From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id iHftMDkYqGAmCQEAgWs5BA (envelope-from ) for ; Fri, 21 May 2021 22:29:45 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id IAqkLDkYqGDPPQAA1q6Kng (envelope-from ) for ; Fri, 21 May 2021 20:29:45 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 291FB1AE2F for ; Fri, 21 May 2021 22:29:45 +0200 (CEST) Received: from localhost ([::1]:38600 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBmC-0006ld-8k for larch@yhetil.org; Fri, 21 May 2021 16:29:44 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52494) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkf-0004dz-Aq for guix-patches@gnu.org; Fri, 21 May 2021 16:28:09 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54498) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkf-0002yb-1p for guix-patches@gnu.org; Fri, 21 May 2021 16:28:09 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBke-0000NG-UK for guix-patches@gnu.org; Fri, 21 May 2021 16:28:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 20/50] gnu: r-annotationhub: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org. Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288481067 (code B ref 48575); Fri, 21 May 2021 20:28:08 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:28 +0000 Received: from localhost ([127.0.0.1]:37735 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk0-0000H2-BS for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:28 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:38830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjN-00009G-Vf for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:50 -0400 Received: by mail-wm1-f54.google.com with SMTP id u4-20020a05600c00c4b02901774b80945cso8061341wmm.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:49 -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=lWp5iRRc16IVy1RyUvSSRWm6Pa0SbaLjN1QS6FjYR9A=; b=c43HmBom37Rtqfqg44njcTzDqfpKbhFpdxdw9K4OYcCIKcQjBGUA7fj4DqvONt9Pym Ckyw1iyZdB6fOYIEs2NkGk0H9BSdMnUOmFgAqCdGadXHS0FkuDuzgNLSP+hNSxY23ATt FDpCd5NFqCEuAv+Ja4/0K/pV5LX19qN25aInqk3Odt0mggpxMmUGWpfxEwDWD+9g8Be4 vkX7KvzLjxrnaLVuXTGHFkC3fNcDKjJ8gDHS6sBnvtaTXYTptCs539qEjB+5h9B+EEuh C7J8TFOzho8AbtjZhX6deudMPNz5oS43GmaX8wiWrq0z9MgQTCyA7D6o4sL6eIwR+g9C UhFQ== 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=lWp5iRRc16IVy1RyUvSSRWm6Pa0SbaLjN1QS6FjYR9A=; b=bY+Z7VxRg047HnaUxS4+ErmXpuO+8/A2ZCuiYALtz7L13TmEETTftkwDcnlTWsCXfG ha2fawc9ZUOBLLQcGndLJAnnKrc34UMzNSRxug4liNW9isOvcx4RQFH3yEzebWIwztZK w7LN6NuvQY4Kjeh9SkcJ8wS8fdMulaqtdCwj3z8QKe4nRioVD0VP6GR1+Xz4/ly9YNsl 7ABnRh5nE1HTd/i8uy5+/aWiri1Owh7FlurGlm/sQS5ac6lQWf7aqfZRb3XxpYwyGpHL k1i0H2WwlYzrVniP1/qjaPBJW+Fls6lyHhldYby41C9sTYdJzjGQlKJoTXr0ko/bGB6H gbvw== X-Gm-Message-State: AOAM530gUPXwibRYP8NU2e8yVAZ7Zb5nwCU4vRxBgC8oScyHblXKQsE9 x97W0ueJUMrRC/Zqd3SRXnAkv17Mw4k= X-Google-Smtp-Source: ABdhPJzCrDN7FYGPYVqCwxCsteKUx7YvaoRRJjrf0VTxc21kvXrJOomk6ckIjD+d4R4iQ8UvN06uFQ== X-Received: by 2002:a7b:c93a:: with SMTP id h26mr10664387wml.141.1621628804467; Fri, 21 May 2021 13:26:44 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.44 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:44 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:52 +0200 Message-Id: <20210521202622.26591-20-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1621628985; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=lWp5iRRc16IVy1RyUvSSRWm6Pa0SbaLjN1QS6FjYR9A=; b=U9dtFsLnF4KYk7QrQvuQ8fW2Wl6Nl6STA9uK1DUfnLeq85sZECj5WgVDVH3/x4n7koboFK tJ412ofVD/+8D5D5xA9iDzS3peWdywBktysbcbpa6/xbJsKRoyr/+gVO+9dftjisgAQC8W lCrJ1XYM6m/b20NZe58bxBlfRwwr5CJ9OE4lYx1nLkvj5zdqM+VbAcX7jj5tViDgMUQpQ5 7a06SmQVQFjW/cMf5VhDo+3z4twv6M19mgX2kCRvt4tdz0bVULaldt835IwCL5Xh5WaaMN xvPvw14VgM1EMwSUy6Sxkpa1zRxm7SPeXFxxAwvvlHTpI2QcmHfAPgvMJ9llTg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1621628985; a=rsa-sha256; cv=none; b=RXBTBCi0KzBgWGo/F4StgxKJuJlIO0V63KGLsIUItYvw/vglIp3RjV0l1FoGG+mrXZyt/Y h4Dpfkff1JRViHYHLUV6mu70e17Kunonee0l+VqoAECTHp1+47XYdXxC3ItgbgX7EsSRWL G9AGPIwlBQJFnQCure+j7ePMzr2s6CSI1EXPuPAWiRnyD1qlMVfgq3YChQu2TB8FwGAhnb 1jsDR2Zij6gYGQEDw4TC0zEyRVdiSKSozf/gJ4eV4q1IX9U0mILlsPwdKku2j4C7cM9svh 89FjND+kbG3DYQjhSGYtWb2D7RaDCpG0dVWhk+QYKMk8huqjsDuDF98yU4mT0A== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=c43HmBom; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.66 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=c43HmBom; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 291FB1AE2F X-Spam-Score: 2.66 X-Migadu-Scanner: scn1.migadu.com X-TUID: ktBzFVbFnuWv * gnu/packages/bioinformatics.scm (r-annotationhub): Move from here... * gnu/packages/bioconductor.scm (r-annotationhub): ...to here. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 41 --------------------------------- 2 files changed, 41 insertions(+), 41 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9619ce5464..4657b0fa8b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1782,6 +1782,47 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-annotationhub + (package + (name "r-annotationhub") + (version "2.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHub" version)) + (sha256 + (base32 + "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) + (properties `((upstream-name . "AnnotationHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) + ("r-curl" ,r-curl) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-interactivedisplaybase" ,r-interactivedisplaybase) + ("r-rappdirs" ,r-rappdirs) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationHub") + (synopsis "Client to access AnnotationHub resources") + (description + "This package provides a client for the Bioconductor AnnotationHub web +resource. The AnnotationHub web resource provides a central location where +genomic files (e.g. VCF, bed, wig) and other resources from standard +locations (e.g. UCSC, Ensembl) can be discovered. The resource includes +metadata about each resource, e.g., a textual description, tags, and date of +modification. The client creates and manages a local cache of files retrieved +by the user, helping with quick and reproducible access.") + (license license:artistic2.0))) + (define-public r-aroma-light (package (name "r-aroma-light") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b367dcae98..1dc2d6f977 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,47 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-annotationhub - (package - (name "r-annotationhub") - (version "2.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationHub" version)) - (sha256 - (base32 - "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) - (properties `((upstream-name . "AnnotationHub"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationHub") - (synopsis "Client to access AnnotationHub resources") - (description - "This package provides a client for the Bioconductor AnnotationHub web -resource. The AnnotationHub web resource provides a central location where -genomic files (e.g. VCF, bed, wig) and other resources from standard -locations (e.g. UCSC, Ensembl) can be discovered. The resource includes -metadata about each resource, e.g., a textual description, tags, and date of -modification. The client creates and manages a local cache of files retrieved -by the user, helping with quick and reproducible access.") - (license license:artistic2.0))) - (define-public r-fastseg (package (name "r-fastseg") -- 2.30.1