From patchwork Tue Oct 31 10:57:19 2023 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: 55716 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 66EF627BBEB; Tue, 31 Oct 2023 10:59:57 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 F2BB227BBE2 for ; Tue, 31 Oct 2023 10:59:56 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTA-0006Si-9L; Tue, 31 Oct 2023 06:59:36 -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 1qxmT4-0006P0-Bz for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:30 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT4-0003YH-1W for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:30 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTb-0005zo-KV; Tue, 31 Oct 2023 07:00:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 01/11] gnu: Add r-r3cseq. References: <39e4b3e1-c4eb-4d32-94f0-8d4d3b0fe19f@mdc-berlin.de> In-Reply-To: <39e4b3e1-c4eb-4d32-94f0-8d4d3b0fe19f@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: Tue, 31 Oct 2023 11:00:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169874999722983 (code B ref 66843); Tue, 31 Oct 2023 11:00:03 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 10:59:57 +0000 Received: from localhost ([127.0.0.1]:47542 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTU-0005yX-OU for submit@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:57 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:45491) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmT7-0005wE-04 for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:33 -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=1698749932; x=1700564333; bh=eJzqktf9fT28MM6 wYk1duVyz8Mkmo9cc1JrZdlSq0rw=; b=Z1Fmcsx9zKtutgK1LilqpH8Rg8XLIp+ vH2RXBeRsohAAAc+cagPUawqelX0lq1DpDttC9jeudZYcQugSAIv4OW96Ym+j/69 hXbSMVkxHsB2FPCIzTE5LZjkBvlBK5F3Nb/LG2XVMVCOTpAzUO9NPJTjZ33eyH6l kKkNbixlQlDY= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id AAC60300195 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:52 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:51 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:19 +0100 Message-ID: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--1.288200-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIpb wG9fIuITrZ8c7WOIyLJdp5evcPexscocsHMOi3Ola87CDXaKRVJITEcvqjcF4EJZ5MDd4/kUssb EkSX6c0npjnMUaEuof69+9utLQN+o27YWB4baXJKFK7CQMC8BwgK0ZgbTOeKUyiLz1Vtc/pWUg5 UD6AlF0sX4oKkYTfsImyiLZetSf8lBgw5G4NYCZN9pjzubZ2rHwrbXMGDYqV8JC+VZi2gQEVheG iOyxgXyzqYBbS279ZVFu7u6uBUVQ5F0DCnnBs3BsyMAlCnHHXJiswA7DwG0jUcjBvGCu1t+awnw IH3axNZN/jdvvDSapShCDgyssE8uo3yYJV8x0OrMUVc0s17dsX/q4TD2v7K1 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.288200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: 38BCDB4C7A4C692AA1C04CDBDF3AE977A1FD050D9E81838C92487DB74EEFA1E12000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-r3cseq): New variable. Change-Id: Ib62db1415ef3988ccef88ad600192246964b4d84 --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) base-commit: d22d2a05c389207f8cdcf824be7738b1499a987c diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3ff0b1127..dee72de2b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7747,6 +7747,38 @@ (define-public r-hpar the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-r3cseq + (package + (name "r-r3cseq") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "r3Cseq" version)) + (sha256 + (base32 "1wpjsiy9qh45h3k5s79w4zhkma5h4gvyf2sa8l934mx0jl16k0q2")))) + (properties `((upstream-name . "r3Cseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-data-table + r-genomeinfodb + r-genomicranges + r-iranges + r-qvalue + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-sqldf + r-vgam)) + (home-page "http://r3cseq.genereg.net/Site/index.html") + (synopsis + "Analysis of Chromosome conformation capture and Next-generation sequencing") + (description + "This package is used for the analysis of long-range chromatin interactions from +3C-seq assay.") + (license license:gpl3))) + (define-public r-raggedexperiment (package (name "r-raggedexperiment") From patchwork Tue Oct 31 10:57:20 2023 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: 55715 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 E8F0527BBEA; Tue, 31 Oct 2023 10:59:55 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 2F7C727BBE2 for ; Tue, 31 Oct 2023 10:59:55 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmT9-0006Qo-4y; Tue, 31 Oct 2023 06:59:35 -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 1qxmT3-0006OV-D7 for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:29 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT3-0003Y9-3m for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:29 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTa-0005zY-PT; Tue, 31 Oct 2023 07:00:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 02/11] gnu: Add r-r4rna. 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: Tue, 31 Oct 2023 11:00:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169874999622971 (code B ref 66843); Tue, 31 Oct 2023 11:00:02 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 10:59:56 +0000 Received: from localhost ([127.0.0.1]:47540 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTU-0005yR-7Q for submit@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:56 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34597) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmT7-0005wG-4o for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:33 -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=1698749933; x=1700564334; bh=iXOBHClnUyh2O110+4gIdflbCSzuI14uOqCmac0L8NM=; b=SEiKAThOclZ0 81UstWXCIFh7xD64fd8rtKZJNUuoetYdaXOWLDIR0ernSQvXCoPZNxMiGPmLem7R 2mIyQtQv1BEOetRGNGu2XyBSTQFpM5n3xy822/1KX/yn8KlCQOlUOlACDKm69nGz nsMbzvOCPAhPRQViGHEPznlYiKD9pgs= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 556D73001C1 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:53 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:52 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:20 +0100 Message-ID: <7d5ca947d109a9ef6a92f861b116242281ed2314.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--5.211400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/Exmr5hqNL1qY5ZGw7wyeH2il Wqs4D9IkPBhEt91+1lhJTjjs9yT6Yo8WMkQWv6iV3LAytsQR4e42j49Ftap9Ee3/K3TeOMBiXf5 sC39gVVFkl4TmW/y09NaUDYe1dhMffCWXRNP0OLA+BKwLZedUQH8FerAT0dJY= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.211400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: 59C5E6E31E6AEB1FA571339F88D5CF173394853F18F91E6D4D7B31CDFCF84D8C2000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-r4rna): New variable. Change-Id: I1bde2a17b0ba4a97fa54161744f048dbfaf2217a --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dee72de2b7..6a3606b399 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7779,6 +7779,29 @@ (define-public r-r3cseq 3C-seq assay.") (license license:gpl3))) +(define-public r-r4rna + (package + (name "r-r4rna") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "R4RNA" version)) + (sha256 + (base32 "1i4c9477xsp3hq5kxydrimhl6g8vshwbqgnhap5n1ykxbsval1pp")))) + (properties `((upstream-name . "R4RNA"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings)) + (home-page "https://www.e-rna.org/r-chie/") + (synopsis "RNA visualization and analysis") + (description + "This package provides a package for RNA basepair analysis, including the +visualization of basepairs as arc diagrams for easy comparison and annotation of +sequence and structure. Arc diagrams can additionally be projected onto +multiple sequence alignments to assess basepair conservation and covariation, +with numerical methods for computing statistics for each.") + (license license:gpl3))) + (define-public r-raggedexperiment (package (name "r-raggedexperiment") From patchwork Tue Oct 31 10:57:21 2023 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: 55721 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 D413327BBE2; Tue, 31 Oct 2023 11:00:13 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 14B0627BBE9 for ; Tue, 31 Oct 2023 11:00:11 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTE-0006Ur-Nw; Tue, 31 Oct 2023 06:59:40 -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 1qxmT9-0006RV-CU for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT7-0003Yp-Kr for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTf-00061F-7l; Tue, 31 Oct 2023 07:00:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 03/11] gnu: Add r-nistunits. 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: Tue, 31 Oct 2023 11:00:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000323048 (code B ref 66843); Tue, 31 Oct 2023 11:00:07 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:03 +0000 Received: from localhost ([127.0.0.1]:47544 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTV-0005ye-5n for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:03 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:47787) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmT7-0005wH-P4 for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:34 -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=1698749934; x=1700564335; bh=LqWr44JAhZZ7Vobc2brzhjiyc9Ht0uuMw+qKjHcB6dY=; b=JCUH2SyedTyw MOFXBXm5eszlXm/6+FMGar6uWOQTUoHFPpmFrEkMrl2VpPprlunws0kEaet1wqV4 sEnVfWmvwNyKAdB+2WNQzz+fcCJBSiDtvsPo/PIHSzABzZZQAbeENYTGtFF9E2HR asqhPmdDXB/0B3mJcwJxQOLEghPETKE= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id EE8403001D3 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:53 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:53 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:21 +0100 Message-ID: <5f1463825ab2765c99232257b57f679ddfff6fd1.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--3.489400-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VNnf JrUSEbFD9gyXL9RSacPCWgf/Z0idjUbpsl4KpyrWfOaYwP8dcX5IvK4LrXs1aQjxoTu0kNRwte+ ocL7MBZcNUccATRyd1KuLQx6TP/2ymDcRJzGLWpLuW/BrYJGl/ULixrsCJ1jTIpz++XQI8PGeAi CmPx4NwGmRqNBHmBveVDC1CbuJXmMqtq5d3cxkNRqXnrxrKCOXe+vOwkjLmlSrHSDJD/CwC02kY y2h30YGCmnZyoUNC1NuN7STVbn7VVw66KJrE41uby7hIM7rOiY7Yn/oXRB7RPhHuXlH8JuIDUEk BTZ8vOLxlyTCXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.489400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: B98175949689A7B6AF87DE1BE843E43849C3626CF5D1CFB45704247205EF1CB22000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-nistunits): New variable. Change-Id: I66328b54045a3125e5f3033605be88e3a1b2646a --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index de31f44dbd..fe8014c381 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9817,6 +9817,27 @@ (define-public r-network supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) +(define-public r-nistunits + (package + (name "r-nistunits") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "NISTunits" version)) + (sha256 + (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a")))) + (properties `((upstream-name . "NISTunits"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=NISTunits") + (synopsis "Fundamental physical constants and unit conversions") + (description + "Fundamental physical constants (quantity, value, uncertainty, unit) for +@acronym{SI, International System of Units} and non-SI units, plus unit +conversions based on the data from @acronym{NIST, National Institute of +Standards and Technology}, USA.") + (license license:gpl3+))) + (define-public r-stabs (package (name "r-stabs") From patchwork Tue Oct 31 10:57:22 2023 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: 55720 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 A4BF727BBED; Tue, 31 Oct 2023 11:00:11 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 2D2B127BBE2 for ; Tue, 31 Oct 2023 11:00:10 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTD-0006Tg-4J; Tue, 31 Oct 2023 06:59:39 -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 1qxmT9-0006RX-Cz for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT9-0003Yx-3r for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTg-00061m-Ow; Tue, 31 Oct 2023 07:00:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 04/11] gnu: Add r-celestial. 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: Tue, 31 Oct 2023 11:00:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000423072 (code B ref 66843); Tue, 31 Oct 2023 11:00:08 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:04 +0000 Received: from localhost ([127.0.0.1]:47553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTb-0005zw-RI for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:04 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:40173) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmT9-0005wO-Dv for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:35 -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=1698749934; x=1700564335; bh=9pD7wsIIQ+a3S0RzC9Gqxl3MyHWpEnDR4d65zWh30+U=; b=GZMzeLTT93W0 ddRhOCVkYt++2thEpv3wYjs4SgR+a5wM2DUMstxeTlTISd8CGAWHPgGb3By4FnC8 6qVShvO6ZYwOx2VhpFTkR2KyPThgS1Ecn5S+Evy4/9scJV9Cl9Wk538On2v4waMz V1d6kxHjgo3N8tjDDpSUGTgBDI+GS/g= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 92D8C3001E3 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:54 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:53 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:22 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10-1.587600-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaY41hcR3BAfxpuHUFrt/n8AE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIFFN3UB4MC3vDzN VDiv90NDXFQkvS/0vidcyle1XTvpymDcRJzGLWpK5x7uAXGEprZiltdER9ZBiU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DOqO5YX0bFi3M03ysyuyqtkLH0P7ffDI3GhKq Bphd0rm//EiXDn4fmZ2R9NjVe6HQB3fKqSDb7uhe1JBUWwI/8BfI6y1CD99H9xSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.587600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: A176BBDEF6AF2307CF2ED3A94D8962C073DC41E84185BB06EBBC3D34735DCAEC2000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-celestial): New variable. Change-Id: I9ab9c6b6c79f2fb12d7391a75e7214bbeba675fc --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fe8014c381..cc3ac02599 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -305,6 +305,30 @@ (define-public r-changepoint ;; Any version of the GPL. (license license:gpl3+))) +(define-public r-celestial + (package + (name "r-celestial") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "celestial" version)) + (sha256 + (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z")))) + (properties `((upstream-name . "celestial"))) + (build-system r-build-system) + (propagated-inputs (list r-nistunits r-pracma r-rann)) + (home-page "https://cran.r-project.org/package=celestial") + (synopsis + "Collection of common astronomical conversion routines and functions") + (description + "This package contains a number of common astronomy conversion routines, +particularly the HMS and degrees schemes, which can be fiddly to convert between +on mass due to the textural nature of the former. It allows users to coordinate +match datasets quickly. It also contains functions for various cosmological +calculations.") + (license license:gpl3))) + ;; The package sources include multiple non-minified JavaScript files and the ;; v5.1.0 variant of d3.js. The d3.js file is not minified. (define-public r-chromomap From patchwork Tue Oct 31 10:57:23 2023 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: 55718 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 BC45527BBE2; Tue, 31 Oct 2023 11:00:05 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 D456D27BBEA for ; Tue, 31 Oct 2023 11:00:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTD-0006UV-DL; Tue, 31 Oct 2023 06:59:39 -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 1qxmT9-0006RW-CV for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT8-0003Yr-G2 for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTg-00061W-4O; Tue, 31 Oct 2023 07:00:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 05/11] gnu: Add r-magicaxis. 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: Tue, 31 Oct 2023 11:00:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000423063 (code B ref 66843); Tue, 31 Oct 2023 11:00:08 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:04 +0000 Received: from localhost ([127.0.0.1]:47549 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTb-0005zh-6g for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:03 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:46981) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmT8-0005wK-KD for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:35 -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=1698749935; x=1700564336; bh=Ha6+VxgIETGTUq+7AN3NmLcqsa1ivIb9HwaX5rYIM3s=; b=ReE8C7L3NO0K ZsFlsozTX9guHyoPTW6Lk0s7KTaZbjO0wL1XIH20Wn3hob+zfYj/Z2G7PeJq8Vo6 cMAxY+BJ7S1QWOLn7Y2FPggci6d4dPXUh8QpOpRI2sswIRbslHuALnEfErtnRVFo suVXQKrjHmGbaiTbV2dsNup4XOz5l18= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 0CD8A3001EB for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:55 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:54 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:23 +0100 Message-ID: <29a0e81be58762636ed2b35edbeb799ef2b01818.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--5.084400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VGb6 PphVtfZgnMBQUHFOVS/uNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIMay5jJvrxqMj8x Vj5MF/3p7MSP7SLpuGIek6stLzp1e1pVckLHgk0Krm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr1m3blLZkutwki3b3ANqrNdOzjhZjUrXtWm4fkaPx78Pt2fTVJ2ch+gg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.084400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: C4E9852FADBB0CB746511CDB1A091D68A03768DA0273076CC60A4231A563E8AD2000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-magicaxis): New variable. Change-Id: I9843dcf90cd6d85799fab688d6dccfcfacfad672 --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index cc3ac02599..b4770f8a53 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -7777,6 +7777,33 @@ (define-public r-magic dimensioned arrays.") (license license:gpl2))) +(define-public r-magicaxis + (package + (name "r-magicaxis") + (version "2.2.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "magicaxis" version)) + (sha256 + (base32 "1gqnivn6qjmf7axdi0pff6a40clklbipcr6qvm6ivzqbqhpbcb7v")))) + (properties `((upstream-name . "magicaxis"))) + (build-system r-build-system) + (propagated-inputs + (list r-celestial + r-mapproj + r-mass + r-plotrix + r-rann + r-sm)) + (home-page "https://cran.r-project.org/package=magicaxis") + (synopsis "Scientific plotting with minor-tick and log minor-tick support") + (description + "This package provides functions to make useful (and pretty) plots for +scientific plotting. Additional plotting features are added for base plotting, +with particular emphasis on making attractive log axis plots.") + (license license:gpl3))) + (define-public r-rmysql (package (name "r-rmysql") From patchwork Tue Oct 31 10:57:24 2023 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: 55725 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 A3DC027BBEA; Tue, 31 Oct 2023 11:00:37 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 0A3DF27BBE2 for ; Tue, 31 Oct 2023 11:00:37 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTM-0006cZ-EY; Tue, 31 Oct 2023 06:59:48 -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 1qxmTB-0006T7-7Q for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmTA-0003ZT-Hy for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:36 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTh-00062B-U4; Tue, 31 Oct 2023 07:00:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 06/11] gnu: Add r-relations. 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: Tue, 31 Oct 2023 11:00:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000623128 (code B ref 66843); Tue, 31 Oct 2023 11:00:09 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:06 +0000 Received: from localhost ([127.0.0.1]:47563 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTd-00060d-OK for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:06 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:38845) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTD-0005xH-2V for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:39 -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=1698749935; x=1700564336; bh=EvfnAPlqdsCabZlW+G6OaJDoAS9LrFq0H7AUZKDa5QE=; b=Wn12+8ZDvPW1 LHF9e5Zrt1IH5hlnWcfT3GWKueyM7SDyno94gUAyuf9bOG5V6sGS79+uoAQKUgXy DO88bnub5oXmxNECGriNNoHc3JLco26gb7ltlkzy7MXNzl0BKxMcFeaAUHyQXvGZ Lyp28YMG+fZB889g2NTc82X071wFSr0= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 6E1533001F7 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:55 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:55 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:24 +0100 Message-ID: <60eed7899047ec5475f7f87e77b7cfbb0d8484d4.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--7.650400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfM0wLVht0qLwQrcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIMay5jJvrxqMmQ9 rT7S4OqN7MSP7SLpuGEnMFskn1/DhMs2EwO0GeddvTnqYKYXTRhDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXmVV1G+Ck2l7+gtHj7OwNO2BSJy8ngwKGfVaVwAjkHhiwJBqaaZzCgSB9G9q5b8P/ZF1W oeLOKxdscUVjVykkzI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.650400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: 976DDCFA458ABEEA08AA6C35A9F79008DD940CF219F03142452B4D672A1CEEBE2000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-relations): New variable. Change-Id: I4bf67353aa7f7221592d274d61c74b83191a6281 --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b4770f8a53..ef43771f47 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3456,6 +3456,27 @@ (define-public r-selectr package is a port of the Python package @code{cssselect}.") (license license:bsd-3))) +(define-public r-relations + (package + (name "r-relations") + (version "0.6-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "relations" version)) + (sha256 + (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq")))) + (properties `((upstream-name . "relations"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster r-sets r-slam)) + (home-page "https://cran.r-project.org/package=relations") + (synopsis "Data structures and algorithms for relations") + (description + "This package provides data structures and algorithms for k-ary relations +with arbitrary domains, featuring relational algebra, predicate functions, and +fitters for consensus relations.") + (license license:gpl2))) + (define-public r-repmis (package (name "r-repmis") From patchwork Tue Oct 31 10:57:25 2023 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: 55723 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 2824127BBEA; Tue, 31 Oct 2023 11:00:24 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 7F09F27BBE2 for ; Tue, 31 Oct 2023 11:00:23 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTF-0006VA-GE; Tue, 31 Oct 2023 06:59:41 -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 1qxmTC-0006TP-DH for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmTB-0003a2-L0 for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTj-00062a-AH; Tue, 31 Oct 2023 07:00:11 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 07/11] gnu: Add r-profmem. 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: Tue, 31 Oct 2023 11:00:11 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000823168 (code B ref 66843); Tue, 31 Oct 2023 11:00:11 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:08 +0000 Received: from localhost ([127.0.0.1]:47575 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTf-00061Q-PL for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:08 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:58639) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTA-0005wX-T3 for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:40 -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=1698749936; x=1700564337; bh=jLett4DbhTTvJbdt5+WVcLI3zmwDHycX2FI/8AcQzzg=; b=cgH2LhOQHI7r YS31+WUTcsGUpnyZXknFAKqdO3Qr9AosZbyABdzcyy5o9Fzzbf7kYPeZV6hye99u ze29XjquA6ZVdMcqdYJYXTQcswsH0pu9Y2uNiOv1Cla9JOZKjW/9mmZH8pxmOeyA bcRXOBIJIuWVIevBCi2ZZYVt5uHV2gU= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 52CA9A0164 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:56 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:55 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:25 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--6.337200-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt0fr6WG4Th9aDDzmS9l9fYoXivwflisSrMIubEPSkNnJbZ1 CAZyZadQ9czwua4Q0W1PSAWHDBcndq2NInS93zS82aDVyTGx/p2a+AJ0Dgp65lCkt7JatNPWeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8hfNjF5BHUO+1uY8Xs6XsBvYwQE3ZJF+bisj3ErVPVfCBBAe vRzHRFvPRmsyDMq6oE= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.337200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: 38CF7FDE9C61A4490EC34CE840BFEB1EE268C3E5F917715F3C098964195119922000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-profmem): New variable. Change-Id: If99cf8e963601e9f0a664f12ef263a064b59b0d6 --- gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ef43771f47..27ea2cdc06 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1266,6 +1266,38 @@ (define-public r-prettydoc highlight styles are supported.") (license license:asl2.0))) +(define-public r-profmem + (package + (name "r-profmem") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "profmem" version)) + (sha256 + (base32 "0gg6ja0ifwn9jj42rw1gnyil55sl9r2y5rjb6yjcvqwd5arajp3l")))) + (properties `((upstream-name . "profmem"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (native-inputs + (list r-r-rsp + r-markdown)) ; for vignettes + (home-page "https://github.com/HenrikBengtsson/profmem") + (synopsis "Simple memory profiling for R") + (description + "This package provides a simple and light-weight API for memory profiling +of R expressions. The profiling is built on top of R's built-in memory profiler +@code{utils::Rprofmem()}, which records every memory allocation done by R (also +native code).") + (license license:lgpl2.1+))) + (define-public r-proj4 (package (name "r-proj4") From patchwork Tue Oct 31 10:57:26 2023 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: 55719 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 0855427BBEA; Tue, 31 Oct 2023 11:00:08 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 56B1A27BBE2 for ; Tue, 31 Oct 2023 11:00:07 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTE-0006Uo-Nb; Tue, 31 Oct 2023 06:59:40 -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 1qxmT9-0006Rr-OS for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT9-0003ZK-GT for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:35 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTh-00061u-5J; Tue, 31 Oct 2023 07:00:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 08/11] gnu: Add r-bench. 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: Tue, 31 Oct 2023 11:00:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000523096 (code B ref 66843); Tue, 31 Oct 2023 11:00:09 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:05 +0000 Received: from localhost ([127.0.0.1]:47555 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTc-000605-FS for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:05 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:48551) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTA-0005wg-T5 for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:38 -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=1698749936; x=1700564337; bh=w3tiHpISS5OTCsHDP3BwSEizyQ1AzYaTCJRdAJKhT4k=; b=XAntrEH1uJ4M RSCjqLHJ8PQW/Dqa80lgzuUJRPSoU2cSl81piFY7yJevY3StSU1sr79aIzYGiKNn N/lijCfromqEtrKCZ5yIA+zl0E4027QOPbvKY2lq8sH8yY7SBrAFM9rxkDoOYIE1 C1J2tFz5uc3eIzrp1akDlCprncXDGEA= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id CA50DA016C for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:56 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:56 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:26 +0100 Message-ID: <0ffb55760837a21200f951b3f4537a98fcead77b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--7.847400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VNnf JrUSEbFDfBP9zL95reczLmfGY6iDkSq+GZ9ZHxIhuW77/y896siFzNNPDc6umBHfiujuTbedvER UVOAFoxh7MSP7SLpuGHG51PW7ogXW5HTg5Su96nQ7lKkz03w06+uLFZZYlisfHxPMjOKY7A+u65 UDD0aDgsRB0bsfrpPIXzYxeQR1Dvt1kV2I/qrMoW+qebJZehdGRWDET34bmZY8FZcR1yLgvVW8a 7326vtt X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.847400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: 9BD6CA10CD73D3FC2A02224AE9D18BCA8C6AC50316AE9EAEE0FFBD0520FDA51E2000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-bench): New variable. Change-Id: I9948ff12729b08dd4016df272777651a6b6de2e0 --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 27ea2cdc06..af9b59c8bf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1481,6 +1481,26 @@ (define-public r-babelwhale volume or copy a file.") (license license:expat))) +(define-public r-bench + (package + (name "r-bench") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bench" version)) + (sha256 + (base32 "05zky7l6103gabv9y0g3qlx8sgkq1sn9yl9jd3x8834cmlh67bmz")))) + (properties `((upstream-name . "bench"))) + (build-system r-build-system) + (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble)) + (home-page "https://bench.r-lib.org/") + (synopsis "High precision timing of R expressions") + (description + "This package provides tools to accurately benchmark and analyze execution +times for R expressions.") + (license license:expat))) + (define-public r-benchmarkmedata (package (name "r-benchmarkmedata") From patchwork Tue Oct 31 10:57:27 2023 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: 55722 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 3366727BBEA; Tue, 31 Oct 2023 11:00:15 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 59CCD27BBEB for ; Tue, 31 Oct 2023 11:00:10 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTK-0006Ze-KR; Tue, 31 Oct 2023 06:59:46 -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 1qxmTB-0006T9-82 for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmTA-0003ZW-Qn for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:36 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTi-00062J-Fn; Tue, 31 Oct 2023 07:00:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 09/11] gnu: Add r-piano. 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: Tue, 31 Oct 2023 11:00:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000723136 (code B ref 66843); Tue, 31 Oct 2023 11:00:10 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:07 +0000 Received: from localhost ([127.0.0.1]:47565 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTe-00060w-AG for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:06 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:55281) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTC-0005wq-LN for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:39 -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=1698749938; x=1700564339; bh=/tgCwzksx3xtX/T3RxYkihTrUv4MgC2NY9zzWe2rhJo=; b=nVCePa3D9jKG RRUUKlpHkci4ZtRVQp+IOttAx+sj7i/xwjJ4Az3k54RdyFotdbXtdCKU3SnAg/1U rgRx63gAuX6h1idzzPLYkbUab1rkT5rt3SenK2eNOZ4aS6afElfRuC9dL5kSigYP iAW22QH8ydM5QoCtOT3OF2iHGALqjtE= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1277C160169 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:57 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:57 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:27 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--3.544300-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt7Qq2pZdbx8PwLYk+NSxc5oGAD6h6FZmEV42zm1Zi+MJ0aU Ngwfxxm57MSP7SLpuGCT1CCst0r53BZy+Ejhkj3TdCok3ibXlQQseQVcTRnF2lwV2iaAfSWcURS Scn+QSXhhJCIHRlO51+gtHj7OwNO3+NBysMVGbo0YaTaQ9eDVL29zZ6HeJSUmZUp8mAF7jR12DM Sc2+IemMrbOdRalcTb0g2m3ky1DN85GF2prpCQKvGuKLl9109KCu4dqSXZ4zd8iatREjfpDE8nb 9DwdQ4C2jbSab1pg0UjxFpwn53SOfhj5CZkmSyI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.544300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: E548DDD1D697CE0A9C755A6497610371F288B5400120C91F9A7EB97DAA5336792000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-piano): New variable. Change-Id: I1bc2387563510c47614748423a3b510adc0486aa --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a3606b399..e2fd9c5016 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9109,6 +9109,43 @@ (define-public r-pfamanalyzer domain isotypes from pfam data.") (license license:expat))) +(define-public r-piano + (package + (name "r-piano") + (version "2.