From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:55:22 2017 Received: (at submit) by debbugs.gnu.org; 14 Aug 2017 20:55:22 +0000 Received: from localhost ([127.0.0.1]:36891 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMOQ-0000MU-0p for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:55:22 -0400 Received: from eggs.gnu.org ([208.118.235.92]:35895) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMON-0000MO-MB for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:55:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dhMOH-0007Ee-HO for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:55:14 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:35881) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dhMOH-0007EY-EE for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:55:13 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:55084) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dhMOG-00056Q-Am for guix-patches@gnu.org; Mon, 14 Aug 2017 16:55:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dhMOC-0007Bn-D2 for guix-patches@gnu.org; Mon, 14 Aug 2017 16:55:12 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21090) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1dhMOC-00079x-7C for guix-patches@gnu.org; Mon, 14 Aug 2017 16:55:08 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744103283307.67728031472063; Mon, 14 Aug 2017 13:55:03 -0700 (PDT) From: Ricardo Wurmus To: guix-patches@gnu.org Subject: [PATCH 00/29] More R packages. Date: Mon, 14 Aug 2017 22:54:58 +0200 Message-Id: <20170814205458.10484-1-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) Hi Guix, here is a series of R package definitions. Ricardo Wurmus (29): gnu: Add r-interactivedisplaybase. gnu: Add r-annotationhub. gnu: Add r-auc. gnu: Add r-calibrate. gnu: Add r-shape. gnu: Add r-globaloptions. gnu: Add r-circlize. gnu: Add r-powerlaw. gnu: Add r-png. gnu: Add r-compare. gnu: Add r-dendextend. gnu: Add r-getoptlong. gnu: Add r-fastmatch. gnu: Add r-ff. gnu: Add r-ffbase. gnu: Add r-prettyunits. gnu: Add r-reshape. gnu: Add r-progress. gnu: Add r-ggally. gnu: Add r-proxy. gnu: Add r-sp. gnu: Add r-rook. gnu: Add r-rmtstat. gnu: Add r-lmoments. gnu: Add r-distillery. gnu: Add r-extremes. gnu: Add r-lmtest. gnu: Add r-inline. gnu: Add r-bbmle. gnu/packages/bioinformatics.scm | 58 ++++ gnu/packages/cran.scm | 588 +++++++++++++++++++++++++++++++++++++++- gnu/packages/image.scm | 24 ++ gnu/packages/web.scm | 24 ++ 4 files changed, 693 insertions(+), 1 deletion(-) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:19 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:19 +0000 Received: from localhost ([127.0.0.1]:36903 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQJ-0000Ng-Cu for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:19 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21030) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQH-0000Na-RA for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:18 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744234898618.8677254726393; Mon, 14 Aug 2017 13:57:14 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 01/29] gnu: Add r-interactivedisplaybase. Date: Mon, 14 Aug 2017 22:56:43 +0200 Message-Id: <20170814205711.10797-1-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9d64294e4..717b5acec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9229,6 +9229,30 @@ distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization.") (license license:artistic2.0))) +(define-public r-interactivedisplaybase + (package + (name "r-interactivedisplaybase") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplayBase" version)) + (sha256 + (base32 + "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7")))) + (properties + `((upstream-name . "interactiveDisplayBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-shiny" ,r-shiny))) + (home-page "http://bioconductor.org/packages/interactiveDisplayBase") + (synopsis "Base package for web displays of Bioconductor objects") + (description + "This package contains the basic methods needed to generate interactive +Shiny-based display methods for Bioconductor objects.") + (license license:artistic2.0))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:23 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:24 +0000 Received: from localhost ([127.0.0.1]:36906 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQN-0000Nt-L8 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:23 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21034) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQL-0000Nn-ER for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:21 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744237700731.6682414167037; Mon, 14 Aug 2017 13:57:17 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 02/29] gnu: Add r-annotationhub. Date: Mon, 14 Aug 2017 22:56:44 +0200 Message-Id: <20170814205711.10797-2-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/bioinformatics.scm (r-annotationhub): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 717b5acec..3571cb96c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9253,6 +9253,40 @@ global-scaling and full-quantile normalization.") Shiny-based display methods for Bioconductor objects.") (license license:artistic2.0))) +(define-public r-annotationhub + (package + (name "r-annotationhub") + (version "2.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHub" version)) + (sha256 + (base32 + "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r")))) + (properties `((upstream-name . "AnnotationHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocinstaller" ,r-biocinstaller) + ("r-httr" ,r-httr) + ("r-interactivedisplaybase" ,r-interactivedisplaybase) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (home-page "http://bioconductor.org/packages/AnnotationHub") + (synopsis "Client to access AnnotationHub resources") + (description + "This package provides a client for the Bioconductor AnnotationHub web +resource. The AnnotationHub web resource provides a central location where +genomic files (e.g. VCF, bed, wig) and other resources from standard +locations (e.g. UCSC, Ensembl) can be discovered. The resource includes +metadata about each resource, e.g., a textual description, tags, and date of +modification. The client creates and manages a local cache of files retrieved +by the user, helping with quick and reproducible access.") + (license license:artistic2.0))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:28 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:28 +0000 Received: from localhost ([127.0.0.1]:36910 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQR-0000OC-Un for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:28 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21071) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQQ-0000O1-Ie for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:26 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744240637642.7607567159382; Mon, 14 Aug 2017 13:57:20 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 03/29] gnu: Add r-auc. Date: Mon, 14 Aug 2017 22:56:45 +0200 Message-Id: <20170814205711.10797-3-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-auc): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index feae80111..c874ff880 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -148,3 +148,27 @@ where the bound function accepts additional arguments.") "This package provides an easy way to fill an environment with active bindings that call a C++ function.") (license license:expat))) + +(define-public r-auc + (package + (name "r-auc") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "AUC" version)) + (sha256 + (base32 + "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) + (properties `((upstream-name . "AUC"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/AUC") + (synopsis "Compute the area under the curve of selected measures") + (description + "This package includes functions to compute the area under the curve of +selected measures: the area under the sensitivity curve (AUSEC), the area +under the specificity curve (AUSPC), the area under the accuracy +curve (AUACC), and the area under the receiver operating characteristic +curve (AUROC). The curves can also be visualized. Support for partial areas +is provided.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:28 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:28 +0000 Received: from localhost ([127.0.0.1]:36912 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQS-0000OE-69 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:28 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21050) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQP-0000O0-Vh for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:26 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744243474725.5238914303627; Mon, 14 Aug 2017 13:57:23 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 04/29] gnu: Add r-calibrate. Date: Mon, 14 Aug 2017 22:56:46 +0200 Message-Id: <20170814205711.10797-4-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-calibrate): New variable. --- gnu/packages/cran.scm | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c874ff880..5ec8d4921 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21,7 +21,8 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) - #:use-module (guix build-system r)) + #:use-module (guix build-system r) + #:use-module (gnu packages statistics)) (define-public r-colorspace (package @@ -172,3 +173,24 @@ curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.") (license license:gpl2+))) + +(define-public r-calibrate + (package + (name "r-calibrate") + (version "1.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "calibrate" version)) + (sha256 + (base32 + "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "http://cran.r-project.org/web/packages/calibrate") + (synopsis "Calibration of scatterplot and biplot axes") + (description + "This is a package for drawing calibrated scales with tick marks +on (non-orthogonal) variable vectors in scatterplots and biplots.") + (license license:gpl2))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:32 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:32 +0000 Received: from localhost ([127.0.0.1]:36915 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQV-0000OX-GT for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:31 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21005) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQT-0000OQ-DF for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:29 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744246200868.489031188183; Mon, 14 Aug 2017 13:57:26 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 05/29] gnu: Add r-shape. Date: Mon, 14 Aug 2017 22:56:47 +0200 Message-Id: <20170814205711.10797-5-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-shape): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5ec8d4921..de7c56f6d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -194,3 +194,22 @@ is provided.") "This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.") (license license:gpl2))) + +(define-public r-shape + (package + (name "r-shape") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "shape" version)) + (sha256 + (base32 + "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/shape") + (synopsis "Functions for plotting graphical shapes") + (description + "This package provides functions for plotting graphical shapes such as +ellipses, circles, cylinders, arrows, ...") + (license license:gpl3+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:33 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:33 +0000 Received: from localhost ([127.0.0.1]:36919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQX-0000Oj-9e for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:33 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21057) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQV-0000OW-8t for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:31 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744249035828.2598127197643; Mon, 14 Aug 2017 13:57:29 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 06/29] gnu: Add r-globaloptions. Date: Mon, 14 Aug 2017 22:56:48 +0200 Message-Id: <20170814205711.10797-6-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-globaloptions): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index de7c56f6d..7179ceb5c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -213,3 +213,23 @@ on (non-orthogonal) variable vectors in scatterplots and biplots.") "This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...") (license license:gpl3+))) + +(define-public r-globaloptions + (package + (name "r-globaloptions") + (version "0.0.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "GlobalOptions" version)) + (sha256 + (base32 + "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0")))) + (properties `((upstream-name . "GlobalOptions"))) + (build-system r-build-system) + (home-page "https://github.com/jokergoo/GlobalOptions") + (synopsis "Generate functions to get or set global options") + (description + "This package provides more controls on the option values such as +validation and filtering on the values, making options invisible or private.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:37 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:37 +0000 Received: from localhost ([127.0.0.1]:36923 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQb-0000P2-Gn for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:37 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21083) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQZ-0000Oq-KG for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:35 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 150274425175844.74085385664307; Mon, 14 Aug 2017 13:57:31 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 07/29] gnu: Add r-circlize. Date: Mon, 14 Aug 2017 22:56:49 +0200 Message-Id: <20170814205711.10797-7-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-circlize): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7179ceb5c..0fc158768 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -233,3 +233,33 @@ ellipses, circles, cylinders, arrows, ...") "This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private.") (license license:gpl2+))) + +(define-public r-circlize + (package + (name "r-circlize") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "circlize" version)) + (sha256 + (base32 + "0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-colorspace" ,r-colorspace) + ("r-globaloptions" ,r-globaloptions) + ("r-shape" ,r-shape))) + (home-page "https://github.com/jokergoo/circlize") + (synopsis "Circular visualization") + (description + "Circular layout is an efficient way for the visualization of huge +amounts of information. This package provides an implementation of circular +layout generation in R as well as an enhancement of available software. The +flexibility of the package is based on the usage of low-level graphics +functions such that self-defined high-level graphics can be easily implemented +by users for specific purposes. Together with the seamless connection between +the powerful computational and visual environment in R, it gives users more +convenience and freedom to design figures for better understanding complex +patterns behind multiple dimensional data.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:40 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:40 +0000 Received: from localhost ([127.0.0.1]:36925 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQd-0000PA-PT for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:39 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21068) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQb-0000Ow-3h for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:37 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744254477200.06941726915227; Mon, 14 Aug 2017 13:57:34 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 08/29] gnu: Add r-powerlaw. Date: Mon, 14 Aug 2017 22:56:50 +0200 Message-Id: <20170814205711.10797-8-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-powerlaw): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0fc158768..83f246d4d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -263,3 +263,28 @@ the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.") (license license:gpl2+))) + +(define-public r-powerlaw + (package + (name "r-powerlaw") + (version "0.70.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "poweRlaw" version)) + (sha256 + (base32 + "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh")))) + (properties `((upstream-name . "poweRlaw"))) + (build-system r-build-system) + (propagated-inputs + `(("r-vgam" ,r-vgam))) + (home-page "https://github.com/csgillespie/poweRlaw") + (synopsis "Tools for the analysis of heavy tailed distributions") + (description + "This package provides an implementation of maximum likelihood estimators +for a variety of heavy tailed distributions, including both the discrete and +continuous power law distributions. Additionally, a goodness-of-fit based +approach is used to estimate the lower cut-off for the scaling region.") + ;; Any of these GPL versions. + (license (list license:gpl2 license:gpl3)))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:42 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:42 +0000 Received: from localhost ([127.0.0.1]:36928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQg-0000PM-0U for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:42 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQd-0000P9-SL for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:40 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744257296891.386433626322; Mon, 14 Aug 2017 13:57:37 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 09/29] gnu: Add r-png. Date: Mon, 14 Aug 2017 22:56:51 +0200 Message-Id: <20170814205711.10797-9-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/image.scm (r-png): New variable. --- gnu/packages/image.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 95a4c91b1..ad9ff4ee0 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -61,6 +61,7 @@ #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system r) #:use-module (srfi srfi-1)) (define-public libpng @@ -176,6 +177,29 @@ APNG patch provides APNG support to libpng.") (sha256 (base32 "1n2lrzjkm5jhfg2bs10q398lkwbbx742fi27zgdgx0x23zhj0ihg")))))) +(define-public r-png + (package + (name "r-png") + (version "0.1-7") + (source (origin + (method url-fetch) + (uri (cran-uri "png" version)) + (sha256 + (base32 + "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) + (build-system r-build-system) + (inputs + `(("libpng" ,libpng) + ("zlib" ,zlib))) + (home-page "http://www.rforge.net/png/") + (synopsis "Read and write PNG images") + (description + "This package provides an easy and simple way to read, write and display +bitmap images stored in the PNG format. It can read and write both files and +in-memory raw vectors.") + ;; Any of these GPL versions. + (license (list license:gpl2 license:gpl3)))) + (define-public pngcrunch (package (name "pngcrunch") -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:46 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:46 +0000 Received: from localhost ([127.0.0.1]:36931 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQk-0000PZ-83 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:46 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21082) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQi-0000PT-84 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:44 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744260012863.8736327853306; Mon, 14 Aug 2017 13:57:40 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 10/29] gnu: Add r-compare. Date: Mon, 14 Aug 2017 22:56:52 +0200 Message-Id: <20170814205711.10797-10-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-compare): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 83f246d4d..25f52a143 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -288,3 +288,24 @@ continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.") ;; Any of these GPL versions. (license (list license:gpl2 license:gpl3)))) + +(define-public r-compare + (package + (name "r-compare") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "compare" version)) + (sha256 + (base32 + "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/compare") + (synopsis "Comparing objects for differences") + (description + "This package provides functions to compare a model object to a +comparison object. If the objects are not identical, the functions can be +instructed to explore various modifications of the objects (e.g., sorting +rows, dropping names) to see if the modified versions are identical.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:47 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:47 +0000 Received: from localhost ([127.0.0.1]:36934 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQl-0000Pn-GZ for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:47 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21007) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQk-0000Pa-M3 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:46 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744262964677.7409043934725; Mon, 14 Aug 2017 13:57:42 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 11/29] gnu: Add r-dendextend. Date: Mon, 14 Aug 2017 22:56:53 +0200 Message-Id: <20170814205711.10797-11-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-dendextend): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 25f52a143..b2502e182 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -309,3 +309,32 @@ comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.") (license license:gpl2+))) + +(define-public r-dendextend + (package + (name "r-dendextend") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "dendextend" version)) + (sha256 + (base32 + "04jz58apibfrkjcrdmw2hmsav6qpb5cs6qdai81k1v1iznfcya42")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fpc" ,r-fpc) + ("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-viridis" ,r-viridis) + ("r-whisker" ,r-whisker))) + (home-page "https://cran.r-project.org/web/packages/dendextend") + (synopsis "Extending 'dendrogram' functionality in R") + (description + "This package offers a set of functions for extending @code{dendrogram} +objects in R, letting you visualize and compare trees of hierarchical +clusterings. You can adjust a tree's graphical parameters (the color, size, +type, etc of its branches, nodes and labels) and visually and statistically +compare different dendrograms to one another.") + ;; Any of these versions + (license (list license:gpl2 license:gpl3)))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:51 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:51 +0000 Received: from localhost ([127.0.0.1]:36937 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQo-0000Q0-P1 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:50 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21032) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQl-0000Pm-EF for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:47 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744265776185.26369483257383; Mon, 14 Aug 2017 13:57:45 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 12/29] gnu: Add r-getoptlong. Date: Mon, 14 Aug 2017 22:56:54 +0200 Message-Id: <20170814205711.10797-12-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-getoptlong): New variable. --- gnu/packages/cran.scm | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b2502e182..abdff54db 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22,7 +22,9 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) - #:use-module (gnu packages statistics)) + #:use-module (gnu packages perl) + #:use-module (gnu packages statistics) + #:use-module (gnu packages web)) (define-public r-colorspace (package @@ -338,3 +340,29 @@ type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) + +(define-public r-getoptlong + (package + (name "r-getoptlong") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "GetoptLong" version)) + (sha256 + (base32 + "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm")))) + (properties `((upstream-name . "GetoptLong"))) + (build-system r-build-system) + (inputs + `(("perl" ,perl))) + (propagated-inputs + `(("r-globaloptions" ,r-globaloptions) + ("r-rjson" ,r-rjson))) + (home-page "https://github.com/jokergoo/GetoptLong") + (synopsis "Parsing command-line arguments and variable interpolation") + (description + "This is yet another command-line argument parser which wraps the +powerful Perl module @code{Getopt::Long} and with some adaptation for easier +use in R. It also provides a simple way for variable interpolation in R.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:53 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:53 +0000 Received: from localhost ([127.0.0.1]:36941 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQr-0000QC-1p for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:53 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21100) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQo-0000Pz-N4 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:51 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744268665525.206818136141; Mon, 14 Aug 2017 13:57:48 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 13/29] gnu: Add r-fastmatch. Date: Mon, 14 Aug 2017 22:56:55 +0200 Message-Id: <20170814205711.10797-13-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-fastmatch): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index abdff54db..c959beee0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -366,3 +366,24 @@ compare different dendrograms to one another.") powerful Perl module @code{Getopt::Long} and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.") (license license:gpl2+))) + +(define-public r-fastmatch + (package + (name "r-fastmatch") + (version "1.1-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastmatch" version)) + (sha256 + (base32 + "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) + (build-system r-build-system) + (home-page "http://www.rforge.net/fastmatch") + (synopsis "Fast match function") + (description + "This package provides a fast @code{match} replacement for cases that +require repeated look-ups. It is slightly faster that R's built-in +@code{match} function on first match against a table, but extremely fast on +any subsequent lookup as it keeps the hash table in memory.") + (license license:gpl2))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:57 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:57 +0000 Received: from localhost ([127.0.0.1]:36944 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQv-0000QP-BV for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:57 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21015) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQt-0000QJ-Ej for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:55 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744271489479.0593935927093; Mon, 14 Aug 2017 13:57:51 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 14/29] gnu: Add r-ff. Date: Mon, 14 Aug 2017 22:56:56 +0200 Message-Id: <20170814205711.10797-14-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-ff): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c959beee0..b1cb0c409 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -387,3 +387,24 @@ require repeated look-ups. It is slightly faster that R's built-in @code{match} function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.") (license license:gpl2))) + +(define-public r-ff + (package + (name "r-ff") + (version "2.2-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "ff" version)) + (sha256 + (base32 + "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb")))) + (build-system r-build-system) + (propagated-inputs `(("r-bit" ,r-bit))) + (home-page "http://ff.r-forge.r-project.org/") + (synopsis "Memory-efficient storage of large data on disk and access functions") + (description + "This package provides data structures that are stored on disk but +behave (almost) as if they were in RAM by transparently mapping only a section +in main memory.") + (license license:gpl2))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:57:59 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:57:59 +0000 Received: from localhost ([127.0.0.1]:36947 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQx-0000Qc-JP for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:59 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21100) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQw-0000QW-At for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:57:58 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 150274427419398.89713439735874; Mon, 14 Aug 2017 13:57:54 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 15/29] gnu: Add r-ffbase. Date: Mon, 14 Aug 2017 22:56:57 +0200 Message-Id: <20170814205711.10797-15-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-ffbase): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b1cb0c409..80ed0bc26 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -408,3 +408,26 @@ any subsequent lookup as it keeps the hash table in memory.") behave (almost) as if they were in RAM by transparently mapping only a section in main memory.") (license license:gpl2))) + +(define-public r-ffbase + (package + (name "r-ffbase") + (version "0.12.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ffbase" version)) + (sha256 + (base32 + "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bit" ,r-bit) + ("r-fastmatch" ,r-fastmatch) + ("r-ff" ,r-ff))) + (home-page "http://github.com/edwindj/ffbase") + (synopsis "Basic statistical functions for package 'ff'") + (description + "This package extends the out of memory vectors of @code{ff} with +statistical functions and other utilities to ease their usage.") + (license license:gpl3))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:03 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:03 +0000 Received: from localhost ([127.0.0.1]:36953 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMR0-0000RJ-QT for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:03 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21110) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMQx-0000Qd-V8 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:00 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744276900455.87655286966026; Mon, 14 Aug 2017 13:57:56 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 16/29] gnu: Add r-prettyunits. Date: Mon, 14 Aug 2017 22:56:58 +0200 Message-Id: <20170814205711.10797-16-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-prettyunits): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 80ed0bc26..637ddfe4f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -431,3 +431,25 @@ in main memory.") "This package extends the out of memory vectors of @code{ff} with statistical functions and other utilities to ease their usage.") (license license:gpl3))) + +(define-public r-prettyunits + (package + (name "r-prettyunits") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "prettyunits" version)) + (sha256 + (base32 + "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-magrittr" ,r-magrittr))) + (home-page "https://github.com/gaborcsardi/prettyunits") + (synopsis "Pretty, human readable formatting of quantities") + (description + "This package provides tools for pretty, human readable formatting of +quantities.") + (license license:expat))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:05 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:05 +0000 Received: from localhost ([127.0.0.1]:36960 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMR3-0000S1-3h for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:05 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21106) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMR1-0000RM-B4 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:03 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 150274427971916.10837415782862; Mon, 14 Aug 2017 13:57:59 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 17/29] gnu: Add r-reshape. Date: Mon, 14 Aug 2017 22:56:59 +0200 Message-Id: <20170814205711.10797-17-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-reshape): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 637ddfe4f..fa75317e9 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -453,3 +453,25 @@ statistical functions and other utilities to ease their usage.") "This package provides tools for pretty, human readable formatting of quantities.") (license license:expat))) + +(define-public r-reshape + (package + (name "r-reshape") + (version "0.8.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "reshape" version)) + (sha256 + (base32 + "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp))) + (home-page "http://had.co.nz/reshape") + (synopsis "Flexibly reshape data") + (description + "Flexibly restructure and aggregate data using just two functions: +@code{melt} and @code{cast}. This package provides them.") + (license license:expat))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:07 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:07 +0000 Received: from localhost ([127.0.0.1]:36968 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMR5-0000Sk-Ei for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:07 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21057) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMR3-0000S5-El for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:05 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744282442347.55478589611744; Mon, 14 Aug 2017 13:58:02 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 18/29] gnu: Add r-progress. Date: Mon, 14 Aug 2017 22:57:00 +0200 Message-Id: <20170814205711.10797-18-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-progress): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fa75317e9..d88202ca5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -475,3 +475,27 @@ quantities.") "Flexibly restructure and aggregate data using just two functions: @code{melt} and @code{cast}. This package provides them.") (license license:expat))) + +(define-public r-progress + (package + (name "r-progress") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "progress" version)) + (sha256 + (base32 + "1fxakchfjr5vj59s9sxynd7crpz97xj42438rmkhkf3rjpyspx59")))) + (build-system r-build-system) + (propagated-inputs + `(("r-prettyunits" ,r-prettyunits) + ("r-r6" ,r-r6))) + (home-page "https://github.com/gaborcsardi/progress") + (synopsis "Terminal progress bars") + (description + "This package provides configurable progress bars. They may include +percentage, elapsed time, and/or