From unknown Wed Jun 18 23:14:14 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#34755 <34755@debbugs.gnu.org> To: bug#34755 <34755@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Remove duplicate r-dnacopy package. Reply-To: bug#34755 <34755@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:14:14 +0000 retitle 34755 [PATCH] gnu: Remove duplicate r-dnacopy package. reassign 34755 guix-patches submitter 34755 Christopher Baines severity 34755 normal tag 34755 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 05 03:14:18 2019 Received: (at submit) by debbugs.gnu.org; 5 Mar 2019 08:14:18 +0000 Received: from localhost ([127.0.0.1]:60533 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1h15DO-0001ZN-DV for submit@debbugs.gnu.org; Tue, 05 Mar 2019 03:14:18 -0500 Received: from eggs.gnu.org ([209.51.188.92]:41311) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1h15DM-0001ZA-DJ for submit@debbugs.gnu.org; Tue, 05 Mar 2019 03:14:17 -0500 Received: from lists.gnu.org ([209.51.188.17]:55943) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1h15DH-0002ii-7x for submit@debbugs.gnu.org; Tue, 05 Mar 2019 03:14:11 -0500 Received: from eggs.gnu.org ([209.51.188.92]:55693) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1h15DG-0001w5-79 for guix-patches@gnu.org; Tue, 05 Mar 2019 03:14:10 -0500 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,UNPARSEABLE_RELAY, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1h15DF-0002gx-G3 for guix-patches@gnu.org; Tue, 05 Mar 2019 03:14:10 -0500 Received: from li622-129.members.linode.com ([212.71.249.129]:59346 helo=mira.cbaines.net) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1h15DF-0002g3-9R for guix-patches@gnu.org; Tue, 05 Mar 2019 03:14:09 -0500 Received: from localhost (cpc102582-walt20-2-0-cust14.13-2.cable.virginm.net [86.27.34.15]) by mira.cbaines.net (Postfix) with ESMTPSA id 4E5CA16450 for ; Tue, 5 Mar 2019 08:14:08 +0000 (GMT) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id c39594ad for ; Tue, 5 Mar 2019 08:14:08 +0000 (UTC) From: Christopher Baines To: guix-patches@gnu.org Subject: [PATCH] gnu: Remove duplicate r-dnacopy package. Date: Tue, 5 Mar 2019 08:14:08 +0000 Message-Id: <20190305081408.17814-1-mail@cbaines.net> X-Mailer: git-send-email 2.20.1 MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 212.71.249.129 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: 1.0 (+) 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: -0.0 (/) This package definition duplicates the earlier definition in the (gnu pac= kages bioinformatics) module. This reverts commit c18dccffa20bf09826758210d457d1df477f959c. * gnu/packages/bioconductor.scm (r-dnacopy): Remove this variable. --- gnu/packages/bioconductor.scm | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.sc= m index ae9d7070c3..dfd3de5901 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -27,7 +27,6 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages cran) #:use-module (gnu packages compression) - #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages maths) #:use-module (gnu packages statistics) @@ -1178,28 +1177,6 @@ Viewer (SAV) files, access data, and generate QC p= lots.") sequencing data.") (license license:gpl2+))) =20 -(define-public r-dnacopy - (package - (name "r-dnacopy") - (version "1.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DNAcopy" version)) - (sha256 - (base32 - "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) - (properties `((upstream-name . "DNAcopy"))) - (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) - (home-page "https://bioconductor.org/packages/DNAcopy") - (synopsis "DNA copy number data analysis") - (description - "This package implements the @dfn{circular binary segmentation} (CB= S) -algorithm to segment DNA copy number data and identify genomic regions w= ith -abnormal copy number.") - (license license:gpl2+))) - ;; This is a CRAN package, but it uncharacteristically depends on a ;; Bioconductor package. (define-public r-htscluster --=20 2.20.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 05 04:25:39 2019 Received: (at 34755-done) by debbugs.gnu.org; 5 Mar 2019 09:25:39 +0000 Received: from localhost ([127.0.0.1]:60572 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1h16KR-0003EK-2b for submit@debbugs.gnu.org; Tue, 05 Mar 2019 04:25:39 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21116) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1h16KP-0003EC-Ig for 34755-done@debbugs.gnu.org; Tue, 05 Mar 2019 04:25:38 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1551777921; cv=none; d=zoho.com; s=zohoarc; b=M0+1UYnX8f1Yp2oHON6MxjLteG+soc0OiKoUZ4PG8M3rep2eRDLoc2AaoSyrdTXYz3b4AUW+zBFmuhc7ObS82WLu+lyC0QLmI13LDH7b5hjj/lX9JTPssgV0eFCuYX4Z2DTLeC1taKtmq+wGaJdaD8OE7ACCQmv5q+HzYaFR7eQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1551777921; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=sJmaGm8VnrBoQIHXrKyiE9W4E4jePU8hX3A9bdpS34s=; b=jIGAmlVv2slPVHZQs0JTGIV+/8ih7zIxEWCIbF/m5RcPQ7qx8nhGshxpy7fF/EQS7V7YfNjymf76oETa5V/kUB60EZIj1vJIgweUUzVLcpKO2EsEt0F//WKsAxkzHY9OWhwgsGGWR6by0ET4Q5GUjq9zT/U+CRri03j4KSX0QXQ= ARC-Authentication-Results: i=1; mx.zoho.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=1551777921; 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; l=470; bh=sJmaGm8VnrBoQIHXrKyiE9W4E4jePU8hX3A9bdpS34s=; b=e22OFXynqPMADKiZaZZHN4eT/mCbPV6ybt2+YaVEzixQEgtNZ/Hq6TnmPOOwouzr /kaqwWB8+aTSJF7I0vAttjlNrJ9xAjc9z5Btidobgm3fF+yw+Xt34ZgFpvuqLnusxJO SIUq7/FBf8xp5NTW8/V8ENbukiGP5Q57ecMte/U8= Received: from localhost (p54AD4ADE.dip0.t-ipconnect.de [84.173.74.222]) by mx.zohomail.com with SMTPS id 1551777920974845.1946107145432; Tue, 5 Mar 2019 01:25:20 -0800 (PST) References: <20190305081408.17814-1-mail@cbaines.net> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Christopher Baines Subject: Re: [bug#34755] [PATCH] gnu: Remove duplicate r-dnacopy package. In-reply-to: <20190305081408.17814-1-mail@cbaines.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: Tue, 05 Mar 2019 10:25:17 +0100 Message-ID: <8736o1wu4i.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: 34755-done Cc: 34755-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 (-) Christopher Baines writes: > This package definition duplicates the earlier definition in the (gnu pac= kages > bioinformatics) module. > > This reverts commit c18dccffa20bf09826758210d457d1df477f959c. > > * gnu/packages/bioconductor.scm (r-dnacopy): Remove this variable. Thanks for noticing this. I=E2=80=99d rather remove the packgae from (gnu packages bioinformatics). = I=E2=80=99ll take care of this today. --=20 Ricardo From unknown Wed Jun 18 23:14:14 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, 02 Apr 2019 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