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "piano" version)) + (sha256 + (base32 "0rm9afgq4n7yinmx09b0xd17wgzhbswm80vcjmmwxr6fv1741xfy")))) + (properties `((upstream-name . "piano"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dt + r-fgsea + r-gplots + r-htmlwidgets + r-igraph + r-marray + r-relations + r-scales + r-shiny + r-shinydashboard + r-shinyjs + r-visnetwork)) + (native-inputs (list r-knitr)) + (home-page "https://varemo.github.io/piano/") + (synopsis "Platform for integrative analysis of omics data") + (description + "Piano performs gene set analysis using various statistical methods, from +different gene level statistics and a wide range of gene-set collections. The +package contains functions for combining the results of multiple runs of gene +set analyses.") + (license license:gpl2+))) + ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs From patchwork Tue Oct 31 10:57:28 2023 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: 55724 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 C985327BBEA; Tue, 31 Oct 2023 11:00:28 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 5F37327BBE2 for ; Tue, 31 Oct 2023 11:00:28 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTM-0006cW-EG; Tue, 31 Oct 2023 06:59:48 -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 1qxmTB-0006T8-7G for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmT9-0003ZR-Sm for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:36 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTh-000622-Hc; Tue, 31 Oct 2023 07:00:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 10/11] gnu: Add r-coregx. 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: Tue, 31 Oct 2023 11:00:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000623106 (code B ref 66843); Tue, 31 Oct 2023 11:00:09 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:06 +0000 Received: from localhost ([127.0.0.1]:47561 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTd-00060T-3A for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:05 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:43665) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTC-0005x4-GJ for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:39 -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=1698749938; x=1700564339; bh=+DOzaNpeQmNJKcUBYCqDRvlx52OjVCrdC6omV0Ixa2U=; b=YeMMdgd308Fj p+fv92aa0Ulrn/9UEtin+En+1my36dfCrz8jWv5TGe/EX12phAK7D+ezf2g/LZ+R KMBhYNmEHtFprlJH9l6nPDfosphjENEYSAGioNXBEoh9ijxW8PpQKjBMswfk8u9O 0issWkt19IJBLUFq66hDNyFrJi1KIFw= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 9EE5516017D for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:58 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:57 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:28 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--14.023100-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRhItcoSAIccJFYR GbK7nAWgKsykCO9ZPU6fXwOj91l33yGl4XmOxPLZOG5AmSMA4voGIsNQKxyHbqshboLxjPXYs28 FPOedmEpST9wVeygStLmth8cTQ473Q3sOMB3Fk1OLzNWBegCW2wgn7iDBesS3CttcwYNipXxjOl t1Pi553v9BIZrOFM/0+e/ht+ujEJs00RHzmU/HJJhOIk2Jg6W8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--14.023100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: D7315A99F6736E0E4F4095B8608D48859C8D6B9705054678853E808FAACEA8FC2000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-coregx): New variable. Change-Id: Ib54ba3c7bebdcc90748d4e4b0b2ce63b7f0fc1b8 --- gnu/packages/bioconductor.scm | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e2fd9c5016..091cf98b5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4422,6 +4422,52 @@ (define-public r-cellid enrichment in single cell data.") (license license:gpl3))) +(define-public r-coregx + (package + (name "r-coregx") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CoreGx" version)) + (sha256 + (base32 "09pv117g8sxhrij960mparrz1r9vx8s20gmpvn1h667kl1bc0jm9")))) + (properties `((upstream-name . "CoreGx"))) + (build-system r-build-system) + (propagated-inputs + (list r-bench + r-biobase + r-biocgenerics + r-biocparallel + r-bumpymatrix + r-checkmate + r-crayon + r-data-table + r-glue + r-lsa + r-matrixgenerics + r-multiassayexperiment + r-piano + r-rlang + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/CoreGx") + (synopsis + "Classes and functions to serve as the basis for other Gx packages") + (description + "This package provides a collection of functions and classes which serve as +the foundation for our lab's suite of R packages, such as PharmacoGx and RadioGx. +It was created to abstract shared functionality from other lab package releases +to increase ease of maintainability and reduce code repetition in current and +future Gx suite programs. Major features include a @code{CoreSet} class, from +which RadioSet and PharmacoSet are derived, along with get and set methods for +each respective slot. Additional functions related to fitting and plotting