the estimated completion time. They work in +terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The +package also provides a C++ API, that works with or without Rcpp.") + (license license:expat))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:12 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:13 +0000 Received: from localhost ([127.0.0.1]:36979 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRA-0000Tt-Nw for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:12 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21032) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMR8-0000TL-R7 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:11 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744287841301.5124543807465; Mon, 14 Aug 2017 13:58:07 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 20/29] gnu: Add r-proxy. Date: Mon, 14 Aug 2017 22:57:02 +0200 Message-Id: <20170814205711.10797-20-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-proxy): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 35d096514..752649337 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -530,3 +530,23 @@ these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.") (license license:gpl2+))) + +(define-public r-proxy + (package + (name "r-proxy") + (version "0.4-17") + (source + (origin + (method url-fetch) + (uri (cran-uri "proxy" version)) + (sha256 + (base32 + "0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/proxy") + (synopsis "Distance and similarity measures") + (description + "This package provides an extensible framework for the efficient +calculation of auto- and cross-proximities, along with implementations of the +most popular ones.") + (license license:gpl2))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:15 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:15 +0000 Received: from localhost ([127.0.0.1]:36982 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRD-0000U6-05 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:15 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21115) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRA-0000Tn-8d for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:12 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744285145998.2026845322684; Mon, 14 Aug 2017 13:58:05 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 19/29] gnu: Add r-ggally. Date: Mon, 14 Aug 2017 22:57:01 +0200 Message-Id: <20170814205711.10797-19-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-ggally): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d88202ca5..35d096514 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -499,3 +499,34 @@ percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The package also provides a C++ API, that works with or without Rcpp.") (license license:expat))) + +(define-public r-ggally + (package + (name "r-ggally") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "GGally" version)) + (sha256 + (base32 + "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b")))) + (properties `((upstream-name . "GGally"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape" ,r-reshape))) + (home-page "https://ggobi.github.io/ggally") + (synopsis "Extension to ggplot2") + (description + "The R package ggplot2 is a plotting system based on the grammar of +graphics. GGally extends ggplot2 by adding several functions to reduce the +complexity of combining geometric objects with transformed data. Some of +these functions include a pairwise plot matrix, a two group pairwise plot +matrix, a parallel coordinates plot, a survival plot, and several functions to +plot networks.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:15 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:16 +0000 Received: from localhost ([127.0.0.1]:36984 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRD-0000U8-Mv for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:15 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21129) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRC-0000U0-4e for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:14 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744290918544.8878954973676; Mon, 14 Aug 2017 13:58:10 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 21/29] gnu: Add r-sp. Date: Mon, 14 Aug 2017 22:57:03 +0200 Message-Id: <20170814205711.10797-21-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-sp): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 752649337..811dd9ba7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -550,3 +550,27 @@ plot networks.") calculation of auto- and cross-proximities, along with implementations of the most popular ones.") (license license:gpl2))) + +(define-public r-sp + (package + (name "r-sp") + (version "1.2-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sp" version)) + (sha256 + (base32 + "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/sp") + (synopsis "Classes and methods for spatial data") + (description + "This package provides classes and methods for spatial data; the classes +document where the spatial location information resides, for 2D or 3D data. +Utility functions are provided, e.g. for plotting data as maps, spatial +selection, as well as methods for retrieving coordinates, for subsetting, +print, summary, etc.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:19 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:19 +0000 Received: from localhost ([127.0.0.1]:36987 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRG-0000UQ-Uk for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:19 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21118) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRE-0000UK-Nf for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:16 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744293742488.3775554882691; Mon, 14 Aug 2017 13:58:13 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 22/29] gnu: Add r-rook. Date: Mon, 14 Aug 2017 22:57:04 +0200 Message-Id: <20170814205711.10797-22-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/web.scm (r-rook): New variable. --- gnu/packages/web.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 5459a3051..2649d68a2 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4879,3 +4879,27 @@ responsive, and powerful applications with minimal effort.") communicate with each other, with Shiny or without (i.e. static @code{.html} files). It currently supports linked brushing and filtering.") (license l:expat))) + +(define-public r-rook + (package + (name "r-rook") + (version "1.