From patchwork Wed Apr 13 14:12:58 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 38560 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 C65E527BBE9; Wed, 13 Apr 2022 15:14:36 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,T_SPF_HELO_TEMPERROR autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 7326A27BBEA for ; Wed, 13 Apr 2022 15:14:21 +0100 (BST) Received: from localhost ([::1]:53580 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nedl4-0000OO-I9 for patchwork@mira.cbaines.net; Wed, 13 Apr 2022 10:14:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:45006) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nedkw-0000OA-AV for guix-patches@gnu.org; Wed, 13 Apr 2022 10:14:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:59578) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nedkw-0002tz-2k for guix-patches@gnu.org; Wed, 13 Apr 2022 10:14:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nedkv-0008Oz-V3 for guix-patches@gnu.org; Wed, 13 Apr 2022 10:14:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54912] [PATCH] gnu: Add r-acme. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 13 Apr 2022 14:14:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54912 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54912@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.164985920432235 (code B ref -1); Wed, 13 Apr 2022 14:14:01 +0000 Received: (at submit) by debbugs.gnu.org; 13 Apr 2022 14:13:24 +0000 Received: from localhost ([127.0.0.1]:53475 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nedkK-0008Nq-59 for submit@debbugs.gnu.org; Wed, 13 Apr 2022 10:13:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:41050) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nedkI-0008Nj-AP for submit@debbugs.gnu.org; Wed, 13 Apr 2022 10:13:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44736) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nedkI-0000LH-4R for guix-patches@gnu.org; Wed, 13 Apr 2022 10:13:22 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:53937) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nedkF-0002q0-DQ for guix-patches@gnu.org; Wed, 13 Apr 2022 10:13:21 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 58649A00E5 for ; Wed, 13 Apr 2022 16:13:15 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1649859194; x=1651673595; bh=pMTB4jkSd5RLlCZS/nhda2vi+wJgBmsBHUS+PpoMsqY=; b=NL8tEIc7w22G FaPHbBtHDTIX1dZXAmTW+/lcERuPrjNQkGdnRXV0KsfXzG9nfcFaxYS7Dahw9UR6 WNvT4/zmwWMhTo8woAW7iWYGgcGzo/qfKFnAjJ/Uu2C7MBxyhJrlEgxmPqnwbZVH O7/YNyzN7nAtlJTNoWRQ9k7Ap+oOan8= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id TCmbTXpdFAkn for ; Wed, 13 Apr 2022 16:13:14 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Wed, 13 Apr 2022 16:13:13 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2375.24; Wed, 13 Apr 2022 16:13:12 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Wed, 13 Apr 2022 16:12:58 +0200 Message-ID: <20220413141258.30929-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26832.000 X-TM-AS-Result: No-10-1.823200-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNLjXXGQy6nlOxa IFENL1fY/p3d+IN6R6/uNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHToQ Rmlq2EaTDTXAQOKjEbg8lXA2BfV9orWL/xQJnm46rm7DrUlmNkIAy6p60ZV62Mhe627A+8aEBpR CTkRk5SfoLR4+zsDTt+GYUedkXNWpH2e5oNkD4KKsgRmdXCz5g99hpb4Evou8koGiTmEnE4S1KU wBpyq5s9IV/qAxPZ91KBCy/jeol3JZn4CDGOXLxEGUQqOTLH5F0CfPGRz/A475iX+rqLWae/WY7 WJgskOpPhxsEgoy4ejPD+71BqIb8 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.823200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26832.000 X-TM-SNTS-SMTP: 8B1EE80EBA60BD8578F3F12D68FDFD542C49CE6B9D3DD9A576E84333CB7866F32000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action 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/bioconductor.scm (r-acme): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..69e9e14dd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11642,6 +11642,36 @@ (define-public r-universalmotif motifs, and others.") (license license:gpl3))) +;; The homepage (http://watson.nci.nih.gov/~sdavis) seems to be inaccessible +;; anymore so I changed it to the Bioconductor page of the package. +(define-public r-acme + (package + (name "r-acme") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACME" version)) + (sha256 + (base32 + "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg")))) + (properties `((upstream-name . "ACME"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-biocgenerics)) + (home-page "https://bioconductor.org/packages/aCGH/") + (synopsis "Calculating microarray enrichment") + (description + "This package implements +@dfn{algorithms for calculating microarray enrichment} (ACME), and it is a set +of tools for analysing tiling array of +@dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip), +DNAse hypersensitivity, or other experiments that result in regions of the +genome showing enrichment. It does not rely on a specific array technology +(although the array should be a tiling array), is very general (can be applied +in experiments resulting in regions of enrichment), and is very insensitive to +array noise or normalization methods. It is also very fast and can be applied +on whole-genome tiling array experiments quite easily with enough memory.") + (license license:gpl2+))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs