From patchwork Mon Mar 15 13:01:26 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27704 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 C1D4D27BC54; Mon, 15 Mar 2021 13:02:42 +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 01ED827BC52 for ; Mon, 15 Mar 2021 13:02:42 +0000 (GMT) Received: from localhost ([::1]:38326 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmrp-0002r9-4e for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:02:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59818) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmrF-0002aL-3b for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51731) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmrE-0006lU-QL for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmrE-00069s-OZ for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 01/10] gnu: r-grohmm: Move to (gnu packages bioconductor). References: <20210315125800.30246-1-zimon.toutoune@gmail.com> In-Reply-To: <20210315125800.30246-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:02:04 +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=B47156.161581332323658 (code B ref 47156); Mon, 15 Mar 2021 13:02:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:03 +0000 Received: from localhost ([127.0.0.1]:35042 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrD-00069P-20 for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:03 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:37389) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr6-00067r-M9 for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:57 -0400 Received: by mail-wm1-f51.google.com with SMTP id f22-20020a7bc8d60000b029010c024a1407so20224263wml.2 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:56 -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:mime-version :content-transfer-encoding; bh=PHRM2lGmgpFY+Fnjv0Taww7I9OQq6F4IjKOWrkgepG4=; b=VLHRNk6LQ6gsqCyjCO9wGYxwYDe/yWzQyMNmWHF6O2f7sYO+u2RyBvrFSDI400vwti MSBNFr1ptfWE6bSPimee9JLMDhH80CtVVY73BRYHGw1RL8J5jk9ZzUESrqCluV7by9aS eMK83JYG0JmtE82GnzERYwhGvR4Zp4A5AUipz4ssnnvXSOKawdxkEPtC9ioakQr6WKqV W2MYo3fdBcoyBMX8xFImM16dQ8OsFXezJ1BX2caNebRf2iEc9wg30Fueqrxw7Ad5HIbN abT7FyoAvE1ghYtZtfLFgM2ggJP8Z/UhYR+Q6Y0QE2RqVnnqMNtxoYwvWmAWXI+us4iE g2Sw== 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:mime-version :content-transfer-encoding; bh=PHRM2lGmgpFY+Fnjv0Taww7I9OQq6F4IjKOWrkgepG4=; b=Te8LMdv9eWb6W4kT6XSWeO1R9TuONKUIQBYwkWqfZx23kDfwep2aC+YJClU6Fvg3sJ l4yFN+t56t72VBd+6/inn5xiwa+s8me8m7wVuc4dI7WYlWCUdeXMO3aPi7Y9jp2Lw1h0 3//vf8ozimOJ+HEZPmHbUkO7guNdwZAkKnFZnnOO2YJqgTk3QqLmEWWxoo3Lap38qJiY 2BQclUrxZibVMmCNtuBLwhzT+y0v7koGT3u6V5/+ny3HgfwhhpKA4LXsZGZC4p1MjNjC TJf8oWfab6iMoORHqTFeSvnjl6UgD6QpHPsGKJ5yWD6OkJzNp7wYefSNmmf9c+tvy9z9 yVjg== X-Gm-Message-State: AOAM532KaSBrVTGoVOWJdGus1rWTikOUT0i3sVAme1DaZUTEGVpjRLd5 3Vp1HbmTmNpq7aJfDeQODLIFV5+fgvA= X-Google-Smtp-Source: ABdhPJyMwWQXQLxIsZRC2NwSLfaCQTejNsOu0zZjjUJntWylt0uyFP9Q4Xxpog5c+Qi2S04v5nxRPg== X-Received: by 2002:a7b:ce16:: with SMTP id m22mr26607300wmc.65.1615813305407; Mon, 15 Mar 2021 06:01:45 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.44 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:44 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:26 +0100 Message-Id: <20210315130134.30302-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 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-grohmm): Move from here... * gnu/packages/bioconductor.scm (r-grohmm): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) base-commit: 1ed435bf394eee1a6cd9c354efb405920c212f0e diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f8e0562b1..55f718d5ab 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8511,6 +8511,33 @@ and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) +(define-public r-grohmm + (package + (name "r-grohmm") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "groHMM" version)) + (sha256 + (base32 + "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) + (properties `((upstream-name . "groHMM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/Kraus-Lab/groHMM") + (synopsis "GRO-seq analysis pipeline") + (description + "This package provides a pipeline for the analysis of GRO-seq data.") + (license license:gpl3+))) + (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b0736d32e4..20a9385604 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,33 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-grohmm - (package - (name "r-grohmm") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "groHMM" version)) - (sha256 - (base32 - "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) - (properties `((upstream-name . "groHMM"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/Kraus-Lab/groHMM") - (synopsis "GRO-seq analysis pipeline") - (description - "This package provides a pipeline for the analysis of GRO-seq data.") - (license license:gpl3+))) - (define-public vsearch (package (name "vsearch") From patchwork Mon Mar 15 13:01:27 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27701 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 48CEE27BC54; Mon, 15 Mar 2021 13:02:15 +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 BECD427BC52 for ; Mon, 15 Mar 2021 13:02:14 +0000 (GMT) Received: from localhost ([::1]:37680 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmrM-0002ZO-9U