From patchwork Mon Mar 8 17:57:54 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27547 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 2314327BC52; Mon, 8 Mar 2021 18:54:48 +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 B840127BC51 for ; Mon, 8 Mar 2021 18:54:46 +0000 (GMT) Received: from localhost ([::1]:47556 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL1h-0001jF-VL for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:45 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59058) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qA-NR for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33231) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9m-0001JW-0E for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9l-0002hF-Vt for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 01/10] gnu: r-genefilter: Move to (gnu packages bioconductor). References: <20210308175558.62461-1-zimon.toutoune@gmail.com> In-Reply-To: <20210308175558.62461-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630510224 (code B ref 47010); Mon, 08 Mar 2021 17:59:01 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:25 +0000 Received: from localhost ([127.0.0.1]:44753 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9A-0002ei-8A for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:24 -0500 Received: from mail-wm1-f51.google.com ([209.85.128.51]:38638) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK98-0002e2-ER for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:22 -0500 Received: by mail-wm1-f51.google.com with SMTP id m20-20020a7bcb940000b029010cab7e5a9fso4342009wmi.3 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:22 -0800 (PST) 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=IJ4IOoDat0pEiMV2kWFZkQJ/yBhVCznWLMPXxWRpF2Y=; b=UVSQgMKVCdP3ddyuuO5U07ckFLecdM+dzBhYPAkDn/Htn5YxhsBDsyNrk/zEsVw4hl AkAzVb4lZLLqK2r7/5TIiJtkwZDI53o/rrCNCaCooPLOZuDMQntMo0EyZa/85FzTj4E+ fFPkt84Hv7V8klhCzLJH/3ECjnX5iO4CI9kPJPLsoYHdN0Rj4GVs2T5ZlXhtgjzb+W0h fdvdF2HXdqNpNLPPMIQLfJQu/URQdpUssvzKdDoFBGgILNNyrt5n0IoXnx70VYCFyIOG m51GNltScctPdWbKyEli304tdJ//pzYLNBa9usIjYI3Vh1wkhGu5CuD9NZ6/bhOPsnPP BgHg== 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=IJ4IOoDat0pEiMV2kWFZkQJ/yBhVCznWLMPXxWRpF2Y=; b=lybe3XvBfS5cTkhTzgyjiDcum+gfaja0q9zsxgVbtsZ2ZB+mwa91UvWiyt9omqElGQ ofjSfdlfX8gt9/uRdDtmBSo9VgrdzNCdZJFXMH5m7mF5Gj1h7XS4+x20d/P61tVyAQBy wMsjRn8M7lyrohwRVl0erj26pRIo9vrshR6Y9THjCpaG/PRjwUFis3iVGcjGsZ43DsYt Zdus80PjzZ0k4JO0RR//PbYbcQjoePyDyTqmLewOE7gorGtTiXm1JpD+i5EesSoif9wH bM179l+hs2fQfh9LSzwWyQCDVHZZhpF1HwMNaz/Qrqf8lD2BPVr6pvWtGgNJKRRVInxT 2eLA== X-Gm-Message-State: AOAM530ffG9y7sU0qaXedQEgRkdz53UJINEa7X3SPKP6fAF7A5lTAcxt P9EZnYnQlDUSTIt2DpHoDTXr5nfwd7I= X-Google-Smtp-Source: ABdhPJz9AmJfI724UzipAbCrr4/D202qwxZa0VPdGsr93rffSRN7mhHmm7+XbxKn9nZ5bcwFLn/ZzA== X-Received: by 2002:a7b:cb99:: with SMTP id m25mr31611wmi.64.1615226296526; Mon, 08 Mar 2021 09:58:16 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.16 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:16 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:54 +0100 Message-Id: <20210308175802.62517-1-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-genefilter): Move from here... * gnu/packages/bioconductor.scm (r-genefilter): ...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 89b191585b..e15984d0e3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,34 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-genefilter + (package + (name "r-genefilter") + (version "1.72.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "genefilter" version)) + (sha256 + (base32 + "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-survival" ,r-survival))) + (home-page "https://bioconductor.org/packages/genefilter") + (synopsis "Filter genes from high-throughput experiments") + (description + "This package provides basic functions for filtering genes from +high-throughput sequencing experiments.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index be07bd18a3..258c3ca409 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,34 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-genefilter - (package - (name "r-genefilter") - (version "1.72.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "genefilter" version)) - (sha256 - (base32 - "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-survival" ,r-survival))) - (home-page "https://bioconductor.org/packages/genefilter") - (synopsis "Filter genes from high-throughput experiments") - (description - "This package provides basic functions for filtering genes from -high-throughput sequencing experiments.") - (license license:artistic2.0))) - (define-public r-deseq2 (package (name "r-deseq2") From patchwork Mon Mar 8 17:57:55 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27540 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 C3FD927BC51; Mon, 8 Mar 2021 18:21:47 +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 E561227BC50 for ; Mon, 8 Mar 2021 18:21:46 +0000 (GMT) Received: from localhost ([::1]:57744 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJKVm-0003d2-2R for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:21:46 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59076) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qS-Qb for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:09 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33232) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9m-0001JY-D5 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9m-0002hN-CT for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 02/10] gnu: r-deseq2: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630510237 (code B ref 47010); Mon, 08 Mar 2021 17:59:02 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:25 +0000 Received: from localhost ([127.0.0.1]:44756 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9A-0002er-Ox for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:25 -0500 Received: from mail-wr1-f52.google.com ([209.85.221.52]:42231) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK98-0002e3-Py for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:23 -0500 Received: by mail-wr1-f52.google.com with SMTP id j2so12399412wrx.9 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:22 -0800 (PST) 