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rook" version)) + (sha256 + (base32 + "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) + (properties `((upstream-name . "Rook"))) + (build-system r-build-system) + (propagated-inputs `(("r-brew" ,r-brew))) + (home-page "http://cran.r-project.org/web/packages/Rook") + (synopsis "Web server interface for R") + (description + "This package contains the Rook specification and convenience software +for building and running Rook applications. A Rook application is an R +reference class object that implements a @code{call} method or an R closure +that takes exactly one argument, an environment, and returns a list with three +named elements: the @code{status}, the @code{headers}, and the @code{body}.") + (license l:gpl2))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:23 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:23 +0000 Received: from localhost ([127.0.0.1]:36991 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRL-0000Ue-8q for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:23 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21121) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRJ-0000UX-0t for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:21 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 150274429646395.19536122037243; Mon, 14 Aug 2017 13:58:16 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 23/29] gnu: Add r-rmtstat. Date: Mon, 14 Aug 2017 22:57:05 +0200 Message-Id: <20170814205711.10797-23-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-rmtstat): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 811dd9ba7..88e275c73 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -574,3 +574,24 @@ Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.") (license license:gpl2+))) + +(define-public r-rmtstat + (package + (name "r-rmtstat") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "RMTstat" version)) + (sha256 + (base32 + "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) + (properties `((upstream-name . "RMTstat"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/RMTstat") + (synopsis "Distributions, statistics and tests derived from random matrix theory") + (description + "This package provides functions for working with the Tracy-Widom laws +and other distributions related to the eigenvalues of large Wishart +matrices.") + (license license:bsd-3))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:24 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:24 +0000 Received: from localhost ([127.0.0.1]:36994 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRM-0000Ur-Hg for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:24 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21079) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRL-0000Uf-JQ for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:24 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744302001990.1270055788362; Mon, 14 Aug 2017 13:58:22 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 25/29] gnu: Add r-distillery. Date: Mon, 14 Aug 2017 22:57:07 +0200 Message-Id: <20170814205711.10797-25-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-distillery): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7bf8e1e13..024796313 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -617,3 +617,24 @@ L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.") (license license:gpl2))) + +(define-public r-distillery + (package + (name "r-distillery") + (version "1.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "distillery" version)) + (sha256 + (base32 + "12m4cacvc18fd3aayc8iih5q6bwsmvf29b55fwp7vs8wp1h8nd8c")))) + (build-system r-build-system) + (home-page "http://www.ral.ucar.edu/staff/ericg") + (synopsis "Functions for confidence intervals and object information") + (description + "This package provides some very simple method functions for confidence +interval calculation and to distill pertinent information from a potentially +complex object; primarily used in common with the packages extRemes and +SpatialVx.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:30 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:30 +0000 Received: from localhost ([127.0.0.1]:36997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRP-0000V4-P1 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:30 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21143) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRJ-0000UZ-Il for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:26 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744299170780.4701620600222; Mon, 14 Aug 2017 13:58:19 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 24/29] gnu: Add r-lmoments. Date: Mon, 14 Aug 2017 22:57:06 +0200 Message-Id: <20170814205711.10797-24-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-lmoments): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 88e275c73..7bf8e1e13 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -595,3 +595,25 @@ print, summary, etc.") and other distributions related to the eigenvalues of large Wishart matrices.") (license license:bsd-3))) + +(define-public r-lmoments + (package + (name "r-lmoments") + (version "1.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "Lmoments" version)) + (sha256 + (base32 + "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79")))) + (properties `((upstream-name . "Lmoments"))) + (build-system r-build-system) + (home-page "http://www.tilastotiede.fi/juha_karvanen.html") + (synopsis "L-moments and quantile mixtures") + (description + "This package contains functions to estimate L-moments and trimmed +L-moments from the data. It also contains functions to estimate the +parameters of the normal polynomial quantile mixture and the Cauchy polynomial +quantile mixture from L-moments and trimmed L-moments.") + (license license:gpl2))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:30 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:30 +0000 Received: from localhost ([127.0.0.1]:36999 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRS-0000VB-4K for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:30 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21132) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRP-0000V3-K7 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:27 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744304693764.4937208675354; Mon, 14 Aug 2017 13:58:24 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 26/29] gnu: Add r-extremes. Date: Mon, 14 Aug 2017 22:57:08 +0200 Message-Id: <20170814205711.10797-26-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-extremes): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 024796313..b1eb91345 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -638,3 +638,28 @@ interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.") (license license:gpl2+))) + +(define-public r-extremes + (package + (name "r-extremes") + (version "2.