From unknown Thu Jun 19 14:15:31 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#47490 <47490@debbugs.gnu.org> To: bug#47490 <47490@debbugs.gnu.org> Subject: Status: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene Reply-To: bug#47490 <47490@debbugs.gnu.org> Date: Thu, 19 Jun 2025 21:15:31 +0000 retitle 47490 [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene reassign 47490 guix-patches submitter 47490 "Hong.Li@mdc-berlin.de" severity 47490 normal tag 47490 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 29 19:05:25 2021 Received: (at submit) by debbugs.gnu.org; 29 Mar 2021 23:05:25 +0000 Received: from localhost ([127.0.0.1]:49830 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lR0wm-0004fa-K4 for submit@debbugs.gnu.org; Mon, 29 Mar 2021 19:05:25 -0400 Received: from lists.gnu.org ([209.51.188.17]:46728) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lR0se-0003T7-Mb for submit@debbugs.gnu.org; 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Tue, 30 Mar 2021 01:00:45 +0200 (CEST) Received: from SW-IT-P-EX1.mdc-berlin.net (mgw1.mdc-berlin.de [141.80.113.54]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Tue, 30 Mar 2021 01:00:45 +0200 (CEST) Received: from SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) by SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2176.2; Tue, 30 Mar 2021 01:00:44 +0200 Received: from SW-IT-P-EX1.mdc-berlin.net ([fe80::b00d:dcd5:bd6c:2cbe]) by SW-IT-P-EX1.mdc-berlin.net ([fe80::b00d:dcd5:bd6c:2cbe%10]) with mapi id 15.01.2176.009; Tue, 30 Mar 2021 01:00:44 +0200 From: "Hong.Li@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene Thread-Topic: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene Thread-Index: AQHXJO9ANMZhPyKDd0e9/3B3BxSB8Q== Date: Mon, 29 Mar 2021 23:00:44 +0000 Message-ID: Accept-Language: en-GB, de-DE, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.52] x-tm-as-product-ver: SMEX-14.0.0.3080-8.6.1012-26060.003 x-tm-as-result: No-10--2.754000-8.000000 x-tmase-matchedrid: 38dH0F6VYpQ25XOhnouJ5RuurbgYp+HQXef5t6q8RcxFdhD9u4+PBJZd R8KtHW+EjSiAYevD2gHGYnTt+EXc1sRb3JaZ4jjzZBiPr4EU8TCoCf7IdvPAJ9iT+ZNwlq8O2Uw BLM8az1Qg/O7wo3r/W8D2FvUjLrtXYlldA0POS1JFEOsMeHJ8N/FNnr4kMg4N+32SXw3QiFyEgp d7r2FIkguvmY78pZoLep94SLzeXS3rW54p25f6q00/Wb3kjwMV+KgiyLtJrSD4/8apt2/jKBaQe ocCrFbEZPG05urt9XfKR3w4E/y0xKjifofrOXymO5SpM9N8NOvrixWWWJYrH0OrZJUSTvYowHlZ tZ51mXTatEOIdonL+Mf7jRM8gUeDU671fEYi3B6AgPRBm277M1apenHQt16IZEx5WD+8HvM57j9 S0tXsDlrnjGyUmNfKzbtNAA9TAe29w9BLQ8Dlv1dlNryGcEYBugRp53kzD5HdjOqvc66oIgeBiF V2jjCF x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10--2.754000-8.000000 x-tmase-version: SMEX-14.0.0.3080-8.6.1012-26060.003 x-tm-snts-smtp: 7AEE3DEF2E12386C1CBBC7108CB2341DEFFD7FC9241C6FDCEF63FFFE30A437E52000:F Content-Type: multipart/alternative; boundary="_000_a1d3b10baf29429fa1bf647a3445cef1mdcberlinde_" MIME-Version: 1.0 Received-SPF: pass client-ip=194.95.234.172; envelope-from=Hong.Li@mdc-berlin.de; helo=b2062.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, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Mon, 29 Mar 2021 19:05:23 -0400 Cc: "Ricardo.Wurmus@mdc-berlin.de" 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 (--) --_000_a1d3b10baf29429fa1bf647a3445cef1mdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable >From 2621d8b89a4406bce271436640b8b7fd7764b8c0 Mon Sep 17 00:00:00 2001 From: hli Date: Tue, 30 Mar 2021 00:53:51 +0200 Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0bcd9a67cd..a8601d7ed2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -619,6 +619,36 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Bi= ostrings objects.") "This package exposes an annotation database generated from Ensembl."= ) (license license:artistic2.0))) +(define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene + (package + (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") + (version "3.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri + "TxDb.Dmelanogaster.UCSC.dm6.ensGene" + version + 'annotation)) + (sha256 + (base32 + "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4")))) + (properties + `((upstream-name + . + "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicfeatures" ,r-genomicfeatures))) + (home-page + "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGen= e") + (synopsis + "Annotation package for TxDb object(s)") + (description + "Exposes an annotation databases generated from UCSC by exposing thes= e as TxDb objects") + (license license:artistic2.0))) + (define-public r-txdb-hsapiens-ucsc-hg19-knowngene (package (name "r-txdb-hsapiens-ucsc-hg19-knowngene") -- 2.17.1 --_000_a1d3b10baf29429fa1bf647a3445cef1mdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
From 2621d8b89a4406bce271436640b8b7fd7764b8c0 Mon Sep 17 00:00:00 2001=
From: hli <hli@mdc-berlin.de>
Date: Tue, 30 Mar 2021 00:53:51 +0200
Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene

---
 gnu/packages/bioconductor.scm | 30 +++++++= ;+++++++++++++++= ;++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm<= br> index 0bcd9a67cd..a8601d7ed2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -619,6 +619,36 @@ as provided by UCSC (hg38, Dec. 2013) and stored i= n Biostrings objects.")
      "This package exposes an annotation dat= abase generated from Ensembl.")
     (license license:artistic2.0)))

+(define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
+  (package
+    (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene&q= uot;)
+    (version "3.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri
+           &nbs= p; "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
+           &nbs= p; version
+           &nbs= p; 'annotation))
+       (sha256
+        (base32
+         "0yij7zyqkmmr133= 89rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
+    (properties
+     `((upstream-name
+        .
+        "TxDb.Dmelanogaster.UC= SC.dm6.ensGene")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationd= bi)
+       ("r-genomicfeatures" ,r= -genomicfeatures)))
+    (home-page
+     "https://bioconductor.org/packages/TxDb.= Dmelanogaster.UCSC.dm6.ensGene")
+    (synopsis
+     "Annotation package for TxDb object(s)&q= uot;)
+    (description
+     "Exposes an annotation databases generat= ed from UCSC by exposing these as TxDb objects")
+    (license license:artistic2.0)))
+
 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
   (package
     (name "r-txdb-hsapiens-ucsc-hg19-knowngene&qu= ot;)
--
2.17.1
--_000_a1d3b10baf29429fa1bf647a3445cef1mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 12 12:38:13 2021 Received: (at 47490-done) by debbugs.gnu.org; 12 Apr 2021 16:38:13 +0000 Received: from localhost ([127.0.0.1]:57879 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lVzZl-00041t-Js for submit@debbugs.gnu.org; Mon, 12 Apr 2021 12:38:13 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21119) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lVzZi-00041i-O8 for 47490-done@debbugs.gnu.org; Mon, 12 Apr 2021 12:38:11 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1618245486; cv=none; d=zohomail.com; s=zohoarc; b=IdQQ3iktl6xINzgYf8cNxhRTZ1D21FtzhLBFOytjsH5SYqWk7uJKRXry4PqUd8BFuknUbK6qne9aquDdm+POsh0MDZTjgxxc4m/s18TEaaMm6zvQQNKuihLMJK6jtHIeORTpS4GpOgl2idEG3FureeYIREWy7qPjINsX0veXBVU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1618245486; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=fP+eOB1Kb2NAsRBbQ/8sNAXVKj1Q+kASpOvdvUpN0k0=; b=IXlX+RJG/AA/1LJlK7KJbXpT/llCOL1isPy1jknZ5Wl8WvdBt1jt2zdUUHCTftcELbhPyMLhXb1l/OjGbK9dY47v9qFjrQKn2I35BZ9GeenNEfg7N520smzJ8yaspRoOpbFBuRNiLwA08MAeBsXOj7Wg8qT0ZT5olu+PMBKYqnY= 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=1618245486; 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; bh=fP+eOB1Kb2NAsRBbQ/8sNAXVKj1Q+kASpOvdvUpN0k0=; b=RS9hDthpkrEPVw9QUtRtBSgNZOK+9YufNcNMR4hgrfjllZVPBk8TV+R6RcxoN7xL 6N7zEkxXPjS9eOaXpojXDMq0zf2Wuema81evuucm71Qs2yLrh4uEx1VJ7mXiFBKP3Hu 4mizFicq+PAB2o2uJyq/bYAb34+qidEWv7ifS3pk= Received: from localhost (p54ad4dc1.dip0.t-ipconnect.de [84.173.77.193]) by mx.zohomail.com with SMTPS id 1618245482579557.1238661695554; Mon, 12 Apr 2021 09:38:02 -0700 (PDT) References: User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: "Li, Hong" Subject: Re: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene In-reply-to: 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: Mon, 12 Apr 2021 18:37:58 +0200 Message-ID: <87fszvv4pl.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47490-done Cc: 47490-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 (-) Li, Hong writes: > From 2621d8b89a4406bce271436640b8b7fd7764b8c0 Mon Sep 17 00:00:00 2001 > From: hli > Date: Tue, 30 Mar 2021 00:53:51 +0200 > Subject: [PATCH] r-txdb-dmelanogaster-ucsc-dm6-ensgene Thank you, I pushed it with minor tweaks and a conventional commit message with commit eb8da54170919bc31946f492da1071dd491e942a. PS: you can generate a commit (or a series of commits) with the expected commit message by running ./etc/committer.scm. -- Ricardo From unknown Thu Jun 19 14:15:31 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, 11 May 2021 11:24:08 +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