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=IOmillYLLCiuQhvwD9JiBVbndlo/RW1bstyP2Nn3cl8=; b=Iaw0OI0M9RgRmbYhqpoeOlCKkqSxVTTnL6VeW89wSpiXTYq83wsQ+lqjy7a/24iJu0 3oUi4Ba5HYk2MpETfjj1ONdQrrYkxG+fZ6okbbioCgXc6HZsfI51xRFL1v+8UsBVqq0u mdbbAXeWjktAeBZrRbN7c5QKO43IeovdAfIWkpggCT0rsSPSIYjJN9erh20d24Zo7Y7Z 7p0ft4+EtH/1Kmctz+iL0g73WiXU/5q5tzc1WAw6LwSXpkk+PCMd0g9xtkus92T1mcf6 UPPZ2OgNa1qpQjAUeHi4qvb8sfuh20uzN0OwVBzuISs40ca8WoKK9q83mhi/nB3egNid ftTg== 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=IOmillYLLCiuQhvwD9JiBVbndlo/RW1bstyP2Nn3cl8=; b=knFshe2oriEJ1M921MDnoJcSwT8TpLxW/bxvA3Tj88U31LjBnRRYjPmCv/2H1LSOVx nE509Sz7aZqP/VTHCRySaVGs83NljoJOqbhzhzOnUyku0N0sEfuerrGSPtEUe+Bxfbyi ctYSG3h+X7NwyRZziAKGx2+0r6IfpKKfZ5uqntzoQwrfV+tXo3XPOD/Y5T82QQGFT9Ee nP0yrIqFN6CXLgZVG+fQsWbkBPrRShdStoSHptMAA47wc8A+oeCjrLhL6hIS7LEkvQva ihJ2WjW9d0pNChw/HvbBfldvxujDcfWGyf1QKpayi36RPe+L8WIX3jNc+SbVGdwVMFUH yE9Q== X-Gm-Message-State: AOAM532j2Feoe5xtZvh5XxS7+CMtPndSgT8ad1i0hc3YADNQZCEcXYta OZd44RNrf6emsWkCuA4/K2KnHumU9F8= X-Google-Smtp-Source: ABdhPJzO0GafZLGyKrR8bJZZyYQm3nZKg6tCE5YbkqYHc/ojhtJjs0W3950qJTG4ronHq08AmVDaaw== X-Received: by 2002:a5d:4002:: with SMTP id n2mr14237058wrp.148.1615226297008; Mon, 08 Mar 2021 09:58:17 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.16 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:16 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:55 +0100 Message-Id: <20210308175802.62517-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-deseq2): Move from here... * gnu/packages/bioconductor.scm (r-deseq2): ...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 e15984d0e3..f2dd4bb70b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,44 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-deseq2 + (package + (name "r-deseq2") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq2" version)) + (sha256 + (base32 + "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) + (properties `((upstream-name . "DESeq2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DESeq2") + (synopsis "Differential gene expression analysis") + (description + "This package provides functions to estimate variance-mean dependence in +count data from high-throughput nucleotide sequencing assays and test for +differential expression based on a model using the negative binomial +distribution.") + (license license:lgpl3+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 258c3ca409..64585127e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,44 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-deseq2 - (package - (name "r-deseq2") - (version "1.30.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq2" version)) - (sha256 - (base32 - "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) - (properties `((upstream-name . "DESeq2"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DESeq2") - (synopsis "Differential gene expression analysis") - (description - "This package provides functions to estimate variance-mean dependence in -count data from high-throughput nucleotide sequencing assays and test for -differential expression based on a model using the negative binomial -distribution.") - (license license:lgpl3+))) - (define-public r-dexseq (package (name "r-dexseq") From patchwork Mon Mar 8 17:57:56 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27545 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 0C6EE27BC50; Mon, 8 Mar 2021 18:54:37 +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 B812527BC52 for ; Mon, 8 Mar 2021 18:54:34 +0000 (GMT) Received: from localhost ([::1]:46876 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL1V-0001SI-Re for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:33 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59068) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qO-Q1 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33233) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9m-0001Jb-Qp for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9m-0002hU-Q1 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630710261 (code B ref 47010); Mon, 08 Mar 2021 17:59:02 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:27 +0000 Received: from localhost ([127.0.0.1]:44761 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9D-0002fP-GB for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:27 -0500 Received: from mail-wr1-f47.google.com ([209.85.221.47]:46781) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK99-0002e5-1b for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:23 -0500 Received: by mail-wr1-f47.google.com with SMTP id a18so12368403wrc.13 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:22 -0800 (PST) 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=i/9dtr60p5NUJjnBPgAH6JZTQEqskEyPpFovnlma3oM=; b=b/AeF79Febdp+9x3kXAsGr2/tQN+FXg2/JseOLdvCb7kCsabj/8ZI+86w7AX1Avt25 47NnGDOJmq5C7yM+iPojfZXH5VE5WHTUEqNXXHyBzGSg0YreqvNLh1WpeH0PNNXTLez2 2uz/jkSk+ggy+d6h2sBbLD/Xyaa33seNlfZCs4OZMquNVC+e6dZbV4klc/v/mgj1BgXt ERIkLTK24EcC1AUk++fisEv2mJXGCW6fwgUqjLHBiwzyeg/iF3r7BGxmlryMPzEIP31X N9AW+Ml7k7LAaYxLeQzLjYvX7G2g/OoJJ5KCe+rDA7M2ZiESiLrwKS9Aix9Flfmf7TSu WDzg== 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=i/9dtr60p5NUJjnBPgAH6JZTQEqskEyPpFovnlma3oM=; b=B41zQSxmoeeCiC+2Y+W4Mp03lAkvjYmNWpB4zRbq3PTh4eLVo/MIu4Gx00scWr2dwp wu36/pbJI7H+F05PDmaCNoiZhKgYfuKQsS6dwM+IzpfPduPPfoCMj1iJdXYGvViv2x0t 3w/lffjkLLygzI1nfwsP5oGbE8XtGlU1FxgWAQMxmR2egZ0lSNmCNoTdrjAr3yqkRkK7 zmT/nf9RH0H9X6rhpL8gUSr1o2i61oV9g32Hqr6maM2EcQMeWHwT8JoLGp/XMv985q6s svziahisAk4uY+FQiEKl0/Db9mF/0ChXKzo94eu2hfyRdQNb1KUhDQ+SYoIJqOW+BHlg sPiA== X-Gm-Message-State: AOAM532SOtUUZfQzO3uRTMQhrL2EuvplDnZhpxtLoplC2H4dDRXNTw7G DMm8rHxe7fhPSHCeiNGVO/IsC5zE0t0= X-Google-Smtp-Source: ABdhPJw2P7A6nXshljTiZVCY6XQHP7hW7W7N6rzA/P88sABrGFIAnvU33l+dpoCxZbX4llaHtBEswg== X-Received: by 2002:a5d:6d06:: with SMTP id e6mr24244598wrq.425.1615226297445; Mon, 08 Mar 2021 09:58:17 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:17 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:56 +0100 Message-Id: <20210308175802.62517-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-dexseq): Move from here... * gnu/packages/bioconductor.scm (r-dexseq): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f2dd4bb70b..883b6df2fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1525,6 +1525,51 @@ differential expression based on a model using the negative binomial distribution.") (license license:lgpl3+))) +(define-public r-dexseq + (package + (name "r-dexseq") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEXSeq" version)) + (sha256 + (base32 + "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) + (properties `((upstream-name . "DEXSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biomart" ,r-biomart) + ("r-deseq2" ,r-deseq2) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-statmod" ,r-statmod) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DEXSeq") + (synopsis "Inference of differential exon usage in RNA-Seq") + (description + "This package is focused on finding differential exon usage using RNA-seq +exon counts between samples with different experimental designs. It provides +functions that allows the user to make the necessary statistical tests based +on a model that uses the negative binomial distribution to estimate the +variance between biological replicates and generalized linear models for +testing. The package also provides functions for the visualization and +exploration of the results.") + (license license:gpl3+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 64585127e6..4fa4a1e354 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,51 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-dexseq - (package - (name "r-dexseq") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DEXSeq" version)) - (sha256 - (base32 - "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) - (properties `((upstream-name . "DEXSeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DEXSeq") - (synopsis "Inference of differential exon usage in RNA-Seq") - (description - "This package is focused on finding differential exon usage using RNA-seq -exon counts between samples with different experimental designs. It provides -functions that allows the user to make the necessary statistical tests based -on a model that uses the negative binomial distribution to estimate the -variance between biological replicates and generalized linear models for -testing. The package also provides functions for the visualization and -exploration of the results.") - (license license:gpl3+))) - (define-public r-annotationforge (package (name "r-annotationforge") From patchwork Mon Mar 8 17:57:57 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27541 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 9C7AC27BC51; Mon, 8 Mar 2021 18:21:55 +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 CCDF627BC50 for ; Mon, 8 Mar 2021 18:21:54 +0000 (GMT) Received: from localhost ([::1]:58570 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJKVu-0003xR-1W for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:21:54 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59066) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qN-QS for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33234) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9n-0001Jc-5O for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9n-0002hb-5Z for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 04/10] gnu: r-annotationforge: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630810268 (code B ref 47010); Mon, 08 Mar 2021 17:59:03 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:28 +0000 Received: from localhost ([127.0.0.1]:44763 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9D-0002fS-Sv for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:28 -0500 Received: from mail-wm1-f51.google.com ([209.85.128.51]:33631) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK99-0002e9-Ej for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:23 -0500 Received: by mail-wm1-f51.google.com with SMTP id w203-20020a1c49d40000b029010c706d0642so8321141wma.0 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:23 -0800 (PST) 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=73OHF4VPjLBZkXsiPHnFAtNkykDl2Hr/CSobNnb6lhY=; b=jIZMow0Uq72in5DMSVImNytYGsb7dI1GHyrnxMA82L2kp9MnzwLFVaSv6zCoa4JDQn okq/hY4XA/CmmnjftyxLb1sd+GyIcKOEf8urh4BqR5757+kyBR4v1PUG1GJFgvW20tZo Y3kecEirgx6P8q6losJa4dhj1pPSKiGVibv5lPLA3G6sHpNEhrOKSLGWzeL33Y5h0r5J PstltCt2cxj3A7k/Izq623L/D+UCYiZYTrt7OBiesjbfZaNaAvepLtrV/7P2ou6QYuGc cs7Kp5pABJWiTJZSUc8NKwqB4FIWdFzORK67JYaOTKGkjbqVdmoJxSdxcvI5FgzdO0OS Un6w== 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=73OHF4VPjLBZkXsiPHnFAtNkykDl2Hr/CSobNnb6lhY=; b=Xv2TM3VjoBGHdQpSzBuCW+8fko4eU5uK1Uhs5AwRkCYAtQV+xfRuNtC6xI2njvz1mj /5Xhxc3oBeDmIi0zLQz6irL5JPIoqT5LbxQQDCLo2qVKpyPvrdcfBhHkCmYsMsR88VXK 01E2AgMT0S2ieaJGtopcXA5pZF6uimdGiqeZrVdEQSgrEvItlFxi03U4/UDH6tUyvExi yYc+0hurLCpnU2PqIaDQXQ7DXTv7M7eZKJJuj5RwMU1B59X5GHLVnfRe2a+IVKOkaJ6g 9hmgSI6Ts7V4u/lnEftP0GLSbDrapmKrIl57JKO7HHr8/hW2spmn4Xl7DjV7Wu5ce4q3 wmIg== X-Gm-Message-State: AOAM532O10xkluKPcDJcRWpio5X1b21+ByRKhxNxasND5UtoTBcaW0ES xqy/VByZL7NNnjqPK5+oa7NyoD8cxnU= X-Google-Smtp-Source: ABdhPJzODC8nRi1qADrzZL4hech027Y7Zov4QJPhtBmjQgIsRVGlUZ2mZ2udGO0bBq1+OUgUyR0Aew== X-Received: by 2002:a7b:cb99:: with SMTP id m25mr31684wmi.64.1615226297906; Mon, 08 Mar 2021 09:58:17 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:17 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:57 +0100 Message-Id: <20210308175802.62517-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-annotationforge): Move from here... * gnu/packages/bioconductor.scm (r-annotationforge): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 883b6df2fb..706b87b207 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,38 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-annotationforge + (package + (name "r-annotationforge") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationForge" version)) + (sha256 + (base32 + "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) + (properties + `((upstream-name . "AnnotationForge"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationForge") + (synopsis "Code for building annotation database packages") + (description + "This package provides code for generating Annotation packages and their +databases. Packages produced are intended to be used with AnnotationDbi.") + (license license:artistic2.0))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4fa4a1e354..3212641af9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,38 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-annotationforge - (package - (name "r-annotationforge") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationForge" version)) - (sha256 - (base32 - "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) - (properties - `((upstream-name . "AnnotationForge"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationForge") - (synopsis "Code for building annotation database packages") - (description - "This package provides code for generating Annotation packages and their -databases. Packages produced are intended to be used with AnnotationDbi.") - (license license:artistic2.0))) - (define-public r-rbgl (package (name "r-rbgl") From patchwork Mon Mar 8 17:57:58 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27539 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 C04A127BC51; Mon, 8 Mar 2021 18:21:39 +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 0508727BC50 for ; Mon, 8 Mar 2021 18:21:39 +0000 (GMT) Received: from localhost ([::1]:56898 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJKVe-0003Ia-5F for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:21:38 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59060) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qK-Pl for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33235) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9n-0001Jm-Jl for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9n-0002hj-J1 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 05/10] gnu: r-rbgl: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630810275 (code B ref 47010); Mon, 08 Mar 2021 17:59:03 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:28 +0000 Received: from localhost ([127.0.0.1]:44765 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9E-0002fZ-6J for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:28 -0500 Received: from mail-wm1-f46.google.com ([209.85.128.46]:51148) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9A-0002eD-0a for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:24 -0500 Received: by mail-wm1-f46.google.com with SMTP id i9so59340wml.0 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:23 -0800 (PST) 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=rdg9WK2Aym8EEXPRrk6vNMips/BhH3sHqhVjjCO+f5M=; b=JHbYK/wMth1ImuluhnViE9/JiZUn+c26MZokdfpc7tBHCQXiRAb3ddSR2JEuPH6T0v tEMwtMJNDJzkL2K9Kewov0FxfCJ+bqSvygd4MeO6FY9XhAI7ACR4SonPQgsjFsaniyG9 SDiHTS2AZ68FRwwaNc9F0tRPguGOwqkU0AioIkFDgKIV71EtEvaADWe14Q+pCHk6VU+w snXmE1xs28QLSRJQf1LAcENyl4pEWViVe8OMcVlCie3KnBktdrWAilRBrJWvH9mM4cNV KJuBsgwMb4LGSO1dRUyIJveEQXvTjArtGWT32NzazFiXNR4RKlzaEavMXEBLbu4eXj7a j6FA== 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=rdg9WK2Aym8EEXPRrk6vNMips/BhH3sHqhVjjCO+f5M=; b=nQmZwDQZCK0ZMTNwfwnh5kp4//+CzTVOGOzotoWuhgUU3QOqXwTeSWD2qhJOpwU5JD oNUWQv4VKbPt/ket8bZ2mTQ5NgjzYp8sa/K3eDYTcLQRJEovqBiBWnMN2IoBFZCyKAuc aYGF2hr3AiPwfDc8/C1KguNkkuGN/+DkvXNQ2qJ+Z4xrQhZ5H9KM7jEUYiKy3yWfWc/z UsshBajx8+yD9naZwe3fBwPazDGlloEGOLh6vcoWXMd1Ie14+DAKHDC2fdnSFlRBcLm5 FxTYA+oXQSkSA9vxKMwwyZhcxxykcFPc7yWpk4ZNulWOawhu6Nv9F00D7jpUNDmVyySs IKMQ== X-Gm-Message-State: AOAM5311UHFuvm1gjBTZwu4KoFZbhSZcCxGa6WK/2CYmWnsNonPqCG1t NKokHsI9w3/k/iJPvT56uYGABnbPOxQ= X-Google-Smtp-Source: ABdhPJx+PK/zCm72hfiTkKM5DEps9EdFApR30iu44SQ9pveFmoBu9z08jS7NRrhNYg8PGqiG/cn6LA== X-Received: by 2002:a7b:c442:: with SMTP id l2mr23369681wmi.69.1615226298374; Mon, 08 Mar 2021 09:58:18 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:18 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:58 +0100 Message-Id: <20210308175802.62517-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-rbgl): Move from here... * gnu/packages/bioconductor.scm (r-rbgl): ...to here. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 706b87b207..0a9dc4f9ba 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1650,6 +1650,29 @@ high-throughput sequencing experiments.") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rbgl + (package + (name "r-rbgl") + (version "1.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RBGL" version)) + (sha256 + (base32 + "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) + (properties `((upstream-name . "RBGL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-graph" ,r-graph))) + (home-page "https://www.bioconductor.org/packages/RBGL") + (synopsis "Interface to the Boost graph library") + (description + "This package provides a fairly extensive and comprehensive interface to +the graph algorithms contained in the Boost library.") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3212641af9..0f96ffc02e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,29 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-rbgl - (package - (name "r-rbgl") - (version "1.66.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "RBGL" version)) - (sha256 - (base32 - "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) - (properties `((upstream-name . "RBGL"))) - (build-system r-build-system) - (propagated-inputs - `(("r-bh" ,r-bh) - ("r-graph" ,r-graph))) - (home-page "https://www.bioconductor.org/packages/RBGL") - (synopsis "Interface to the Boost graph library") - (description - "This package provides a fairly extensive and comprehensive interface to -the graph algorithms contained in the Boost library.") - (license license:artistic2.0))) - (define-public r-gseabase (package (name "r-gseabase") From patchwork Mon Mar 8 17:57:59 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27544 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 9860827BC51; Mon, 8 Mar 2021 18:54:23 +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 D3CF227BC50 for ; Mon, 8 Mar 2021 18:54:22 +0000 (GMT) Received: from localhost ([::1]:46326 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL1K-0001C9-2V for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:22 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59072) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qQ-PL for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33236) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9n-0001KK-WD for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9n-0002hq-Vp for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 06/10] gnu: r-gseabase: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630910283 (code B ref 47010); Mon, 08 Mar 2021 17:59:03 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:29 +0000 Received: from localhost ([127.0.0.1]:44767 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9E-0002fg-Mq for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:29 -0500 Received: from mail-wr1-f50.google.com ([209.85.221.50]:41746) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9A-0002eF-DL for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:25 -0500 Received: by mail-wr1-f50.google.com with SMTP id f12so12400329wrx.8 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:24 -0800 (PST) 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=bjwocVYIJU7VQ13OY1ZxpOU2foAZsN4OKaBYsrlY1jw=; b=sI1Q8k7SVuCgwKhr56bnOGCNyYcM6HkksQftPYVoF1TftPbmicPgU3lEg8g57G9/iZ iAbKMUWtrBmDu+xPf6Ubbj2rQXjiDalm8F9UWEPUotgWrYc6bBhCkpaRKh+V6cCloeDY WjYdVVIVzVWm4CqR2g4D5QPIruoaQ9Wn35kRphyETgO60gwf+r4bFmZXE+j+huiDinTm CJDvIN9jgPKGW6xGK+UFejn/0FOl+gyP/ajsZKJjig4BoRRf7oVinE1FAN1Cij/4l+ST oEVJn0XGU9EHeJTLRN7uzUYH10QtWPDSPdXVLYtatTq7BLrFgdPD8Zu2dB0lzbwAq/8e fZUg== 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=bjwocVYIJU7VQ13OY1ZxpOU2foAZsN4OKaBYsrlY1jw=; b=EI0SajFY1wqrDzE1Feax2Zp4I+PqBOmPHolLgp3RRyt8KIiptXhY7UEIVyQ1FSUHp2 EbWG2hRBQKSJzcKLouPL3JBpryVdLkq0tKKSIqXT+2ndvk6RrRzc1co6B8FQC6pWN+qR rca0TPJRr6z0byLk2dUokcJFX9lmOW2gkYSrk5doKqm2nnlPnz6WSltj+sqRkfgQbLNi VWGHcyJWuKiAi3xX2ibZeY83Ny3Aay7FPlowmNHMV6TMSdNz+Ekt9MaPOLE299rWi0Pi oVsTAyLK1cOzbLmP3pghWr6SjIEAX3K17cNafxuXLD5/B2R7vI07t+rvDmi+WYGR70SF k6UA== X-Gm-Message-State: AOAM530LTFuT/zmASYJ4OUvL6ev5LGR1yXzH5g0KLMQwJN+VMvibmbQU WA0JVQxa6oodJl2J7+VZla0TSxc6sAQ= X-Google-Smtp-Source: ABdhPJzJ0CGaJU3poSY1B3RLehFqqzv0fdV5T9MH+/K55rYnSyLVwOovmSbUtVg33CflThdjYV6hLQ== X-Received: by 2002:adf:b30f:: with SMTP id j15mr24092143wrd.132.1615226298814; Mon, 08 Mar 2021 09:58:18 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.18 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:18 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:59 +0100 Message-Id: <20210308175802.62517-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-gseabase): Move from here... * gnu/packages/bioconductor.scm (r-gseabase): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a9dc4f9ba..a17c6beeef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1630,6 +1630,35 @@ exploration of the results.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-gseabase + (package + (name "r-gseabase") + (version "1.52.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GSEABase" version)) + (sha256 + (base32 + "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) + (properties `((upstream-name . "GSEABase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-graph" ,r-graph) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GSEABase") + (synopsis "Gene set enrichment data structures and methods") + (description + "This package provides classes and methods to support @dfn{Gene Set +Enrichment Analysis} (GSEA).") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0f96ffc02e..23b8ce6892 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,35 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-gseabase - (package - (name "r-gseabase") - (version "1.52.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GSEABase" version)) - (sha256 - (base32 - "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) - (properties `((upstream-name . "GSEABase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GSEABase") - (synopsis "Gene set enrichment data structures and methods") - (description - "This package provides classes and methods to support @dfn{Gene Set -Enrichment Analysis} (GSEA).") - (license license:artistic2.0))) - (define-public r-category (package (name "r-category") From patchwork Mon Mar 8 17:58:00 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27542 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 E3A8027BC51; Mon, 8 Mar 2021 18:22:03 +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 1E04B27BC50 for ; Mon, 8 Mar 2021 18:22:03 +0000 (GMT) Received: from localhost ([::1]:59432 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJKW2-0004Ib-Aa for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:22:02 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59070) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qP-QW for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:09 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33237) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9o-0001KM-Dm for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9o-0002hx-DP for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 07/10] gnu: r-category: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630910290 (code B ref 47010); Mon, 08 Mar 2021 17:59:04 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:29 +0000 Received: from localhost ([127.0.0.1]:44769 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9F-0002fo-1w for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:29 -0500 Received: from mail-wr1-f51.google.com ([209.85.221.51]:37747) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9A-0002eG-Rp for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:25 -0500 Received: by mail-wr1-f51.google.com with SMTP id v15so12412671wrx.4 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:24 -0800 (PST) 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=Hfwe981xk/fEpxYQtDfziH+EYmZh/iF2HCkCZqkuZoQ=; b=dt7SGIhzhqtofYI6PvdWykaBkHM+wGrIYrE0pwBrmoHrl0G0v1ITOmk11wFTPcpF2o QP7Wb8o2d0M5FqZ+n0aBAXq0vjbftbTw10St4TaZy+yViy4nHt8PEYuipUlWgqX4bbyC lRlpvUGV3+Vbl4WrvMjsznqhlZOlFkpBw6YoS9WC12sa8b22Bis8cjkn/TY3EeuToOrI suGGDQNAeT/hJAfdylMo+9vJWF3j4IummUz6JCyspsE6dxELeVj7AJ+1QlAT9pYpY/Lo BrFm45Z0j4aaLd23fOFNyJ4OIbkYqSNlTdC93Pr/V71253t2m8BsZO+9CcNlhPZvyjTi Hy6g== 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=Hfwe981xk/fEpxYQtDfziH+EYmZh/iF2HCkCZqkuZoQ=; b=n6j6mxboSMDb8Mqbt/3y7seBYvysZXpo+P2ooWsHpafnxfekayugClZRUaZ3k++Onl TdfNiyDd3PbDg7KGHZCcDfW8i4zFpIhrqwgeMt1OsuU2CnRsgWkbpnBzWeP6L3npv0HC AVtQhcsWiug7YgPOL75xJFxKaFw9UOE8F6ARhdos5Bpv/3ZWIXqDzS05C7KfK9WCl05n ufEt7os41yxF4eRSEAFCAtFFyjm7jx+n+4lvhGQYms5SlMij4YljTen0dqG/pgUc/5Oc J0NbiuWv9RZxY4dgPJwOzqvKULb7686lZhhgM8AzbosGYl3Z06zZVYQGad8TNsxVUKMD LFWg== X-Gm-Message-State: AOAM53327lM0gcNPEpeSrOq2XKyXrzU0Uf8XBaIaud6v5sRfnjGtzSdx DPldLymhQ34N/XHKAUHSq+X6aSpoTLE= X-Google-Smtp-Source: ABdhPJy7aqmO73n45ZUNPSSW74dHU//a/nBsrUwYs4jiF/bb3Vuj88p14DggZqeX05xpbsfKgslKZg== X-Received: by 2002:a5d:54c4:: with SMTP id x4mr23705778wrv.329.1615226299264; Mon, 08 Mar 2021 09:58:19 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.18 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:18 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:58:00 +0100 Message-Id: <20210308175802.62517-7-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-category): Move from here... * gnu/packages/bioconductor.scm (r-category): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a17c6beeef..4e3dd25d61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1519,6 +1519,37 @@ microarrays.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-category + (package + (name "r-category") + (version "2.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Category" version)) + (sha256 + (base32 + "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) + (properties `((upstream-name . "Category"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-graph" ,r-graph) + ("r-gseabase" ,r-gseabase) + ("r-matrix" ,r-matrix) + ("r-rbgl" ,r-rbgl) + ("r-dbi" ,r-dbi))) + (home-page "https://bioconductor.org/packages/Category") + (synopsis "Category analysis") + (description + "This package provides a collection of tools for performing category +analysis.") + (license license:artistic2.0))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 23b8ce6892..6b32f3416c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,37 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-category - (package - (name "r-category") - (version "2.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Category" version)) - (sha256 - (base32 - "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) - (properties `((upstream-name . "Category"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-graph" ,r-graph) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix) - ("r-rbgl" ,r-rbgl) - ("r-dbi" ,r-dbi))) - (home-page "https://bioconductor.org/packages/Category") - (synopsis "Category analysis") - (description - "This package provides a collection of tools for performing category -analysis.") - (license license:artistic2.0))) - (define-public r-gostats (package (name "r-gostats") From patchwork Mon Mar 8 17:58:01 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27546 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 7F33F27BC50; Mon, 8 Mar 2021 18:54:38 +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 1305427BC55 for ; Mon, 8 Mar 2021 18:54:35 +0000 (GMT) Received: from localhost ([::1]:46920 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL1W-0001TH-8a for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:34 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59074) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qR-Q7 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33238) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9o-0001KO-Q6 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9o-0002i5-Pb for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 08/10] gnu: r-gostats: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630910297 (code B ref 47010); Mon, 08 Mar 2021 17:59:04 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:29 +0000 Received: from localhost ([127.0.0.1]:44771 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9F-0002fv-Db for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:29 -0500 Received: from mail-wr1-f41.google.com ([209.85.221.41]:38485) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9B-0002eJ-EH for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:25 -0500 Received: by mail-wr1-f41.google.com with SMTP id d15so12427931wrv.5 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:25 -0800 (PST) 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=Vz7z94cH8deYOCBCGw+8DMufxLXy126NaQu9IWedgZg=; b=NgBdeUBnGPWsjQhtapeoNxWp3IJdChWsuLryNB/7iznXb1XlX4pxRxSnGmG3ocVZHc +1kboFUshbxUOqcGQx/LpYGClVFeieXNe8DD4mHO/urcnnUP5BM3eQh1pxDS1xrqV6TD ZtwO/xAGeoLQeNR0fjI4482HBrhZXyvqrdocXiqOoMwrICBRUm9FkhvRQucGfnRTHRwI EWPBZ/eyYmGy0h7wJO27F4EYpJRzWuRRdSRbovKfbeO6Hem+7hiNczit+KmKCkE4SDof gqvucWcEUDIQxyQy7ebfsOE4qSotsAzzdgJH62U89TBJEZyBJGoEVIwx49hDBH7db+Zk yRTQ== 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=Vz7z94cH8deYOCBCGw+8DMufxLXy126NaQu9IWedgZg=; b=fynRfNlvHDPTmvfk2/ys9Wvb/N4bTLC2b4uEno5QDxSOD6SDTIKTWQVsAo+2JX3jCg j/A8PO7A186eAE2ykNSsqE3bqlILKj917vChOrFQ/xZjnvZwR9oUf8oW536UjeK++DSx oR++0S1IPCCEMEOqdJ9EUY0d/Yi84peSxn9RqmDNPs3rUhhI6rqvTGcVv0whdTMzcUAd YG8x535uc9IVZU+u6ATE51zld20hYKnr71S2ZQvYe4z46A2LClEt4PQw/YX8dqUp5zWu Myj0ZfFug63iRqEWwBveJBOcOHW4v++m910CUFkPjpF00j8E4H2yg122KT4cG74MrtqC 6sSA== X-Gm-Message-State: AOAM5336c59LRM2v5BU49a0cguPTv6RikhaKiTbm+QntP354wLGTeWgr gRPJQQeiGzv2g8GkIhu6WzoBsL1Awok= X-Google-Smtp-Source: ABdhPJy4JyB9MBMNdi2hfVBkMNMEnyahnZqpaodX4uh0IeaT50b/Mn6gZW5VPXLb10tF5od5YodmBg== X-Received: by 2002:adf:f3cc:: with SMTP id g12mr24767969wrp.118.1615226299788; Mon, 08 Mar 2021 09:58:19 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:19 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:58:01 +0100 Message-Id: <20210308175802.62517-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-gostats): Move from here... * gnu/packages/bioconductor.scm (r-gostats): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4e3dd25d61..4f4088db27 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1661,6 +1661,37 @@ exploration of the results.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-gostats + (package + (name "r-gostats") + (version "2.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOstats" version)) + (sha256 + (base32 + "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) + (properties `((upstream-name . "GOstats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-annotationforge" ,r-annotationforge) + ("r-biobase" ,r-biobase) + ("r-category" ,r-category) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rbgl" ,r-rbgl))) + (home-page "https://bioconductor.org/packages/GOstats") + (synopsis "Tools for manipulating GO and microarrays") + (description + "This package provides a set of tools for interacting with GO and +microarray data. A variety of basic manipulation tools for graphs, hypothesis +testing and other simple calculations.") + (license license:artistic2.0))) + (define-public r-gseabase (package (name "r-gseabase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6b32f3416c..186b051865 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,37 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-gostats - (package - (name "r-gostats") - (version "2.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GOstats" version)) - (sha256 - (base32 - "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) - (properties `((upstream-name . "GOstats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-annotationforge" ,r-annotationforge) - ("r-biobase" ,r-biobase) - ("r-category" ,r-category) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rbgl" ,r-rbgl))) - (home-page "https://bioconductor.org/packages/GOstats") - (synopsis "Tools for manipulating GO and microarrays") - (description - "This package provides a set of tools for interacting with GO and -microarray data. A variety of basic manipulation tools for graphs, hypothesis -testing and other simple calculations.") - (license license:artistic2.0))) - (define-public r-shortread (package (name "r-shortread") From patchwork Mon Mar 8 17:58:02 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27543 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 B681F27BC50; Mon, 8 Mar 2021 18:54:06 +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 C955D27BC51 for ; Mon, 8 Mar 2021 18:54:04 +0000 (GMT) Received: from localhost ([::1]:45866 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL11-00010H-Si for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:03 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59062) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qL-Ow for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33239) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9p-0001KQ-6d for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9p-0002iC-6A for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 09/10] gnu: r-shortread: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522631010304 (code B ref 47010); Mon, 08 Mar 2021 17:59:05 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:30 +0000 Received: from localhost ([127.0.0.1]:44773 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9F-0002g2-Pb for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:30 -0500 Received: from mail-wr1-f47.google.com ([209.85.221.47]:35336) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9B-0002eK-Ty for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:26 -0500 Received: by mail-wr1-f47.google.com with SMTP id l12so12415752wry.2 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:25 -0800 (PST) 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=qTG2WYw8O0RVcetU4sk65HmZE3LBPPAxun/yQIaIFJI=; b=s14W27df3fNJMO+bvRtr2UpursykI2lkX2QdSs1QXwFFs2KxwGPJUOTSYqzMamfnlj any0cQhay7Av2jiP8Pm82Hy50hQ+aS8XCaKfjyzzJPop64Lu2ob6qUWSSHPXLMHVXjHV HAaX/13gXWnznpIqg8lc60hEn3NsWAF9UDScVlbl4k32Isizfl+oz98+KJBnJoJEyYCA dcq4qvCas9HYcqnUuLgGfsPQ99PfEkNWYkXLjPBrhFoWcb+5syK7ldn+sD3Ne7A+anoS G6RGLLzrKJ/amu97/4UsxnLPMk5WtAF08LnaSd+YRdU573Owq6fIaJgHUDk9m/xz395O PRhw== 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=qTG2WYw8O0RVcetU4sk65HmZE3LBPPAxun/yQIaIFJI=; b=fedIzlWvj8mW4aR0nuEOcAcxzw1aahC7P4nFPMLHz2Re/JcAjzP67sdM7UAaaun15x j9bz6p0ohs76q/f61oXGajqWZOFFjbQcKzXfHP6sVPIk5bh5epFxVZ+czlEOEDFoMoEN pE+JnNfPy3EqWWAbgdTaZH3uEQkKyKlZ0IAq0pEMA2mVnw6Z/4cxLo5i+vubQ8u9F5zQ VZ0bq5Uf/vy34Hsc6beSB/8ttfhTeJRjklG+RdIA9Rz27gp3NJV8/D5EHVkTMoG7uEkj sKdpiiMzUK76cD+UYx3lvjITHaipnpjaZD2VpOfnSgGisBud6R6lPNmV28J3AxXUwP7H vDuQ== X-Gm-Message-State: AOAM531QGQYLPIHED0kiBP/wvZ2burzOZPR83g2D+ylRqhDxfbmLbE9C 5THVIPQb2JWtwZB2od63MiIlNRGk2zg= X-Google-Smtp-Source: ABdhPJzRfy2mNzk67fE+ukzrzh4/AbTMUg2/uh3vhU66itQwHr0wqlAwU4P+fm8l9rn/h4sxIjcOXQ== X-Received: by 2002:a5d:404f:: with SMTP id w15mr25207479wrp.106.1615226300344; Mon, 08 Mar 2021 09:58:20 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:20 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:58:02 +0100 Message-Id: <20210308175802.62517-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 --------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f4088db27..05077b422e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-shortread + (package + (name "r-shortread") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ShortRead" version)) + (sha256 + (base32 + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + (properties `((upstream-name . "ShortRead"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ShortRead") + (synopsis "FASTQ input and manipulation tools") + (description + "This package implements sampling, iteration, and input of FASTQ files. +It includes functions for filtering and trimming reads, and for generating a +quality assessment report. Data are represented as +@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of +purposes. The package also contains legacy support for early single-end, +ungapped alignment formats.") + (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 186b051865..fda4516052 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,49 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-shortread - (package - (name "r-shortread") - (version "1.48.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ShortRead" version)) - (sha256 - (base32 - "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) - (properties `((upstream-name . "ShortRead"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/ShortRead") - (synopsis "FASTQ input and manipulation tools") - (description - "This package implements sampling, iteration, and input of FASTQ files. -It includes functions for filtering and trimming reads, and for generating a -quality assessment report. Data are represented as -@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of -purposes. The package also contains legacy support for early single-end, -ungapped alignment formats.") - (license license:artistic2.0))) - (define-public r-systempiper (package (name "r-systempiper") From patchwork Mon Mar 8 17:58:28 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27548 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 78D1327BC51; Mon, 8 Mar 2021 18:54:48 +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 9A61227BC50 for ; Mon, 8 Mar 2021 18:54:46 +0000 (GMT) Received: from localhost ([::1]:47522 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL1h-0001iW-SA for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:45 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59064) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qM-Pp for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33240) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9p-0001KS-JW for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9p-0002iJ-Im for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 10/10] gnu: r-systempiper: Move to (gnu packages bioconductor). References: <20210308175558.62461-1-zimon.toutoune@gmail.com> In-Reply-To: <20210308175558.62461-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522631810327 (code B ref 47010); Mon, 08 Mar 2021 17:59:05 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:38 +0000 Received: from localhost ([127.0.0.1]:44776 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9O-0002gV-72 for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:38 -0500 Received: from mail-wr1-f50.google.com ([209.85.221.50]:46817) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9M-0002gH-T1 for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:37 -0500 Received: by mail-wr1-f50.google.com with SMTP id a18so12369170wrc.13 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:36 -0800 (PST) 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=0RRv5HfAiTFHQ133fZ83VCRpAgyEe5DMYV+eXN3ApF4=; b=iWlIhxn0taaN2/lFFKYtZzqUjSIi7vdH0k0PefqfMfJHz2/xRCbRrK6d58PLn6vTix uMe9Ljy5lLs2WGti2u4TJAMqI8D2hgGi/h2N/uGXjNFnSCWfijGvKo3JPAxzwVhGTL3a 8DjeF/xf4Aup4cBbLvnqMJDCwhalCSdNoYe+oQ8/rK9ZasVPfP0ooBHeHhTnpscuYF/K +ovJLeOQ1b3QhCmitQPt1MIefxB8anQwiXeHF8+beOUcfeUGSIalgC11O8r5vrtgcS9o ItoBGazzE5V/A2T8Q5L6QUHMqj74hdsJGSk8XtFBMMXJY0h1t2hdE/MURh9IgVcax5uc mRmg== 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=0RRv5HfAiTFHQ133fZ83VCRpAgyEe5DMYV+eXN3ApF4=; b=IUORoCweTDlmx0jj9LiFEHZCcoUcvpvTsLGIN2LaBs5f4YFlwBvNENdN+GUp7ZiSLd 8EAapsN4JkB3sY6IRCGQioHMXJUpEIb12JWan6zPGB8GSm+GSKjH5NiDb0bjWJlYWaAa g1isOoYGhO0WpRMNygUPw2FJkhAJ5H/DCOVr31dlekaUeg+2R1iXh+ckVCNjTwJmU04u nKjxSQMrOvT18LZJFPH/ZeFVjaumZblW3R3W57vqmoZ3d8C+zu+oqziEPrHlzV7kuah7 bJdWUWccQ73rhgRRSFRpgTOQmIV41sSlouT1izRPBNc0xSf40aJJZ4Ozy9ik+asjWLH4 A+uw== X-Gm-Message-State: AOAM533vmqd/S8rjNaqcmAO+f4CwV3XKNWRrBaQLo4plTKQE5gKMeCE/ Fxg3TMMmed4e+/lMJ51T/r3+xb7CN9A= X-Google-Smtp-Source: ABdhPJyMM+qbUmjGmfbojaXf2A575yyAqmmbsmf7EBCNKqFz/abU2+EJc/Qu7ajPKuNxhEJAybF52Q== X-Received: by 2002:a5d:638f:: with SMTP id p15mr23764706wru.220.1615226311353; Mon, 08 Mar 2021 09:58:31 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id y18sm12325034wrw.39.2021.03.08.09.58.30 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:31 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:58:28 +0100 Message-Id: <20210308175828.62579-1-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-systempiper): Move from here... * gnu/packages/bioconductor.scm (r-systempiper): ...to here. --- gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 54 --------------------------------- 2 files changed, 54 insertions(+), 54 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 05077b422e..d7be5e66a2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1888,6 +1888,60 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-systempiper + (package + (name "r-systempiper") + (version "1.24.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeR" version)) + (sha256 + (base32 + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) + (properties `((upstream-name . "systemPipeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-assertthat" ,r-assertthat) + ("r-batchtools" ,r-batchtools) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-dot" ,r-dot) + ("r-edger" ,r-edger) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gostats" ,r-gostats) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-pheatmap" ,r-pheatmap) + ("r-rjson" ,r-rjson) + ("r-rsamtools" ,r-rsamtools) + ("r-rsvg" ,r-rsvg) + ("r-shortread" ,r-shortread) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-yaml" ,r-yaml) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tgirke/systemPipeR") + (synopsis "Next generation sequencing workflow and reporting environment") + (description + "This R package provides tools for building and running automated +end-to-end analysis workflows for a wide range of @dfn{next generation +sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. +Important features include a uniform workflow interface across different NGS +applications, automated report generation, and support for running both R and +command-line software, such as NGS aligners or peak/variant callers, on local +computers or compute clusters. Efficient handling of complex sample sets and +experimental designs is facilitated by a consistently implemented sample +annotation infrastructure.") + (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 fda4516052..072c0582be 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,60 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-systempiper - (package - (name "r-systempiper") - (version "1.24.3") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "systemPipeR" version)) - (sha256 - (base32 - "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) - (properties `((upstream-name . "systemPipeR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-assertthat" ,r-assertthat) - ("r-batchtools" ,r-batchtools) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-dot" ,r-dot) - ("r-edger" ,r-edger) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-gostats" ,r-gostats) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rjson" ,r-rjson) - ("r-rsamtools" ,r-rsamtools) - ("r-rsvg" ,r-rsvg) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-yaml" ,r-yaml) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/tgirke/systemPipeR") - (synopsis "Next generation sequencing workflow and reporting environment") - (description - "This R package provides tools for building and running automated -end-to-end analysis workflows for a wide range of @dfn{next generation -sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. -Important features include a uniform workflow interface across different NGS -applications, automated report generation, and support for running both R and -command-line software, such as NGS aligners or peak/variant callers, on local -computers or compute clusters. Efficient handling of complex sample sets and -experimental designs is facilitated by a consistently implemented sample -annotation infrastructure.") - (license license:artistic2.0))) - (define-public r-grohmm (package (name "r-grohmm")