for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:02:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59792) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmrD-0002ZE-3M for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51726) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmrC-0006kG-Rq for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmrC-00069H-Q1 for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 02/10] gnu: r-biocviews: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:02:02 +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=B47156.161581331523577 (code B ref 47156); Mon, 15 Mar 2021 13:02:02 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:01:55 +0000 Received: from localhost ([127.0.0.1]:35029 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr4-000685-Nb for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:55 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:51028) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr2-00067f-LQ for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:53 -0400 Received: by mail-wm1-f50.google.com with SMTP id g25so8055814wmh.0 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=omMJYiCVL2E3Z/tWmTGMzaR/ZOTwUc4d+iQZrtx9dYg=; b=Z5M3yfPe4v/d1LXgs5/u8Pgd6SRhh652I+b8d1C6vwfOSKHKs2fygKR/7GdolBoudi co6rb7bMpQ/GK+jMM9MKqKXVbg7AjAnBQMvE7FWrhWrnCe2cn08Dnf3KgDr5Xd5oaVES eWR/0J8nXWneNlcX/b4hVr70PROD2KKLXIClh+gcdLk+E/stL4BQLi3HrPzA+GhO2z+l u9kzzb5OlovyGDeuhxJysBJmODnQIA3HmP5Y61AubwPxahyVKgqbQ8J4zSAHU7b9zqqj GXqKXjj25Qxi4ORD3WkpGQINsN7dMmjL/eunYQmMv7vxfn4i6bstr2wUDf5szh728gvI tSDA== 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=omMJYiCVL2E3Z/tWmTGMzaR/ZOTwUc4d+iQZrtx9dYg=; b=rXbfwkzGhl+EmZSCAxtXU/HSyyBaFS3vOUC39HyIjgsrC9JFU6wcjkJ9rjvkSbhkE/ rJVe0kFUJKhhjQbWLSzjHbHZsDkMUN3EoUJJWKaNpZAD2jhBkEtuc1LK30G0yVA5N8yW e6ro/0kCcPKFYmD4J6VCbHn67lT2eVxqmYJAcqqd+78Q3TRi+BT2b7jJe37HM/YQCn5k bKynKece0DJ3FsjzhzK6RSd5kuxdp8SYnEabjiNkfOIe2Ssld0i4q+IeY1UMmA9FMXpV 2bzKlM2JIVToRTEbFryn6l4A7E49wKwOY9EwASOa7CGhDUAmyqbkoxvYlecT6V2poAl6 VxYg== X-Gm-Message-State: AOAM5331FtCn5r1sn1OUpwvrU4jDehTAZm6OBNJpjiyUeChDtYUWrsbh 9T+TxM8sCRHH8iEtVnge8HV+XT56ijw= X-Google-Smtp-Source: ABdhPJxBFzqowwSwTzo2C/CnHJim1naszhzC7cdEK5df9Z1Iyq9iTBQy7RtmjvYWiqg6RB9LPtMzyg== X-Received: by 2002:a1c:21c3:: with SMTP id h186mr25039485wmh.32.1615813306526; Mon, 15 Mar 2021 06:01:46 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:45 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:27 +0100 Message-Id: <20210315130134.30302-2-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-biocviews): Move from here... * gnu/packages/bioconductor.scm (r-biocviews): ...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 55f718d5ab..4761474b04 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-biocviews + (package + (name "r-biocviews") + (version "1.58.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biocViews" version)) + (sha256 + (base32 + "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) + (properties + `((upstream-name . "biocViews"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-graph" ,r-graph) + ("r-rbgl" ,r-rbgl) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml) + ("r-runit" ,r-runit))) + (home-page "https://bioconductor.org/packages/biocViews") + (synopsis "Bioconductor package categorization helper") + (description "The purpose of biocViews is to create HTML pages that +categorize packages in a Bioconductor package repository according to keywords, +also known as views, in a controlled vocabulary.") + (license license:artistic2.0))) + (define-public r-experimenthub (package (name "r-experimenthub") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 20a9385604..cc6e40283b 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-biocviews - (package - (name "r-biocviews") - (version "1.58.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biocViews" version)) - (sha256 - (base32 - "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) - (properties - `((upstream-name . "biocViews"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-graph" ,r-graph) - ("r-rbgl" ,r-rbgl) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml) - ("r-runit" ,r-runit))) - (home-page "https://bioconductor.org/packages/biocViews") - (synopsis "Bioconductor package categorization helper") - (description "The purpose of biocViews is to create HTML pages that -categorize packages in a Bioconductor package repository according to keywords, -also known as views, in a controlled vocabulary.") - (license license:artistic2.0))) - (define-public r-biocstyle (package (name "r-biocstyle") 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") From patchwork Mon Mar 15 13:01:29 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27706 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 8637D27BC54; Mon, 15 Mar 2021 13:03:37 +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 97C6D27BC52 for ; Mon, 15 Mar 2021 13:03:36 +0000 (GMT) Received: from localhost ([::1]:38632 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmsh-00034B-3z for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:35 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60046) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032T-L7 for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51746) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsA-0007Hw-QQ 