From patchwork Fri Oct 28 05:02:34 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: 44166 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 85DF527BBEA; Fri, 28 Oct 2022 06:05:49 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED 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 BA26327BBE9 for ; Fri, 28 Oct 2022 06:05:48 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ooHWK-0007wZ-73; Fri, 28 Oct 2022 01:03:04 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ooHWI-0007tO-Ro for guix-patches@gnu.org; Fri, 28 Oct 2022 01:03:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ooHWI-0002hv-Kf for guix-patches@gnu.org; Fri, 28 Oct 2022 01:03:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ooHWH-0000B0-U5; Fri, 28 Oct 2022 01:03:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58828] [PATCH 1/2] gnu: Add r-dmwr2. References: <4e23676adf3142d98f2120e6da966f18@mdc-berlin.de> In-Reply-To: <4e23676adf3142d98f2120e6da966f18@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 28 Oct 2022 05:03:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58828 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <58828@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 58828-submit@debbugs.gnu.org id=B58828.1666933379664 (code B ref 58828); Fri, 28 Oct 2022 05:03:01 +0000 Received: (at 58828) by debbugs.gnu.org; 28 Oct 2022 05:02:59 +0000 Received: from localhost ([127.0.0.1]:59958 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooHWF-0000Ad-1E for submit@debbugs.gnu.org; Fri, 28 Oct 2022 01:02:59 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:55773) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooHWC-0000AH-TT for 58828@debbugs.gnu.org; Fri, 28 Oct 2022 01:02:58 -0400 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; s=mdc; t=1666933369; x=1668747770; bh=tbSgXRCLU/rNdtA q3k5hqX3zhNxCL5CDmXmfbKwh+y8=; b=GAQNHS7WjzQx38r2zUcGwt1r6jUZJKg i5VFPeDzjCsbtI0IeF9wfDflUGVCs/yWLTJbOzTAqO2ws9GlmdmDEsYhhDfGvqML rwyXFYhx/wK9yM5a1OT+gJxUPmn1HiqGXqqQgp723KOpjt9tQquJ3h+FBvDO7yy/ OLHWUj5R4jCY= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 953FA1602FF for <58828@debbugs.gnu.org>; Fri, 28 Oct 2022 07:02:49 +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 15.1.2507.13; Fri, 28 Oct 2022 07:02:48 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 28 Oct 2022 07:02:34 +0200 Message-ID: <20221028050235.5355-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27228.005 X-TM-AS-Result: No-10--7.901400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEFVB oFHq1/NXRRa406V/YwyBUGewL2YXt6/a/Ug5qXLHwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHY87 NwWBxSvgqJVjgDINn3Mign5HsLTCTuJXEeLLJ6+yrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr1yeoN417uL8ZTpDBUYNQIoB9YHPBYCvC1RSLsSQVpP0G7zMyqCH0DtQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.901400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27228.005 X-TM-SNTS-SMTP: 20C89532BDD2F9257082FD703A2BEF15963F40CFF83DA06970995D56FFCCA1602002:F 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: , Sender: "Guix-patches" Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-dmwr2): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260 diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f969da5b3c..eb4532a62a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -402,6 +402,36 @@ (define-public r-dixontest Gaussian quadrature for a numerical solution.") (license license:gpl3))) +(define-public r-dmwr2 + (package + (name "r-dmwr2") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "DMwR2" version)) + (sha256 + (base32 + "1vzfbz2k05j8r2hpig3d2grb99rnnh2s1sviii3prcyqicxfh0i9")))) + (properties `((upstream-name . "DMwR2"))) + (build-system r-build-system) + (propagated-inputs + (list r-class + r-dbi + r-dplyr + r-quantmod + r-readr + r-rpart + r-xts + r-zoo)) + (home-page "https://github.com/ltorgo/DMwR2") + (synopsis + "Functions and data for the second edition of \"Data Mining with R\"") + (description + "This package provides functions and data accompanying the second edition +of the book \"Data Mining with R, learning with case studies\" by Luis Torgo, +published by CRC Press.") + (license license:gpl2+))) + (define-public r-emdist (package (name "r-emdist") From patchwork Fri Oct 28 05:02:35 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: 44165 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 333D227BBEB; Fri, 28 Oct 2022 06:04:53 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 D48DE27BBE9 for ; Fri, 28 Oct 2022 06:04:50 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ooHWL-0007zm-FU; Fri, 28 Oct 2022 01:03:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ooHWI-0007tN-R1 for guix-patches@gnu.org; Fri, 28 Oct 2022 01:03:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ooHWI-0002hy-Hh for guix-patches@gnu.org; Fri, 28 Oct 2022 01:03:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ooHWI-0000B9-Al; Fri, 28 Oct 2022 01:03:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58828] [PATCH 2/2] gnu: Add r-debcam. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 28 Oct 2022 05:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58828 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <58828@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 58828-submit@debbugs.gnu.org id=B58828.1666933380670 (code B ref 58828); Fri, 28 Oct 2022 05:03:02 +0000 Received: (at 58828) by debbugs.gnu.org; 28 Oct 2022 05:03:00 +0000 Received: from localhost ([127.0.0.1]:59960 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooHWF-0000Af-El for submit@debbugs.gnu.org; Fri, 28 Oct 2022 01:02:59 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37803) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ooHWD-0000AJ-DJ for 58828@debbugs.gnu.org; Fri, 28 Oct 2022 01:02:58 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1666933370; x=1668747771; bh=YnxYg/VVo7GncjESmtxcD9hYPjomMTknp0uNTOwdUVs=; b=hRt2dxw8sNM3 7v/QJQVFRxJTrKy9MIPb9NS+gZNBUNkg64mP5+YTaGA3VHyyEVG5awmBEQ+ktKEs 6kA276XJRQ94/fGaogos1QHrbQvxoV3/WFp4OWeoRliehFg817WXztKfOwhTGIBp NRuBEdRzFAQ+F2e6l65Q644gwCqVq7c= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id A571816030D for <58828@debbugs.gnu.org>; Fri, 28 Oct 2022 07:02:50 +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 15.1.2507.13; Fri, 28 Oct 2022 07:02:48 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 28 Oct 2022 07:02:35 +0200 Message-ID: <20221028050235.5355-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.0 In-Reply-To: <20221028050235.5355-1-madalinionel.patrascu@mdc-berlin.de> References: <20221028050235.5355-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27228.005 X-TM-AS-Result: No-10--5.698900-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkELz3 f1m0xqkLGBKlWUwuGkbjvWTUyWSXIpT6aKfZ6tn9a87CDXaKRVJITEcvqjcF4EJZ5MDd4/kUhEz I3+mkzid7MSP7SLpuGLg539/y6ey+Kq9drOoruLzd+fuf9kcapsHT/vGF3gHJocwYjaqIPvDHD8 r2CM9/xWRBr3/XRWat1Cr+bWkJx9HQ3sOMB3Fk1OLzNWBegCW2wgn7iDBesS3CttcwYNipXxjOl t1Pi553Tv+WDxelXuEKNcr/7E+wBf42sFrtVVKcUyHwSBIPWXA= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.698900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27228.005 X-TM-SNTS-SMTP: 5D5302CA5BCB9971B6C7F6EDA0E4BA2A407D43D101BD85483CED74DD8C2A06C22002:F 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: , Sender: "Guix-patches" Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-debcam): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b8535250f9..994b3b0137 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -48,6 +48,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) + #:use-module (gnu packages java) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -3051,6 +3052,45 @@ (define-public r-dearseq set analyses, and can deal with repeated or longitudinal data.") (license license:gpl2))) +(define-public r-debcam + (package + (name "r-debcam") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "debCAM" version)) + (sha256 + (base32 + "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7")))) + (properties `((upstream-name . "debCAM"))) + (build-system r-build-system) + (inputs (list openjdk)) + (propagated-inputs + (list r-apcluster + r-biobase + r-biocparallel + r-corpcor + r-dmwr2 + r-geometry + r-nmf + r-nnls + r-pcapp + r-rjava + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/debCAM") + (synopsis "Deconvolution by convex analysis of mixtures") + (description + "This package is an R implementation for fully unsupervised deconvolution +of complex tissues. @code{DebCAM} provides basic functions to perform unsupervised +deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis +of Mixtures} and some auxiliary functions to help understand the subpopulation- +specific results. It also implements functions to perform supervised deconvolution +based on prior knowledge of molecular markers, S matrix or A matrix. Combining +molecular markers from CAM and from prior knowledge can achieve semi-supervised +deconvolution of mixtures.") + (license license:gpl2))) + (define-public r-decipher (package (name "r-decipher")