From patchwork Mon Mar 15 13:01:33 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27707 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 5F9F027BC54; Mon, 15 Mar 2021 13:03:39 +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 76F2B27BC52 for ; Mon, 15 Mar 2021 13:03:38 +0000 (GMT) Received: from localhost ([::1]:38644 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmsj-00034o-N5 for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60048) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032U-KW for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51745) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsA-0007Hu-DR for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmsA-0006C8-AF for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 08/10] gnu: r-genomeinfodb: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47156 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47156@debbugs.gnu.org Cc: zimoun Received: via spool by 47156-submit@debbugs.gnu.org id=B47156.161581332623699 (code B ref 47156); Mon, 15 Mar 2021 13:03:02 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:06 +0000 Received: from localhost ([127.0.0.1]:35047 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrF-0006AA-Jt for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:06 -0400 Received: from mail-wm1-f46.google.com ([209.85.128.46]:51867) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr8-00067u-5s for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:59 -0400 Received: by mail-wm1-f46.google.com with SMTP id l19so8065730wmh.1 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:58 -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=Eg3m3OW/xIfJd6vlNIo04T+VxoB8rPoJZ3zsaRSkkfs=; b=iZkTzekcfhvWkteADz/22S1wkjFFCEG3RfWqUHOy8Li9ROaMXEL+3meY6VfQTz12g5 N0lj6GkeGRUSv6EOreZWaxOOCzesUqjDLBpCdV0sx8cJ7jTzCfy3IehBTYF/2DJ+BRxW yyJnoGa2jFDpvb9tX2dQe9xNnpYv8N92C6UvG7jK0Tj89s5GO40gzRHbF9vK3R9SJXbc 1dLpgg6B8rlrcnikpHkQXNhHiJJGpCK56Xd8Cm/i5zKYayl8TQI+dN4pOQx0qXVd84E7 W7EpZL81R1r4bTb4jcCAus+tCv2HQ6FNuDkUoUQrVwnBPqwF/XbZaeRAOtEdnH7dfA90 VK9w== 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=Eg3m3OW/xIfJd6vlNIo04T+VxoB8rPoJZ3zsaRSkkfs=; b=HMas+lA+iXgR4aoeKteKyrm2n7OitjFFoNkAUxNWV+LEORouVkzRl/nL/nUyraS4Py Mf9+eGldkMEu+y90brPg2DfperWwDIEV0Db9jyYkaIH7qY7LUrlUtO0tCeiz7wMAybqw inEnPSutWq16ZdhJ3cEHu9xvQ7JSLUKnPlG3vWItTCatCKSx4tna1xtBJdj9wK3bJIfV 7S6XeGHPBbrehnWATpR44x4xMI4WH9YlrIVEifh+3TZ+Jg02hZbvuBQGtVFJaDtfhSGj EJOMq1pujgH5lukqucpOUFCD57VSBucpEPXr6ryKqVLyBE9cPdm1awr8VVdfR0rRRmzv zCrQ== X-Gm-Message-State: AOAM530dbCP419ehS5dwRaURgOZJ5+SKJvuxiYFLO6EM+AVHWNTfQGG+ 2SCT8cQsSQM5n9pHIOChs8ZntI5vDbM= X-Google-Smtp-Source: ABdhPJzPqh60MfyRBqXVtO4Kq+B1FxWxsZY8jmdbE98WJmJr2+dGsl1E5VZotbshB52U44/4Mbc3bA== X-Received: by 2002:a05:600c:204f:: with SMTP id p15mr26102176wmg.165.1615813310628; Mon, 15 Mar 2021 06:01:50 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:49 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:33 +0100 Message-Id: <20210315130134.30302-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315130134.30302-1-zimon.toutoune@gmail.com> References: <20210315130134.30302-1-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-genomeinfodb): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53f025ec61..b4456d13c8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1712,6 +1712,36 @@ exploration of the results.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomeinfodb + (package + (name "r-genomeinfodb") + (version "1.26.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDb" version)) + (sha256 + (base32 + "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v")))) + (properties + `((upstream-name . "GenomeInfoDb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodbdata" ,r-genomeinfodbdata) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomeInfoDb") + (synopsis "Utilities for manipulating chromosome identifiers") + (description + "This package contains data and functions that define and allow +translation between different chromosome sequence naming conventions (e.g., +\"chr1\" versus \"1\"), including a function that attempts to place sequence +names in their natural, rather than lexicographic, order.") + (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 25ade2b9db..ff6996011e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,36 +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-genomeinfodb - (package - (name "r-genomeinfodb") - (version "1.26.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomeInfoDb" version)) - (sha256 - (base32 - "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v")))) - (properties - `((upstream-name . "GenomeInfoDb"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodbdata" ,r-genomeinfodbdata) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomeInfoDb") - (synopsis "Utilities for manipulating chromosome identifiers") - (description - "This package contains data and functions that define and allow -translation between different chromosome sequence naming conventions (e.g., -\"chr1\" versus \"1\"), including a function that attempts to place sequence -names in their natural, rather than lexicographic, order.") - (license license:artistic2.0))) - (define-public r-edger (package (name "r-edger")