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-0006CF-Np for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 04/10] gnu: r-bioccheck: 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=B47156.161581332723708 (code B ref 47156); Mon, 15 Mar 2021 13:03:02 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:07 +0000 Received: from localhost ([127.0.0.1]:35049 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrG-0006AC-67 for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:06 -0400 Received: from mail-wr1-f48.google.com ([209.85.221.48]:42396) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr8-00067w-Im for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:59 -0400 Received: by mail-wr1-f48.google.com with SMTP id j2so8628235wrx.9 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=4hxht/01l6LN9BCFmQcL3Tlr6AzFXVEUTCRpq8rUGao=; b=iCGUjpFPbPs3asrIXrP1dweugBzL7MPd6OwZjkmYZpsd2QURO0aEx6UBiusKwWits6 UIu5xL8aGki2s06Qrcav2ccK800eYrRoOF7aPD4YYu2a0RCIkRamWMNO4IDNs7ozamLU bq/zyyNwpbYE3ndIV/EjJVNQ0aFHB8bSINUEZ3NwiQHh+jg9XBtH+ig+TJsS0TEZx+x3 lRAtwlSwqdjvuDyDZo8uNfOkEuMyD/ypcR2ktdV5eBYiYJOrL3BoLgpIBAEJlYB87BRG q3x8s+2tXd1peH9q7QW9ueHwgk70uLj5gvUlfuAZq9CTpDaufnBJiuOTvpO7mywH29HO DAAw== 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=4hxht/01l6LN9BCFmQcL3Tlr6AzFXVEUTCRpq8rUGao=; b=nBoLWeNHtFnKmwKWu4SJ4JBXJcUJri43nMks0Hm1p/KtMDK6CasArizqAqA4S+a1ea ehrn/srPL2eyOkrNvcb6OgY52DuAoqC7ZnxUkTe4L7LGPCzBbBkp3UFAM1zOZ9X42soM JGKWJog/+oCwaxSdX6FSpXJxqFF14C+bXjFP3Um9udNhzJoK91ITYDcgJljoBg9iSPkw fctMMkSLU8gnIBlq1dGvt1Ssc73nOhoTR7YGAHqvL1exBL3QEbQirtz26wzIy/CIobcc PWw3GMmXA37vwbgy2yNQZqyCtSk8o7j9/rkaFY0iJcmA0uQYtd/tgvdwGy6+1KzPpS2R s8DQ== X-Gm-Message-State: AOAM530pdE/P2hnFMWUPIidaS6u9pmiMBuWIw8WFmQmOmYEvd1+AOLgv phckWXLjiHPWOYUg5J1KE1fX/kbnhqM= X-Google-Smtp-Source: ABdhPJyIMrGXTHOxXDpBE6JPEeBqlC7XxeGdo8LVEhNBhsys1xz1jXTC4lgxx4bO9sySyD4kqdWAvQ== X-Received: by 2002:a5d:6290:: with SMTP id k16mr26167488wru.177.1615813307924; 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.21.2021.03.15.06.01.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:47 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:29 +0100 Message-Id: <20210315130134.30302-4-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-bioccheck): Move from here... * gnu/packages/bioconductor.scm (r-bioccheck): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 --------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91d02639a3..7c97e52312 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8452,6 +8452,55 @@ microarray data.") monograph.") (license license:artistic2.0))) +(define-public r-bioccheck + (package + (name "r-bioccheck") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocCheck" version)) + (sha256 + (base32 + "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) + (properties + `((upstream-name . "BiocCheck"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; This package can be used by calling BiocCheck() from + ;; within R, or by running R CMD BiocCheck . This phase + ;; makes sure the latter works. For this to work, the BiocCheck + ;; script must be somewhere on the PATH (not the R bin directory). + (add-after 'install 'install-bioccheck-subcommand + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (dest-dir (string-append out "/bin")) + (script-dir + (string-append out "/site-library/BiocCheck/script/"))) + (mkdir-p dest-dir) + (symlink (string-append script-dir "/checkBadDeps.R") + (string-append dest-dir "/checkBadDeps.R")) + (symlink (string-append script-dir "/BiocCheck") + (string-append dest-dir "/BiocCheck"))) + #t))))) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-knitr" ,r-knitr) + ("r-optparse" ,r-optparse) + ("r-biocmanager" ,r-biocmanager) + ("r-biocviews" ,r-biocviews) + ("r-stringdist" ,r-stringdist))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocCheck") + (synopsis "Executes Bioconductor-specific package checks") + (description "This package contains tools to perform additional quality +checks on R packages that are to be submitted to the Bioconductor repository.") + (license license:artistic2.0))) + (define-public r-biocgraph (package (name "r-biocgraph") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad3ae204e1..d8d64818d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,55 +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-bioccheck - (package - (name "r-bioccheck") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocCheck" version)) - (sha256 - (base32 - "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) - (properties - `((upstream-name . "BiocCheck"))) - (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - ;; This package can be used by calling BiocCheck() from - ;; within R, or by running R CMD BiocCheck . This phase - ;; makes sure the latter works. For this to work, the BiocCheck - ;; script must be somewhere on the PATH (not the R bin directory). - (add-after 'install 'install-bioccheck-subcommand - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (dest-dir (string-append out "/bin")) - (script-dir - (string-append out "/site-library/BiocCheck/script/"))) - (mkdir-p dest-dir) - (symlink (string-append script-dir "/checkBadDeps.R") - (string-append dest-dir "/checkBadDeps.R")) - (symlink (string-append script-dir "/BiocCheck") - (string-append dest-dir "/BiocCheck"))) - #t))))) - (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocCheck") - (synopsis "Executes Bioconductor-specific package checks") - (description "This package contains tools to perform additional quality -checks on R packages that are to be submitted to the Bioconductor repository.") - (license license:artistic2.0))) - (define-public r-s4vectors (package (name "r-s4vectors") From patchwork Mon Mar 15 13:01:30 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27703 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 6A1F327BC54; Mon, 15 Mar 2021 13:02:27 +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 AE28527BC52 for ; Mon, 15 Mar 2021 13:02:26 +0000 (GMT) Received: from localhost ([::1]:37738 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmrZ-0002bR-T3 for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:02:25 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59810) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmrE-0002Zr-Kj for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51730) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmrE-0006lN-Cv for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmrE-00069l-8L for guix-patches@gnu.org; Mon, 15 Mar 2021 09:02:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 05/10] gnu: r-s4vectors: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:02:04 +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=B47156.161581332323650 (code B ref 47156); Mon, 15 Mar 2021 13:02:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:03 +0000 Received: from localhost ([127.0.0.1]:35036 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr8-00068a-Tk for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:02 -0400 Received: from mail-wm1-f52.google.com ([209.85.128.52]:53131) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr4-00067l-D9 for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:01:55 -0400 Received: by mail-wm1-f52.google.com with SMTP id d191so8048848wmd.2 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:54 -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=/+6AunnG0DDWTKnpRJDXXd345iWPkWrSTnkN3r6Mbq8=; b=HfAVPX9hFzdabgi2ZqDAnF/w1tVbK2Omx2aF6Ptfr7bpoVLTrUr9teJ2/XBTslBK6Y 0xh8KWs0/jo21HugJTIBxkcJheWx7kZRHm77MXFqgIXtDnIJI/L/z8HJRNze3jNIPjXJ juDuCjG7PlI/KyJ5GIx9I6iqqPWl9tX1EaGGuMojUgz43dOuQKjB1kvKcPNCElPGVwJn Eh8DPCqhbncgLRNaKdKwQ4/hrVtWsafM6rxz3CH5we0xmeMfwyjuxMwpD6hrP7ul+nHW aHRJyENAu65EwA+bGMf6mAjzjue0lvsRSJxKlZ7dX0V4ubaGDF+TpfBK43tzewybclKF Q4zQ== 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=/+6AunnG0DDWTKnpRJDXXd345iWPkWrSTnkN3r6Mbq8=; b=UyKrseElwYtgKNvpdENxlY3ipjZbYzF71qUHlmQ9zPO775HDR9kNRxHD3kbogRzYFC 0uD89bQOR/tkWAwYJx3FhO8ZfTJuUtwE9VtgEzulHI3O78DDDw9ZwOls2mrTmXENUJBX WCKL2zf0tqlvzn78sCfLjbNkJOwcYhfmRs/OjjQiKD7uydTHuC43BQrkWt3ahUUof8GP NYvjvTjo5CmPPs5Uu8DuiV/VvvpBaA94JtXDiolnIKQ8o0ybL87ACvBneJ+ysFZ8raFM UHQuvlTLRWavRpJvKIlDKdGdl/cCdV3TdBqyA8wYXQneVFyKCNV8NoFPx17SCAXBMtyc sknQ== X-Gm-Message-State: AOAM531d/fXe0ZxXYS4oRtneAlgZ3QGIwP3CKV81Li97detXPpwsoHj/ RO9OqDDw03lIwjffTx6fvxlTM2yVL9M= X-Google-Smtp-Source: ABdhPJxYDam4/QBMkNTpte0slzS0vdCWVVIrFI2u7LVpSBUbx2/w6aBRDxc82VXv7tUCqONrfA51HA== X-Received: by 2002:a1c:7f84:: with SMTP id a126mr26411827wmd.151.1615813308552; Mon, 15 Mar 2021 06:01:48 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:48 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:30 +0100 Message-Id: <20210315130134.30302-5-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-s4vectors): Move from here... * gnu/packages/bioconductor.scm (r-s4vectors): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 28 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c97e52312..ed34a9308a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen +;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -9154,6 +9155,33 @@ generated.") routines.") (license license:lgpl2.0+))) +(define-public r-s4vectors + (package + (name "r-s4vectors") + (version "0.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "S4Vectors" version)) + (sha256 + (base32 + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) + (properties + `((upstream-name . "S4Vectors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/S4Vectors") + (synopsis "S4 implementation of vectors and lists") + (description + "The S4Vectors package defines the @code{Vector} and @code{List} virtual +classes and a set of generic functions that extend the semantic of ordinary +vectors and lists in R. Package developers can easily implement vector-like +or list-like objects as concrete subclasses of @code{Vector} or @code{List}. +In addition, a few low-level concrete subclasses of general interest (e.g. +@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the +S4Vectors package itself.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on preprocessorcore, which is a ;; Bioconductor package. (define-public r-wgcna diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d8d64818d2..1fcb436f0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,33 +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-s4vectors - (package - (name "r-s4vectors") - (version "0.28.