl0PhlTbB4g25g== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.154400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-SNTS-SMTP: F3147DF224C2DE3C9880C42731710D818FE1D1709EA7EE621A967E858D6886912002: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 (--) * gnu/packages/bioconductor.scm (r-organism-dplyr): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d2ca413e9..ed9e4df73d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5017,6 +5017,45 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) +(define-public r-organism-dplyr + (package + (name "r-organism-dplyr") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Organism.dplyr" version)) + (sha256 + (base32 + "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as")))) + (properties `((upstream-name . "Organism.dplyr"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-annotationfilter + r-biocfilecache + r-dbi + r-dbplyr + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rsqlite + r-s4vectors + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/Organism.dplyr") + (synopsis "Dplyr-based access to Bioconductor annotation resources") + (description + "This package provides an alternative interface to Bioconductor @code{ +annotation} resources, in particular the gene identifier mapping functionality +of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate +functionality of the @code{TxDb} packages (e.g., +@code{TxDb.Hsapiens.UCSC.hg38.knownGene}).") + (license license:artistic2.0))) + (define-public r-organismdbi (package (name "r-organismdbi") base-commit: 706b3ef38b2f7ce9f05aa56e2eaaaf1c19e25f90 -- 2.37.2 From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 23 06:05:31 2022 Received: (at 57340-done) by debbugs.gnu.org; 23 Aug 2022 10:05:31 +0000 Received: from localhost ([127.0.0.1]:42664 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQQmo-0005al-Qc for submit@debbugs.gnu.org; Tue, 23 Aug 2022 06:05:31 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQQml-0005ac-09 for 57340-done@debbugs.gnu.org; Tue, 23 Aug 2022 06:05:28 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1661249125; cv=none; d=zohomail.com; s=zohoarc; b=fYsveACvknbIHMWXBswc074pegwQOI3kA70yA+zBbjE1tvl2qv4fV/1QoeCPrwe2l91bIv3CCCK0MIneV9eRDswS7HpY++1tSZXDsJeBE/9exi8SuzCZEJqILZ1LHxxVNZsIgn1MmVHWqYo9dNfi4HGxqrtZnAOlk6fUXRGi/TE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1661249125; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=xkqMSdMfzL0WmFZlFPc2EE2R8/FDLWIFC1L9o2ywI6c=; b=jlx7QZO7yFeKV4kgfcx9rz5yrUG5IsgorjD24gnjO4H8TpfZSGpUSFRswiGHy3pRIdOfqz78+d5bhYQOfRvLbXWYRJux8yrS972fq3EYDVvfkRnkinUHHEwI0XmL5k98/kPLX8vu9btkok7zC7NoCuGwNuLvTVZDQnLd3vW1JtE= 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=1661249125; 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=xkqMSdMfzL0WmFZlFPc2EE2R8/FDLWIFC1L9o2ywI6c=; b=BYiRE2neY5tKkJB60zfadzm1U5M7ZwcjJ8u4vHfjg2k2kzi4qkI6jI7vUvO1dkeK nFi9eVMANm8/89+/Jh8vlb6OXX4K8mnbF5iFXt0gd177wb5mVWL+W9KdLXD1IYn0twe k39Fk27sNGEzqp7Rz+d18fKd+Nh3iEj/+KEsFXM4= Received: from localhost (84-109-142-46.pool.kielnet.net [46.142.109.84]) by mx.zohomail.com with SMTPS id 1661249123956421.1070784634187; Tue, 23 Aug 2022 03:05:23 -0700 (PDT) References: <20220822112627.32123-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#57340] [PATCH] gnu: Add r-organism-dplyr. Date: Tue, 23 Aug 2022 12:05:09 +0200 In-reply-to: <20220822112627.32123-1-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: <87o7wbz34v.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: 57340-done Cc: 57340-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: > * gnu/packages/bioconductor.scm (r-organism-dplyr): New variable. Applied, thank you! --=20 Ricardo From unknown Tue Jun 24 05:10:16 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 20 Sep 2022 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