From patchwork Mon Mar 15 13:01:28 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27702 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 EBB0827BC54; Mon, 15 Mar 2021 13:02:24 +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 74AAA27BC52 for ; Mon, 15 Mar 2021 13:02:24 +0000 (GMT) Received: from localhost ([::1]:37712 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmrX-0002am-He for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:02:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59806) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmrE-0002ZN-1W for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51729) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmrD-0006kz-Pz for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmrD-00069X-LM for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 03/10] gnu: r-biocstyle: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:02:03 +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=B47156.161581331923599 (code B ref 47156); Mon, 15 Mar 2021 13:02:03 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:01:59 +0000 Received: from localhost ([127.0.0.1]:35033 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr8-00068X-FD for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:58 -0400 Received: from mail-wr1-f47.google.com ([209.85.221.47]:38141) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr3-00067i-0K for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:54 -0400 Received: by mail-wr1-f47.google.com with SMTP id d15so8648840wrv.5 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:52 -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=eMoPV5iDE66FoOaSRWK51AGPY3jrggFY64e/4ntxPRE=; b=c8bmLw4V40y3iN/GEFwWspzDLQ+paTAEMJQc7b8sDzmRRcxFFkmp+7So/BeXeGMTv1 tsQsdDQeuy66vSI+nC6fS/tBFNRD3Jd7EJal1mPozHfd2kSgbl3ceMyCalij/fE45SMX LSyGQETIrPugWmZJbEdweMnkKyAprbMp/xi/EZfTM7NcEKyoC4aMPtjZ/ioXN14d+ZRS heGdSDJC63ICqAR5csfzyIvnHl8y55ifDRNzAPNET1nshaWo8uVE0j2v/hJkf2GiuEnT fuOLfA67BdVD+i6brm7j/w7Q0Wavb9SrTP56MAyca5X6o8qFfm6WdQXrzyYAOUCAQB0m wo0g== 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=eMoPV5iDE66FoOaSRWK51AGPY3jrggFY64e/4ntxPRE=; b=QtxsicsDOdN1LYOFLVZTUrXxHG01BcYLZoIUyhw7fqvGu1FCHFO6CNVsA2eIrHsOad GO0N/lTLSLiuVUPMP/0vW7dlCL/kjmr+J3TXh0drqkgpth1vCMnze2c7CisE4i9YFChy 93OuJ1iyqWFUAHlW99TNkG5y34uho3k66ekalBgoyzhYC+RgROgdK4hQP/g2EhZ2w71v hv4xBpjhIf2EfN2gq/ACBmiyYhkwCLHZocTrau9GFDjBWl0KC3KpKY8x/C1wCKb9eV/a Z0uw0zuPIU4wh/+CuRtdT5Kby6S1/oXO/W2IMia07qr04cUWM525AdgozkkjSegziT9Z nB8Q== X-Gm-Message-State: AOAM5321wZBp4EaIf2urgYxbXDcdGAm6kHoJ43vUNJ3qILqHcHycqJQK 6msQoashC00m4+KPFxZIkqyRylVryQM= X-Google-Smtp-Source: ABdhPJzGGwdjw5levEkwe+qkIZgBDZNvmWyWLBq9mMePnw2z7j+Ea+Sm48GsbvWj6Xi88/xoSdFbpA== X-Received: by 2002:adf:b1c9:: with SMTP id r9mr27985306wra.51.1615813307096; Mon, 15 Mar 2021 06:01:47 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.46 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:46 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:28 +0100 Message-Id: <20210315130134.30302-3-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-biocstyle): Move from here... * gnu/packages/bioconductor.scm (r-biocstyle): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4761474b04..91d02639a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8477,6 +8477,34 @@ monograph.") different graph related packages produced by Bioconductor.") (license license:artistic2.0))) +(define-public r-biocstyle + (package + (name "r-biocstyle") + (version "2.18.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocStyle" version)) + (sha256 + (base32 + "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) + (properties + `((upstream-name . "BiocStyle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocmanager" ,r-biocmanager) + ("r-bookdown" ,r-bookdown) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocStyle") + (synopsis "Bioconductor formatting styles") + (description "This package provides standard formatting styles for +Bioconductor PDF and HTML documents. Package vignettes illustrate use and +functionality.") + (license license:artistic2.0))) + (define-public r-biocviews (package (name "r-biocviews") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cc6e40283b..ad3ae204e1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,34 +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-biocstyle - (package - (name "r-biocstyle") - (version "2.18.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocStyle" version)) - (sha256 - (base32 - "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) - (properties - `((upstream-name . "BiocStyle"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-bookdown" ,r-bookdown) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocStyle") - (synopsis "Bioconductor formatting styles") - (description "This package provides standard formatting styles for -Bioconductor PDF and HTML documents. Package vignettes illustrate use and -functionality.") - (license license:artistic2.0))) - (define-public r-bioccheck (package (name "r-bioccheck")