From patchwork Fri May 21 20:25:53 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29465 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 6AEEE27BC81; Fri, 21 May 2021 21:29:23 +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 9E4A527BC78 for ; Fri, 21 May 2021 21:29:22 +0100 (BST) Received: from localhost ([::1]:38424 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBlp-0006e2-GF for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:29:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52512) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkg-0004hb-LJ for guix-patches@gnu.org; Fri, 21 May 2021 16:28:10 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54499) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkf-0002yu-DZ 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 1lkBkf-0000NN-AQ for guix-patches@gnu.org; Fri, 21 May 2021 16:28:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 21/50] gnu: r-fastseg: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:09 +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=B48575.16216288491074 (code B ref 48575); Fri, 21 May 2021 20:28:09 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:29 +0000 Received: from localhost ([127.0.0.1]:37737 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk0-0000HA-PU for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:29 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:51727) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjO-00009R-BZ for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:51 -0400 Received: by mail-wm1-f42.google.com with SMTP id u133so11744876wmg.1 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:50 -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=sbY4kmXYlvZqB3uWJBCYUX61JhV9giynZDkg9CH2Aog=; b=s/p4mkArmGmZ9h1ODqv6YGHylh0EYE0dO1WVq2UHrLcXi8Omwcv9VB2XFhTNqNzq9O nlYrD3oTMjLIHUzOPC8u5TvPzVrRAEutoAjkEEPtqExGBYEjprJKCJ8J6BWUbsEAPTGw 94ID8Dvjug3Or+v8tqmDmG4mHfYk7V3gjo31DWTqFjvFIGDUPUnKDo+QnL9nol4mvuU0 eqaYMiRzefdd3lMZMZIHzZLb1AXcKjc75DvoVyC/R0xbMWn7owANwlk2aHrQV3Y9fsEB JlSRYhZQfa5x0bv5BDGGReb6Wt3RLvi/J+2b8nFWKbqGeoiUiT0WjBzHTJd17k4fbdI4 Glqw== 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=sbY4kmXYlvZqB3uWJBCYUX61JhV9giynZDkg9CH2Aog=; b=G7R3wYSt6jXnK0u+XcYsxIhJBc9nRsfG/xH3vSbTQUkM8fRIfn25bcrzTrh0/0f1Og T58iQD3M/MyoOsnxrSqsi17u3usA6bf8KmfqRH2DY0q4z/SHq990T/SoCUWeFtVRurrX vDuiF1CgOSBYecXLyerJxGTxf3i/GBkDUWshlCNeto82ITmhZlbYBDzECm3jLGjv2JI6 Yzogk510SYlZZn9ulS8QI2O9gbUl4ku46TnaTQQQuKiYN2BFlpic5jcfI4y8APYUg/J1 wPniFt1Ny/EU+xpMm6y6LnPcayZu6EFHy1zmy+NBPywLSjNn2gZLHPRH22C6/yugPfGg o1rQ== X-Gm-Message-State: AOAM532gFNTe3FinrhRi8GaSGOPpn1vvUbexjJhdyDsKeTcBbXNRS5k3 l5p754cTtCfzJXbAHvYWYY7lTH4J6WE= X-Google-Smtp-Source: ABdhPJzsxPlK5QpHHy8G+lL970XSJsZfwGSN6EG4kGIAdyMXQr0vBH5EV2ndanJg9ukskzp7Gj9qDQ== X-Received: by 2002:a05:600c:4f95:: with SMTP id n21mr10812579wmq.74.1621628804900; 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 22:25:53 +0200 Message-Id: <20210521202622.26591-21-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-fastseg): Move from here... * gnu/packages/bioconductor.scm (r-fastseg): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4657b0fa8b..313ed7e36f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2236,6 +2236,36 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1dc2d6f977..33680c283d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,36 +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-fastseg - (package - (name "r-fastseg") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "fastseg" version)) - (sha256 - (base32 - "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") - (synopsis "Fast segmentation algorithm for genetic sequencing data") - (description - "Fastseg implements a very fast and efficient segmentation algorithm. -It can segment data from DNA microarrays and data from next generation -sequencing for example to detect copy number segments. Further it can segment -data from RNA microarrays like tiling arrays to identify transcripts. Most -generally, it can segment data given as a matrix or as a vector. Various data -formats can be used as input to fastseg like expression set objects for -microarrays or GRanges for sequencing data.") - (license license:lgpl2.0+))) - (define-public r-keggrest (package (name "r-keggrest")