From patchwork Fri May 21 20:25:39 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29485 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 AF37F27BC81; Fri, 21 May 2021 21:32:02 +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 3A01D27BC78 for ; Fri, 21 May 2021 21:32:02 +0100 (BST) Received: from localhost ([::1]:44268 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBoP-0002Ot-DQ for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:32:01 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52420) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkZ-0004JI-OR for guix-patches@gnu.org; Fri, 21 May 2021 16:28:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54484) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkZ-0002vs-HI 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-0000Lb-Ci for guix-patches@gnu.org; Fri, 21 May 2021 16:28:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 07/50] gnu: r-msnbase: 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=B48575.1621628831937 (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]:37706 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBji-0000Ex-UZ for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:11 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:45720) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjI-00008X-3G for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:45 -0400 Received: by mail-wm1-f48.google.com with SMTP id s5-20020a7bc0c50000b0290147d0c21c51so7796208wmh.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=sEI0QpP50D3ePFXyCNJNLyhBWd55pfePWc1v0CRAHCo=; b=r/KAWHTXPALECbbo/K4IW6oKfbiqbp/AYPe/DiG4u2VE/CgelvzNTB0z2mhmLfTuoz /76zSrAOCo0o7Dmchzz7fJMTOUQ6cAspT05yW5ziyzQ272jAX3d95pWOiy4e5WbVxLm2 QC4M/vexpLLsGRzHVpBZ+JmCVpItZAudt8sxglgQxo8Ra1LFbOVtu3dW+qaG4WBJ0rKK ge/a4lAHMz+RxTFa22nzHGSSpdHiLP45+eS2mioSqdRBzafZyg4heNsf/fe9JP79lZbF JenU+jLPzvq3CIhskbmNKXGiQsoE8rSSIDH9LCWjHi+5E4arQPDP6BX5x0/WjIB7k/4D iZeg== 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=sEI0QpP50D3ePFXyCNJNLyhBWd55pfePWc1v0CRAHCo=; b=hQWBgvslkvARgfGQR+2x3flD17Q+VYK7MEGSxGbUau7qcoQhQwX4pDWg9KG/DMr4lt CmmUwlDXgJ+55D0R3cBFCDcarpLwgIwClrnrDgb91Io5dMaU2Acopw2opoESGXQTre5U LFMMSQO45xlH6Lkg8Ejjy7YJVvNamoa51/gs7ye71M+bSLAOSUXYCWk1dH4xOqvUqh+M KmX83EjmhqPC9z2z6GQbTY6ueHUYQb9a4wTO8PePXGnrj8X+AOqOXFQfoK3fi9p2fZGD Q9pRQ95gnCQnZUSvO5CA0IB89z+Yrkk4EoXaIKrkK0B0b+x+bYrLCxeG4H6cw/DyVVY/ 6g0Q== X-Gm-Message-State: AOAM5301jfpTm2jJ6sfjgijyD5lVEcQyEcotnDQAybkb5MfwYzC97mgg Iylq2ev9JIJCQQEUFzRkjkAjXuWWDRM= X-Google-Smtp-Source: ABdhPJzuV55gxxU+38dCx7hGx2eq8hj8QreiEB/+sqR5Jilz7z8Qew6FaDVVJrw91reNnMRFNgAABA== X-Received: by 2002:a05:600c:4f0b:: with SMTP id l11mr10528436wmq.126.1621628798628; Fri, 21 May 2021 13:26:38 -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 22:25:39 +0200 Message-Id: <20210521202622.26591-7-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/bioinformatics.scm (r-msnbase): Move from here... * gnu/packages/bioconductor.scm (r-msnbase): ...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 b5787cb207..58c8336ce5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2312,6 +2312,51 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnbase + (package + (name "r-msnbase") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnbase" version)) + (sha256 + (base32 + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) + (properties `((upstream-name . "MSnbase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-digest" ,r-digest) + ("r-ggplot2" ,r-ggplot2) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-maldiquant" ,r-maldiquant) + ("r-mass" ,r-mass) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-pcamethods" ,r-pcamethods) + ("r-plyr" ,r-plyr) + ("r-preprocesscore" ,r-preprocesscore) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-vsn" ,r-vsn) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/lgatto/MSnbase") + (synopsis "Base functions and classes for MS-based proteomics") + (description + "This package provides basic plotting, data manipulation and processing +of mass spectrometry based proteomics data.") + (license license:artistic2.0))) + (define-public r-msnid (package (name "r-msnid") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5c2abe6e94..28893c40e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9230,51 +9230,6 @@ the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) -(define-public r-msnbase - (package - (name "r-msnbase") - (version "2.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnbase" version)) - (sha256 - (base32 - "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) - (properties `((upstream-name . "MSnbase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/lgatto/MSnbase") - (synopsis "Base functions and classes for MS-based proteomics") - (description - "This package provides basic plotting, data manipulation and processing -of mass spectrometry based proteomics data.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light")