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "S4Vectors" version)) - (sha256 - (base32 - "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) - (properties - `((upstream-name . "S4Vectors"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/S4Vectors") - (synopsis "S4 implementation of vectors and lists") - (description - "The S4Vectors package defines the @code{Vector} and @code{List} virtual -classes and a set of generic functions that extend the semantic of ordinary -vectors and lists in R. Package developers can easily implement vector-like -or list-like objects as concrete subclasses of @code{Vector} or @code{List}. -In addition, a few low-level concrete subclasses of general interest (e.g. -@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the -S4Vectors package itself.") - (license license:artistic2.0))) - (define-public r-iranges (package (name "r-iranges") From patchwork Mon Mar 15 13:01:31 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27709 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 8168727BC54; Mon, 15 Mar 2021 13:03:57 +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 E5D3027BC52 for ; Mon, 15 Mar 2021 13:03:53 +0000 (GMT) Received: from localhost ([::1]:39204 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmsz-0003MJ-2j for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:53 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60040) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032Q-Ky for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51747) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsB-0007Hx-8X 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 1lLmsB-0006CM-63 for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 06/10] gnu: r-iranges: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:03 +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=B47156.161581332723715 (code B ref 47156); Mon, 15 Mar 2021 13:03:03 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:07 +0000 Received: from localhost ([127.0.0.1]:35051 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrG-0006AL-R5 for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:07 -0400 Received: from mail-wr1-f47.google.com ([209.85.221.47]:42738) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmr9-000683-HH for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:00 -0400 Received: by mail-wr1-f47.google.com with SMTP id x13so5646106wrs.9 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:01:59 -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=eqc+9cvsgDprbsNpPrLnaDaAZehsN4tKi8aEh4epFBc=; b=P0iBUy8gwaWxNtDieWdjpoIiAUe5jbo7v8JDyfGR4JBxRUroV1XkHjxbMDA719HtGM 6Wu34EWzdnj6irc9c+hqJ4q+44RdZL981BeAY5xVHHH8wuK4priZMyfJFXZeZR+WQgO3 RDFz3jkDb/5jXn30xoegbLEz6+V3LKLubhkdX2/m0OCfJSXSFyF+il+/5N97+c4ZkRx8 2Twh8zNXR9en2/ww8p7VH8rCC6/Y78dDGRyGzKhjBLXL5ZPg7l4q7QsbHyPNYY8CvLbd 6lUVgmSxHY2DOpZAq34bCnhP9ljPpAN0euIhB3FSGjRbD0sOSwryEzoP17Ny/ddOY5hA sISg== 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=eqc+9cvsgDprbsNpPrLnaDaAZehsN4tKi8aEh4epFBc=; b=Dia2n7ZXtiOpUaekoFrSx/6qK9ASxfiiJSuOi08A6WV/AnyKrZ8M2V03FMxckZfynV l0arVG1Ljp5qiWK3FK935NcRRZNUJpVRkHsrTNsJHW6t8ykrz1CI7a/QQqMiOwFLcFCy R8imtrRfdGcX9MdPA7LGG2C1IwZSC97N2VvYH5wAAPlqjyx5ezgPwBKfMXbKxMfmHvuv 5acaXMho1ovOQ+B9sCQMXkEAn6rL5LviUObZAVP6bhzuYKul6e8sKlIPeHPBmg8HhijK xtG/wKWhO/F4rAKV1TmKfFed95D9jhA7Hvyam1Z4229iOJAXLe8ByVD8/7grQ7TCGodF k5Lw== X-Gm-Message-State: AOAM5312Y9RAL8N2BnsQYga/ZoAAL45q+FyakcDjcL6qgJkCqD9vs7Tk gOrRMnJnwb/5UuZN1GXNnNfs36aGIiE= X-Google-Smtp-Source: ABdhPJwxJLkULV/FSVLRmXoaEnT4JGMp1L7J6/KhmMgJUrFhyTcmWLyKLeCBuj3OoCeJIlz1Hv5azg== X-Received: by 2002:a5d:6ca6:: with SMTP id a6mr26870834wra.179.1615813309118; Mon, 15 Mar 2021 06:01:49 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:48 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:31 +0100 Message-Id: <20210315130134.30302-6-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-iranges): Move from here... * gnu/packages/bioconductor.scm (r-iranges): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 30 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed34a9308a..68c5ed7768 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins +;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -1244,6 +1245,35 @@ and evaluate clustering results.") arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-iranges + (package + (name "r-iranges") + (version "2.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "IRanges" version)) + (sha256 + (base32 + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) + (properties + `((upstream-name . "IRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/IRanges") + (synopsis "Infrastructure for manipulating intervals on sequences") + (description + "This package provides efficient low-level and highly reusable S4 classes +for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more +generally, data that can be organized sequentially (formally defined as +@code{Vector} objects), as well as views on these @code{Vector} objects. +Efficient list-like classes are also provided for storing big collections of +instances of the basic classes. All classes in the package use consistent +naming and share the same rich and consistent \"Vector API\" as much as +possible.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1fcb436f0d..36ecf47467 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,35 +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-iranges - (package - (name "r-iranges") - (version "2.