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "extRemes" version)) + (sha256 + (base32 + "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm")))) + (properties `((upstream-name . "extRemes"))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-distillery" ,r-distillery) + ("r-lmoments" ,r-lmoments))) + (home-page "http://www.assessment.ucar.edu/toolkit/") + (synopsis "Extreme value analysis") + (description + "ExtRemes is a suite of functions for carrying out analyses on the +extreme values of a process of interest; be they block maxima over long blocks +or excesses over a high threshold.") + (license license:gpl2+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:33 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:33 +0000 Received: from localhost ([127.0.0.1]:37004 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRV-0000VU-B4 for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:33 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21139) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRT-0000VN-V2 for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:32 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 15027443073901012.8392263443534; Mon, 14 Aug 2017 13:58:27 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 27/29] gnu: Add r-lmtest. Date: Mon, 14 Aug 2017 22:57:09 +0200 Message-Id: <20170814205711.10797-27-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-lmtest): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b1eb91345..8200ccfaf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22,6 +22,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages gcc) #:use-module (gnu packages perl) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -663,3 +664,28 @@ SpatialVx.") extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.") (license license:gpl2+))) + +(define-public r-lmtest + (package + (name "r-lmtest") + (version "0.9-35") + (source + (origin + (method url-fetch) + (uri (cran-uri "lmtest" version)) + (sha256 + (base32 + "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-zoo" ,r-zoo))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/lmtest") + (synopsis "Testing linear regression models") + (description + "This package provides a collection of tests, data sets, and examples for +diagnostic checking in linear regression models. Furthermore, some generic +tools for inference in parametric models are provided.") + ;; Either version is okay + (license (list license:gpl2 license:gpl3)))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:35 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:36 +0000 Received: from localhost ([127.0.0.1]:37008 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRX-0000Vm-Lc for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:35 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21004) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRV-0000VT-EO for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:33 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744310098125.08106580728031; Mon, 14 Aug 2017 13:58:30 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 28/29] gnu: Add r-inline. Date: Mon, 14 Aug 2017 22:57:10 +0200 Message-Id: <20170814205711.10797-28-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-inline): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8200ccfaf..9e50eed3c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -689,3 +689,23 @@ diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.") ;; Either version is okay (license (list license:gpl2 license:gpl3)))) + +(define-public r-inline + (package + (name "r-inline") + (version "0.3.14") + (source (origin + (method url-fetch) + (uri (cran-uri "inline" version)) + (sha256 + (base32 + "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/inline") + (synopsis "Functions to inline C, C++, Fortran function calls from R") + (description + "This package provides functionality to dynamically define R functions +and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and +@code{.Call} calling conventions.") + ;; Any version of the LGPL. + (license license:lgpl3+))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 14 16:58:36 2017 Received: (at 28089) by debbugs.gnu.org; 14 Aug 2017 20:58:36 +0000 Received: from localhost ([127.0.0.1]:37010 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRX-0000Vo-SK for submit@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:36 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21141) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dhMRW-0000Vb-4M for 28089@debbugs.gnu.org; Mon, 14 Aug 2017 16:58:34 -0400 Received: from localhost (port-92-200-82-5.dynamic.qsc.de [92.200.82.5]) by mx.zohomail.com with SMTPS id 1502744312913956.1738134280059; Mon, 14 Aug 2017 13:58:32 -0700 (PDT) From: Ricardo Wurmus To: 28089@debbugs.gnu.org Subject: [PATCH 29/29] gnu: Add r-bbmle. Date: Mon, 14 Aug 2017 22:57:11 +0200 Message-Id: <20170814205711.10797-29-rekado@elephly.net> X-Mailer: git-send-email 2.13.3 In-Reply-To: <20170814205711.10797-1-rekado@elephly.net> References: <20170814205711.10797-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * gnu/packages/cran.scm (r-bbmle): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9e50eed3c..e604799c4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -709,3 +709,28 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and @code{.Call} calling conventions.") ;; Any version of the LGPL. (license license:lgpl3+))) + +(define-public r-bbmle + (package + (name "r-bbmle") + (version "1.0.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "bbmle" version)) + (sha256 + (base32 + "014h6mw16gv4acs2p78dy7lla7s428n633aybsb1mbi6250dg0p8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-numderiv" ,r-numderiv))) + (home-page "http://cran.r-project.org/web/packages/bbmle") + (synopsis "Tools for General Maximum Likelihood Estimation") + (description + "Methods and functions for fitting maximum likelihood models in R. This +package modifies and extends the @code{mle} classes in the @code{stats4} +package.") + ;; Any version of the GPL + (license (list license:gpl2 license:gpl3)))) -- 2.13.3 From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 17 12:03:58 2017 Received: (at 28089-done) by debbugs.gnu.org; 17 Aug 2017 16:03:58 +0000 Received: from localhost ([127.0.0.1]:42992 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1diNH4-0001mu-9N for submit@debbugs.gnu.org; Thu, 17 Aug 2017 12:03:58 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21010) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1diNH2-0001mn-W1 for 28089-done@debbugs.gnu.org; Thu, 17 Aug 2017 12:03:57 -0400 Received: from localhost (141.80.245.197 [141.80.245.197]) by mx.zohomail.com with SMTPS id 1502985835138449.71003357699215; Thu, 17 Aug 2017 09:03:55 -0700 (PDT) References: <20170814205711.10797-1-rekado@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: 28089-done@debbugs.gnu.org Subject: Re: [PATCH 01/29] gnu: Add r-interactivedisplaybase. In-reply-to: <20170814205711.10797-1-rekado@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 17 Aug 2017 18:03:52 +0200 Message-ID: <874lt6ji53.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 28089-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) I’ve pushed these patches to master. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Fri Jun 13 10:49:25 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 15 Sep 2017 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator