From patchwork Tue Mar 5 08:14:08 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 1346 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 05E7F16D1C; Tue, 5 Mar 2019 08:15:14 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,UNPARSEABLE_RELAY, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id B17D716D19 for ; Tue, 5 Mar 2019 08:15:13 +0000 (GMT) Received: from localhost ([127.0.0.1]:39413 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1h15EH-00026o-2H for patchwork@mira.cbaines.net; Tue, 05 Mar 2019 03:15:13 -0500 Received: from eggs.gnu.org ([209.51.188.92]:55806) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1h15E7-000242-T1 for guix-patches@gnu.org; Tue, 05 Mar 2019 03:15:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1h15E6-0003Oe-3t for guix-patches@gnu.org; Tue, 05 Mar 2019 03:15:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:46989) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1h15E5-0003OM-W6 for guix-patches@gnu.org; Tue, 05 Mar 2019 03:15:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1h15E5-0001ac-Ns for guix-patches@gnu.org; Tue, 05 Mar 2019 03:15:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#34755] [PATCH] gnu: Remove duplicate r-dnacopy package. Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 05 Mar 2019 08:15:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 34755 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 34755@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15517736586041 (code B ref -1); Tue, 05 Mar 2019 08:15:01 +0000 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 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 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches This package definition duplicates the earlier definition in the (gnu packages 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.scm 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 plots.") sequencing data.") (license license:gpl2+))) -(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} (CBS) -algorithm to segment DNA copy number data and identify genomic regions with -abnormal copy number.") - (license license:gpl2+))) - ;; This is a CRAN package, but it uncharacteristically depends on a ;; Bioconductor package. (define-public r-htscluster