From patchwork Mon Mar 15 18:08:57 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27808 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 27E3027BC54; Mon, 15 Mar 2021 18:38:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 42D0327BC52 for ; Mon, 15 Mar 2021 18:38:15 +0000 (GMT) Received: from localhost ([::1]:58526 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLs6Y-0003Pb-FI for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 14:38:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37746) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLrfH-0007If-DN for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:53650) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLrfH-0003Md-02 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLrfG-0004ok-R6 for guix-patches@gnu.org; Mon, 15 Mar 2021 14:10:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 03/10] gnu: r-genomicranges: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 18:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47171@debbugs.gnu.org Cc: zimoun Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161583177018411 (code B ref 47171); Mon, 15 Mar 2021 18:10:02 +0000 Received: (at 47171) by debbugs.gnu.org; 15 Mar 2021 18:09:30 +0000 Received: from localhost ([127.0.0.1]:36947 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLrek-0004ms-0s for submit@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:30 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:33657) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLred-0004lS-Oj for 47171@debbugs.gnu.org; Mon, 15 Mar 2021 14:09:24 -0400 Received: by mail-wm1-f51.google.com with SMTP id w203-20020a1c49d40000b029010c706d0642so2718818wma.0 for <47171@debbugs.gnu.org>; Mon, 15 Mar 2021 11:09:23 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=xeLBVlZt0/Pn5u7gI2OgMDwB9DVPZwQs3bjdjPUIMq0=; b=PPovfXbTHK/3fpONOSURTyci7633G7nzg8gv4+etH0bA+3XCR/lassdcuVjiGvRu0L rV/SoVi8uzzKcdo4ZZzcbcpAKp+UaFThgT8qeSbekAdo0kqxEFM8qLMAn+uYhAyJuuIj 9yQ0yIlPfzjoexZ83Nys6aW+IMl+44OzLC5dM3BcISL62FhKZa+cjU7Sk9bhcR3CAiJ7 VJOvCcNK4SvZtOgjRlZHPPI5RlIL26Iq56MNDiECt45f2vVzrWRe28RRAumHtgmeiQtj j+JYKi35hvHJlbUK0JXfgF36WMDSkGTnI0dfVokFEgwO/VyjhdmZnhYvZpjpxCZhJ66+ 18Gg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=xeLBVlZt0/Pn5u7gI2OgMDwB9DVPZwQs3bjdjPUIMq0=; b=sgon+GqC3KNATKkOUCdRqp1BeB3JoiOyaYvIOS9O4nCdUOwnyKH7ChlDvQMAfgWOHz IX42EXKYKiCf7SrBTzSztgZElNwbZC+6hH+acF6mS3VSkg0BFzBoXyp/7pNskcbXxyd9 Npea+Roods8Y9vWeRhFYd9QlLNZFlEDL4btjQfFdG7e61nEQ2xZQabmOopsdTr4Fv7ay 31UQXM6E0X7HphTaayr2VlTzV6vbSvgF7sPvrGKWXOmlmHmO7E8VNCj7tAxU39R1/87U VmaNKeAFcSfqncnGdSjLgR3ovgTB5wg+CduP3fkx/ABpcFTL3KQ9HtbtWrPk9NDVS4cL u5Pg== X-Gm-Message-State: AOAM531ASHFbDejEk4296OfHlG9ZR1wHKv/fU1IcOAdBSCMZWulAn535 Yavx6/MmQeut2B4NCU5VWKHyxoC1Ei8= X-Google-Smtp-Source: ABdhPJzSVXVmm4YQrZ/v0k2HyoKaqrd0E1LBaGXeWnCUcY2P1+yRSUTGHx2B7AdIlfJiRyEH3sQDaQ== X-Received: by 2002:a1c:318b:: with SMTP id x133mr912251wmx.154.1615831758140; Mon, 15 Mar 2021 11:09:18 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id s11sm438851wme.22.2021.03.15.11.09.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 11:09:17 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 19:08:57 +0100 Message-Id: <20210315180904.8346-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315180904.8346-1-zimon.toutoune@gmail.com> References: <20210315180904.8346-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 * gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdb2f7c7ac..ec273cae70 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1770,6 +1770,37 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicranges + (package + (name "r-genomicranges") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicRanges" version)) + (sha256 + (base32 + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + (properties + `((upstream-name . "GenomicRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicRanges") + (synopsis "Representation and manipulation of genomic intervals") + (description + "This package provides tools to efficiently represent and manipulate +genomic annotations and alignments is playing a central role when it comes to +analyzing high-throughput sequencing data (a.k.a. NGS data). The +GenomicRanges package defines general purpose containers for storing and +manipulating genomic intervals and variables defined along a genome.") + (license license:artistic2.0))) + (define-public r-gostats (package (name "r-gostats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65db983461..4889c148e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,37 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicranges - (package - (name "r-genomicranges") - (version "1.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicRanges" version)) - (sha256 - (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) - (properties - `((upstream-name . "GenomicRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicRanges") - (synopsis "Representation and manipulation of genomic intervals") - (description - "This package provides tools to efficiently represent and manipulate -genomic annotations and alignments is playing a central role when it comes to -analyzing high-throughput sequencing data (a.k.a. NGS data). The -GenomicRanges package defines general purpose containers for storing and -manipulating genomic intervals and variables defined along a genome.") - (license license:artistic2.0))) - (define-public r-biobase (package (name "r-biobase")