dose +response curves, quantifying statistical correlation and calculating +@acronym{AUC, area under the curve} or @acronym{SF, survival fraction} are +included.") + (license license:gpl3+))) + (define-public r-coverageview (package (name "r-coverageview") From patchwork Tue Oct 31 10:57:29 2023 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: 55717 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 9434F27BBEC; Tue, 31 Oct 2023 11:00:04 +0000 (GMT) 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_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 91B3B27BBE2 for ; Tue, 31 Oct 2023 11:00:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qxmTE-0006Us-Po; Tue, 31 Oct 2023 06:59:40 -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 1qxmTB-0006TA-F5 for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:38 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qxmTB-0003Zs-7C for guix-patches@gnu.org; Tue, 31 Oct 2023 06:59:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qxmTi-00062S-T2; Tue, 31 Oct 2023 07:00:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66843] [PATCH 11/11] gnu: Add r-radiogx. 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: Tue, 31 Oct 2023 11:00:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66843 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <66843@debbugs.gnu.org> Cc: Ricardo Wurmus X-Debbugs-Original-Xcc: Ricardo Wurmus Received: via spool by 66843-submit@debbugs.gnu.org id=B66843.169875000823155 (code B ref 66843); Tue, 31 Oct 2023 11:00:10 +0000 Received: (at 66843) by debbugs.gnu.org; 31 Oct 2023 11:00:08 +0000 Received: from localhost ([127.0.0.1]:47568 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTe-000617-U5 for submit@debbugs.gnu.org; Tue, 31 Oct 2023 07:00:07 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:48139) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxmTC-0005xB-Tc for 66843@debbugs.gnu.org; Tue, 31 Oct 2023 06:59:40 -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=1698749939; x=1700564340; bh=hIcf/wDB7WjB/mDQ07RkhLRu6VLfUGN1QxPPauy5fm8=; b=XVyvGW7ZQzaK 68PCSwL5E0h6a7HkRf3mvwQxT4Yw9wmrhc/jCL8iz6r+OnfeDdQv4LTexAug4oSe lbPRq6JrabBvpZoGVRxZzTpdEYZ5UCBXUlaBvPjF7itAJBomtnB4RQeG1zBEkR9K FZ88Wvu0/Md+pTaZNnKRvEZOcS8j5hs= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 2D07F1601A9 for <66843@debbugs.gnu.org>; Tue, 31 Oct 2023 11:58:59 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 11:58:58 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 31 Oct 2023 11:57:29 +0100 Message-ID: <38e1b856e05a09c4d90277f2d78f64f1528ffadf.1698749849.git.madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.41.0 In-Reply-To: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> References: <4d5576bdd09911a6a51bbe87a1b905bd07ca0c4b.1698749849.git.madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-AS-Result: No-10--1.602500-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCTiEPRj9j9rvwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v995kRsYEJuFqY5ZGw7wyeH/2F l7Kds1UCNuhQLalU3H4EqI9LvsCXAHZVDA3E+C7t6qtvKiCnRdgFkGmUzEj/OVUwmVL0cK7NJUQ /LWiKU2VslxAfd+6tXElOOOz3JPpijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7RcGDc Hb4niEwjAOGEc80lEySxrvsbmIlGAv9X15xtOFprzkJV7AWni49t5KqRulQaYNHgmB1rzokMX3H XoffYLYDQMfbCHhtWlkoJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.602500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27968.007 X-TM-SNTS-SMTP: FD946929D8FD16D6E29261E95FAF07F43E3654C642CA07539333E4B6A98085A82000: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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-radiogx): New variable. Change-Id: I8fd06a18bd68f9a3baa2cc129d62aef06528bc97 --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 091cf98b5c..69adea13e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7848,6 +7848,50 @@ (define-public r-r4rna with numerical methods for computing statistics for each.") (license license:gpl3))) +(define-public r-radiogx + (package + (name "r-radiogx") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RadioGx" version)) + (sha256 + (base32 "18zqfnwjil4mv7fgh4wvnniyybmyqkg0hk2wc57rcn0mlppa3602")))) + (properties `((upstream-name . "RadioGx"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biobase + r-biocgenerics + r-biocparallel + r-catools + r-coregx + r-data-table + r-downloader + r-magicaxis + r-matrixstats + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/RadioGx") + (synopsis "Analysis of large-scale radio-genomic data") + (description + "This package is a computational tool box for radio-genomic analysis which +integrates radio-response data, radio-biological modelling and comprehensive +cell line annotations for hundreds of cancer cell lines. The @code{RadioSet} +class enables creation and manipulation of standardized datasets including +information about cancer cells lines, radio-response assays and dose-response +indicators. Included methods allow fitting and plotting dose-response data +using established radio-biological models along with quality control to validate +results. Additional functions related to fitting and plotting dose response +curves, quantifying statistical correlation and calculating @acronym{AUC, area +under the curve} or @acronym{SF, survival fraction} are included.") + (license license:gpl3))) + (define-public r-raggedexperiment (package (name "r-raggedexperiment")