From patchwork Tue May 24 18:08:50 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 39597 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 845C327BBEA; Tue, 24 May 2022 19:10:17 +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_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, SPF_HELO_PASS 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 142F127BBE9 for ; Tue, 24 May 2022 19:10:17 +0100 (BST) Received: from localhost ([::1]:37332 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ntYz2-0003NR-63 for patchwork@mira.cbaines.net; Tue, 24 May 2022 14:10:16 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50670) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ntYyp-0003NG-Kq for guix-patches@gnu.org; Tue, 24 May 2022 14:10:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:59404) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ntYyp-0005Qq-Bl for guix-patches@gnu.org; Tue, 24 May 2022 14:10:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ntYyo-0003NF-RS; Tue, 24 May 2022 14:10:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55615] [PATCH] gnu: Add r-pscbs. 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(license license:gpl3+))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-aroma-light, r-dnacopy.. +(define-public r-pscbs + (package + (name "r-pscbs") + (version "0.66.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PSCBS" version)) + (sha256 + (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (properties `((upstream-name . "PSCBS"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-aroma-light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r-cache + r-r-methodss3 + r-r-oo + r-r-utils)) + (native-inputs + (list r-r-rsp ;used to build vignettes + r-r-devices)) + (home-page "https://github.com/HenrikBengtsson/PSCBS") + (synopsis "Analysis of Parent-Specific DNA Copy Numbers") + (description + "Segmentation of allele-specific DNA copy number data and detection of +regions with abnormal copy number within each parental chromosome. Both +tumor-normal paired and tumor-only analyses are supported.") + (license license:gpl2+))) + (define-public r-protgenerics (package (name "r-protgenerics")