From patchwork Fri May 21 20:25:40 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29459 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 995EF27BC81; Fri, 21 May 2021 21:28:21 +0100 (BST) 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_H4, 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 1285027BC78 for ; Fri, 21 May 2021 21:28:21 +0100 (BST) Received: from localhost ([::1]:36194 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBkq-0004wm-7V for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:28:20 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52424) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBka-0004KB-4q for guix-patches@gnu.org; Fri, 21 May 2021 16:28:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54485) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkZ-0002w1-TI for guix-patches@gnu.org; Fri, 21 May 2021 16:28:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkZ-0000Li-Pw for guix-patches@gnu.org; Fri, 21 May 2021 16:28:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:03 +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=B48575.1621628831944 (code B ref 48575); Fri, 21 May 2021 20:28:03 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:11 +0000 Received: from localhost ([127.0.0.1]:37708 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjj-0000F4-Aw for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:11 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:45726) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjI-00008Y-Jd for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: by mail-wm1-f54.google.com with SMTP id s5-20020a7bc0c50000b0290147d0c21c51so7796219wmh.4 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:44 -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=FpMwdoUajN9MlX1EuMrEntzImgJjKlsOi0ZsYhyH0JM=; b=YGwFhuJKZjIWPmx3uMxKPLW7LkagKPP9ifXCjmlayAkJODC4QzwwRmoE5kPzSGMdOD iUi0egdSgC+WVaygyQYrya9thH3jIUdqOxBnuDoAW+OENNtpzX5XSFmh5XJwpRZkX1F7 ljeereC5x98XVzJV7SoVJByjbKHBTBAtH9mX6Xib5D4nGKpNIiUqZiJmjTxpp/aPZEiL MRLkuT2NnJGDVKTrkC5cs+BRnqO8JOTyLhxT5mnZWioQactMtEN6JX0MnRfc0Sws9NI0 m2P/FgZSzo2W/KXYXXu+0LNIIC1m5obfJuhQsh7SPXEUCqFpcrLHYpsf4ML78C7HC67/ sf0Q== 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=FpMwdoUajN9MlX1EuMrEntzImgJjKlsOi0ZsYhyH0JM=; b=hbwGGsEG/BgMox0uAugrxLSnyiR9eZC/co3EUIhQ3JSrUPRu59yJ990qOgdJAvtQLn pB//dDwDfphor+3z8V8J8olVtyuNcAOupsOq1/2C4ePycNBLwQNF2zJDcuUU2il+CJIR U3zxld6DCYEVy/0+UWJjafjn1nyz78mxTOepaItVmyMBiu81akha0u/iARJGXhUJnqM9 Jo8jFxdH3yjje46gyl9zbl50/hK29eQpFGMTyQS+JSL+vBy53susklRVPfBS9iGreRpq RAT36yFBZcz5hfGhKuWfWhtDafHfK8UdsWn+nApRU3xauiwS5hiDqGVXXLZvwThEClGK q7EA== X-Gm-Message-State: AOAM533BwF1/mMQsKcdlxQ0eXkIs/gBi+afRN+WlDAkqVWNiC1sdJIU4 7Wp+wPLkJLtAS6ec9TzusFPXXEk2H1Y= X-Google-Smtp-Source: ABdhPJyXBvBW1pfFNJk2S8n2rdKz2IiIHMY8qgg0v1zhqHbsd9ObYegx337yUleKXB5My42p9aELuA== X-Received: by 2002:a7b:c5cd:: with SMTP id n13mr10317337wmk.97.1621628799042; Fri, 21 May 2021 13:26:39 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:38 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:40 +0200 Message-Id: <20210521202622.26591-8-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 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/cran.scm (r-samr): Move from here... * gnu/packages/bioconductor.scm (r-samr): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 30 ------------------------------ 2 files changed, 31 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 58c8336ce5..f9aa34d254 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -2604,6 +2605,36 @@ built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis "Significance analysis of Microarrays") + (description + "This is a package for significance analysis of Microarrays for +differential expression analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8709cd21fa..e5d1db7cb6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33,7 +33,6 @@ ;;; Copyright © 2020 Magali Lemes ;;; Copyright © 2020 Simon Tournier ;;; Copyright © 2020 Aniket Patil -;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -28629,35 +28628,6 @@ indicator, a quantitative variable or a survival time.") ;; Any version of the LGPL (license license:lgpl3+))) -(define-public r-samr - (package - (name "r-samr") - (version "3.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "samr" version)) - (sha256 - (base32 - "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) - (properties `((upstream-name . "samr"))) - (build-system r-build-system) - (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) - (home-page "https://statweb.stanford.edu/~tibs/SAM/") - (synopsis "Significance analysis of Microarrays") - (description - "This is a package for significance analysis of Microarrays for -differential expression analysis, RNAseq data and related problems.") - ;; Any version of the LGPL - (license license:lgpl3+))) - (define-public r-randomforestsrc (package (name "r-randomforestsrc")