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "IRanges" version)) - (sha256 - (base32 - "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) - (properties - `((upstream-name . "IRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/IRanges") - (synopsis "Infrastructure for manipulating intervals on sequences") - (description - "This package provides efficient low-level and highly reusable S4 classes -for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more -generally, data that can be organized sequentially (formally defined as -@code{Vector} objects), as well as views on these @code{Vector} objects. -Efficient list-like classes are also provided for storing big collections of -instances of the basic classes. All classes in the package use consistent -naming and share the same rich and consistent \"Vector API\" as much as -possible.") - (license license:artistic2.0))) - (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") From patchwork Mon Mar 15 13:01:32 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27710 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 6C2D527BC54; Mon, 15 Mar 2021 13:04:07 +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 6BEAC27BC52 for ; Mon, 15 Mar 2021 13:04:06 +0000 (GMT) Received: from localhost ([::1]:39726 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmtB-0003b2-K7 for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:04:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60044) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032S-KX for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51748) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsB-0007Hy-Mz 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 1lLmsB-0006CU-KH for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 07/10] gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:03 +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=B47156.161581332823723 (code B ref 47156); Mon, 15 Mar 2021 13:03:03 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:08 +0000 Received: from localhost ([127.0.0.1]:35053 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrH-0006AS-EF for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:07 -0400 Received: from mail-wr1-f46.google.com ([209.85.221.46]:35976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrA-00068B-6P for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:00 -0400 Received: by mail-wr1-f46.google.com with SMTP id y16so8663310wrw.3 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:02:00 -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=rPPUdFVPfI3K1oKTHQw2hWCuXTWwwYOBaqfc5RWqbTU=; b=KR1NqAZl15540wcIyv6rN3MYU++bCpKfaZ8OJkwDIcsJV6TqdADqTpMXa2CiBflTJe xm3rsjnX+W2ZwLmjtyh3kwQu2vvoN5FKSXTSqa/x4t5IL7G4llwQewk/fmLeR8b7FQAM LjG9BFneJtV9RV2ysrt8V4QIi/iC83atJdtF1n37FwLwrGPcZfADGQnXY5BkPRctr+rG aFxb+FWYtC0X0QDeXZu0FPutUxuTCorVUGVIcTHedOaVbveL1FSsyvCS6OZnpIr8hi6G qklRHAFeZtD/i9AByTvmcHudNdCUdPh6wcIIm+2VO+5PtVW5ZH9+wduZtl8ZlzryoL7d QMuw== 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=rPPUdFVPfI3K1oKTHQw2hWCuXTWwwYOBaqfc5RWqbTU=; b=XjiI6NwfKR3mtF/zckCNc5Ufxc9onHWv9XghYrTwifzKgmvLPVf6mfUj5t5yJsilCO ojmBp0kWeSWhhGdfFI7FPb1qQe2bVK5lzbJqCtO1/iv50LgkPxJXQ6DxBjyemEL+LByv aR99bxfy83QBXBdtwBeErSXoO02Rpf7mjiprLfSoO5bj7FX/gKxszAQ/meJXij27SD/r FAjAVPYNaJoLxbdaLUgR3+GmB6BWM7X1ViuYhAVtoSZLzQ1Sq59OOqddoIpyumgoj8Nf 1VFVXRrbA4Wikr4yFP573QADxPfrsriFqlnHN6oIvDH0i/OADLQx2Hr9R0mjcDEwIHgO Y72A== X-Gm-Message-State: AOAM533V9TsuHFvLqJccHowCI8cvVIDUgzR+7jk1odZTaB+uUwwpsUkM HCza+zrAQo3WmknCAGqORTfgX9znyig= X-Google-Smtp-Source: ABdhPJw4addtXhIt1MoAkfcE5AgNfD/HO1I52ui6EODpD4a5IcOQ437Xhu3BF9WzN63En6eIrSHGOA== X-Received: by 2002:a5d:5051:: with SMTP id h17mr26819967wrt.80.1615813309703; Mon, 15 Mar 2021 06:01:49 -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 14:01:32 +0100 Message-Id: <20210315130134.30302-7-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-genomeinfodbdata): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here. [source]: Use 'bioconductor-uri'. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 20 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68c5ed7768..53f025ec61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft +;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -391,6 +392,25 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-genomeinfodbdata + (package + (name "r-genomeinfodbdata") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) + (sha256 + (base32 + "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) + (properties + `((upstream-name . "GenomeInfoDbData"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/GenomeInfoDbData") + (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") + (description "This package contains data for mapping between NCBI taxonomy +ID and species. It is used by functions in the GenomeInfoDb package.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36ecf47467..25ade2b9db 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,29 +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-genomeinfodbdata - (package - (name "r-genomeinfodbdata") - (version "1.2.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://bioconductor.org/packages/release/" - "data/annotation/src/contrib/GenomeInfoDbData_" - version ".tar.gz")) - (sha256 - (base32 - "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) - (properties - `((upstream-name . "GenomeInfoDbData"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/GenomeInfoDbData") - (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") - (description "This package contains data for mapping between NCBI taxonomy -ID and species. It is used by functions in the GenomeInfoDb package.") - (license license:artistic2.0))) - (define-public r-genomeinfodb (package (name "r-genomeinfodb") 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") From patchwork Mon Mar 15 13:01:34 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27708 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 6715427BC55; Mon, 15 Mar 2021 13:03:56 +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 2134527BC54 for ; Mon, 15 Mar 2021 13:03:55 +0000 (GMT) Received: from localhost ([::1]:39308 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmt0-0003PG-Af for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:54 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60042) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032R-LR for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51749) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsC-0007Hz-4v 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 1lLmsC-0006Cb-2Y for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 09/10] gnu: r-edger: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:04 +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=B47156.161581332823729 (code B ref 47156); Mon, 15 Mar 2021 13:03:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:08 +0000 Received: from localhost ([127.0.0.1]:35055 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrI-0006Aa-0N for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:08 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:37398) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrB-00068Q-MX for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:02 -0400 Received: by mail-wm1-f51.google.com with SMTP id f22-20020a7bc8d60000b029010c024a1407so20224467wml.2 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:02:01 -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=934bcbrdffuahjUu3IX2GMxYkAsHi5dsEE/SASFznFA=; b=eOmH3tWGxGhlPyXeMLhBSP4+M1B5SPXFZwQzyTRhQqnnxXRIllCARGpjV9Bn7lHRCE 3t6lamyEUz2YmlLwWe5YlqglbqgMLGxWLdh08cWZpC5IYPdYQ35Vq4BPQaZXllYvEGRm 6j8QSN6lOHG5iTllzGpRYWUClE0GObMOVHE0jRoJJKK7oeZde/8n1XyoT40SoYpSle9F x87My3akfTwWry4swfvVR6AegnPwExd+1KBl6F4TqxULQ15WjWWztV7zMm6a3cNKOuX0 BKP6/GvsgBMlq8uD690YC+7EYHz82I8Xy1xu/j/WBNksX8L/ZFWPHFb6lsDgg3wWHYUp 152g== 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=934bcbrdffuahjUu3IX2GMxYkAsHi5dsEE/SASFznFA=; b=aQOhRime9aQkjtqcSf13sK6nonx5X6xCeWHr2E1rB+zjac3Voq8PLgTkd+h1EfUe+M lxOlWExuFWRe4hrdzINv3f79zDBD4Z5OiaCE6dQFRb4ODHO9OIRZ0cQNjSlremjI0AQi 6Va2HwvBpPHyWwSd1/0tDdVKJhVFXkestDllsDClhMHye+0yoKprHQhoK1hdM4ouM1gn /rS9lkdOmHeZGkfaoF7IjfWxOxjUUDAiAtW8Es5/4U9iNjwM7gHwS+LQcksXGTg4cV81 yv2KPTxrwDGDOCqF+k7ugGCPcAWCy8ohq2sgQ7K26mC5JCeFQkrcuu6+ZreG6q+kdftr Pfqw== X-Gm-Message-State: AOAM530gWfIzZJ8OzPMTBBLdLby4/DUl7IuIkWFA3vkkSw7lS71/XWsV AlxEtciuH8PM70zsawKOu1RmjXNmQng= X-Google-Smtp-Source: ABdhPJxNqZJFLO8INh+invR0Zxlhc3nWA7pckQds7udEiVKaAcd9DiptP7i45JaPgq81sc6U4Uf6Ww== X-Received: by 2002:a1c:400b:: with SMTP id n11mr25682401wma.167.1615813311169; Mon, 15 Mar 2021 06:01:51 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.50 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:50 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:34 +0100 Message-Id: <20210315130134.30302-9-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-edger): Move from here... * gnu/packages/bioconductor.scm (r-edger): ...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 b4456d13c8..fb0127b7ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1684,6 +1684,34 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edger + (package + (name "r-edger") + (version "3.32.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "edgeR" version)) + (sha256 + (base32 + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) + (properties `((upstream-name . "edgeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-statmod" ,r-statmod))) ;for estimateDisp + (home-page "http://bioinf.wehi.edu.au/edgeR") + (synopsis "EdgeR does empirical analysis of digital gene expression data") + (description "This package can do differential expression analysis of +RNA-seq expression profiles with biological replication. It implements a range +of statistical methodology based on the negative binomial distributions, +including empirical Bayes estimation, exact tests, generalized linear models +and quasi-likelihood tests. It be applied to differential signal analysis of +other types of genomic data that produce counts, including ChIP-seq, SAGE and +CAGE.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6996011e..dc0d7a2906 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-edger - (package - (name "r-edger") - (version "3.32.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "edgeR" version)) - (sha256 - (base32 - "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) - (properties `((upstream-name . "edgeR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp - (home-page "http://bioinf.wehi.edu.au/edgeR") - (synopsis "EdgeR does empirical analysis of digital gene expression data") - (description "This package can do differential expression analysis of -RNA-seq expression profiles with biological replication. It implements a range -of statistical methodology based on the negative binomial distributions, -including empirical Bayes estimation, exact tests, generalized linear models -and quasi-likelihood tests. It be applied to differential signal analysis of -other types of genomic data that produce counts, including ChIP-seq, SAGE and -CAGE.") - (license license:gpl2+))) - (define-public r-variantannotation (package (name "r-variantannotation") From patchwork Mon Mar 15 13:01:58 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27705 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 C86C627BC52; Mon, 15 Mar 2021 13:03:33 +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 5A17D27BC55 for ; Mon, 15 Mar 2021 13:03:28 +0000 (GMT) Received: from localhost ([::1]:38608 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmsZ-000333-It for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60050) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032V-LC for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51750) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsC-0007I2-J8 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 1lLmsC-0006Cj-Gb for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 10/10] gnu: r-variantannotation: Move to (gnu packages bioconductor). References: <20210315125800.30246-1-zimon.toutoune@gmail.com> In-Reply-To: <20210315125800.30246-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:04 +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=B47156.161581333723750 (code B ref 47156); Mon, 15 Mar 2021 13:03:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:17 +0000 Received: from localhost ([127.0.0.1]:35058 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrQ-0006B0-KQ for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:17 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:34392) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrL-0006AJ-VG for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:12 -0400 Received: by mail-wm1-f47.google.com with SMTP id n11-20020a05600c4f8bb029010e5cf86347so2262755wmq.1 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:02:11 -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:mime-version :content-transfer-encoding; bh=UktbsVBAxsuPXyhqSuueZQiphjwVwYsVljVSaG2Z2Tc=; b=edF4R77ZkiHa4vfNDeHXJZqowUqd0svzEy4067TgH1fiytTWH6H9bDEyFXL55rCmAq Uuyd0PUx49ZQ9sJD7dgj0PL9Cgv+umX8vFnyKMq8+AieKO+P1wWpVsmMOXj6dwJVkm3H 2Gz5God75zfkpMlfmNg00S6lfLPelhJcWikUnFp/Yrhp2CcGXfQVxDVaSvh0cKpYoU92 91Cb/p5NPrDAN4PCA53CLSNeujnT1+OnElzAqdzJhqmgx7ySbpnhVBrWDWhSBMWKJQ34 4xIXy8msNmGHZTwPILc0iUXmrFfabB9Kh7OqzKHxFQSKjl4fY9gUzXRS8tBegsnjA1Rj 0zsw== 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:mime-version :content-transfer-encoding; bh=UktbsVBAxsuPXyhqSuueZQiphjwVwYsVljVSaG2Z2Tc=; b=XAa3RiYqXwb9B2UNA0bk3pf7jvfuN/mIIvBatDdF+xdzowbjGy5k5LMzp1nI0NWuUJ wfIGD77Y/eFt4Elvpg33zXUhD58i2ADU7az93QkC7hFdRfOPcms9+oJRoirg5uAcs6gx CGzTRAHSsNJjJVKSZfFcRnoFYlwcefLgRgxzbhu/q7FGiDqVXFCpSAnrTp8tebRRLQji O/KSRClrfJpczHf787NjjO0sNYynPOGgEhfs7tCQDptDYuhqjXGU9EJ8D8SbWtUuviOG RnfLEU77cMW3MkI2TMn/QmiYNmCyGk++A0nNEyLuhGnLNhZHUv1xiWx0gtVeND/CBrAm VIaQ== X-Gm-Message-State: AOAM533/VoHD22R51GGCNk3KLG2VABIWHKPjW9BOGgJFtAN4b4RuBAk0 PIg4HqMfoZY0pOI6QYHsloqbQtr58og= X-Google-Smtp-Source: ABdhPJx4oxitsYHCy5LmVF4hSrJMTe1vNieEiWvuL6hXBGMnmyfCzcytaiDJH1unenLyyG4XUoM+wA== X-Received: by 2002:a1c:3d46:: with SMTP id k67mr20794739wma.188.1615813320909; Mon, 15 Mar 2021 06:02:00 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id c9sm18682463wrr.78.2021.03.15.06.02.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:02:00 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:58 +0100 Message-Id: <20210315130158.30365-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 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-variantannotation): Move from here... * gnu/packages/bioconductor.scm (r-variantannotation): ...to here. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 --------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb0127b7ca..c4df090a05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2051,6 +2051,44 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-variantannotation + (package + (name "r-variantannotation") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "VariantAnnotation" version)) + (sha256 + (base32 + "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) + (properties + `((upstream-name . "VariantAnnotation"))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/VariantAnnotation") + (synopsis "Package for annotation of genetic variants") + (description "This R package can annotate variants, compute amino acid +coding changes and predict coding outcomes.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dc0d7a2906..78df3091fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,44 +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-variantannotation - (package - (name "r-variantannotation") - (version "1.36.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "VariantAnnotation" version)) - (sha256 - (base32 - "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) - (properties - `((upstream-name . "VariantAnnotation"))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/VariantAnnotation") - (synopsis "Package for annotation of genetic variants") - (description "This R package can annotate variants, compute amino acid -coding changes and predict coding outcomes.") - (license license:artistic2.0))) - (define-public r-limma (package (name "r-limma")