diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1101 |
1 files changed, 1100 insertions, 1 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 423bb5b54f..847e3ccacb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com> @@ -10,6 +10,8 @@ ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com> +;;; Copyright © 2018 Leo Famulari <leo@famulari.name> +;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,10 +32,14 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages algebra) #:use-module (gnu packages base) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) + #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages gl) @@ -41,6 +47,8 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages haskell) #:use-module (gnu packages image) + #:use-module (gnu packages javascript) + #:use-module (gnu packages lisp) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -276,6 +284,642 @@ the embedded @code{RapidXML} C++ library.") into a pipeline of data manipulation and visualisation.") (license license:gpl3))) +(define-public r-httpuv + (package + (name "r-httpuv") + (version "1.4.5") + (source (origin + (method url-fetch) + (uri (cran-uri "httpuv" version)) + (sha256 + (base32 + "1ddpcarzf694h0gy5pdz7l5glqfv4hr9dmxb4vw7yqd0bga174gi")))) + (build-system r-build-system) + (native-inputs + `(("r-rcpp" ,r-rcpp) + ("pkg-config" ,pkg-config))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-later" ,r-later) + ("r-promises" ,r-promises))) + (home-page "https://github.com/rstudio/httpuv") + (synopsis "HTTP and WebSocket server library for R") + (description + "The httpuv package provides low-level socket and protocol support for +handling HTTP and WebSocket requests directly from within R. It is primarily +intended as a building block for other packages, rather than making it +particularly easy to create complete web applications using httpuv alone.") + ;; This package includes third-party code that was originally released + ;; under various non-copyleft licenses. Full licensing information can be + ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE + (license license:gpl3+))) + +(define-public r-jsonlite + (package + (name "r-jsonlite") + (version "1.5") + (source (origin + (method url-fetch) + (uri (cran-uri "jsonlite" version)) + (sha256 + (base32 + "00lfg464jhf7k01bal9pcjvbdf5cxk6xi2h46hccp1x3h883g434")))) + (build-system r-build-system) + (home-page "http://arxiv.org/abs/1403.2805") + (synopsis "Robust, high performance JSON parser and generator for R") + (description + "The jsonlite package provides a fast JSON parser and generator optimized +for statistical data and the web. It offers flexible, robust, high +performance tools for working with JSON in R and is particularly powerful for +building pipelines and interacting with a web API. In addition to converting +JSON data from/to R objects, jsonlite contains functions to stream, validate, +and prettify JSON data. The unit tests included with the package verify that +all edge cases are encoded and decoded consistently for use with dynamic data +in systems and applications.") + (license license:expat))) + +(define-public r-servr + (package + (name "r-servr") + (version "0.11") + (source (origin + (method url-fetch) + (uri (cran-uri "servr" version)) + (sha256 + (base32 + "0yj3p1risf269n25dd56lqv82dsxv6a0aq4bcc1ddn9wv7h2xdfi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-httpuv" ,r-httpuv) + ("r-jsonlite" ,r-jsonlite) + ("r-mime" ,r-mime) + ("r-xfun" ,r-xfun))) + (home-page "https://github.com/yihui/servr") + (synopsis "Simple HTTP server to serve static files or dynamic documents") + (description + "Servr provides an HTTP server in R to serve static files, or dynamic +documents that can be converted to HTML files (e.g., R Markdown) under a given +directory.") + (license license:expat))) + +(define-public r-htmltools + (package + (name "r-htmltools") + (version "0.3.6") + (source (origin + (method url-fetch) + (uri (cran-uri "htmltools" version)) + (sha256 + (base32 + "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/rstudio/htmltools/pull/68 + ;; The resource files are in the store and have mode 444. After + ;; copying the files R fails to remove them again because it doesn't + ;; have write access to them. + (add-after 'unpack 'copy-files-without-mode + (lambda _ + (substitute* "R/html_dependency.R" + (("file.copy\\(from, to, " prefix) + (string-append prefix + "copy.mode = FALSE, "))) + #t))))) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/htmltools") + (synopsis "R tools for HTML") + (description + "This package provides tools for HTML generation and output in R.") + (license license:expat))) + +(define-public r-htmlwidgets + (package + (name "r-htmlwidgets") + (version "1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "htmlwidgets" version)) + (sha256 + (base32 + "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i")))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-yaml" ,r-yaml))) + (home-page "https://github.com/ramnathv/htmlwidgets") + (synopsis "HTML Widgets for R") + (description + "HTML widgets is a framework for creating HTML widgets that render in +various contexts including the R console, R Markdown documents, and Shiny web +applications.") + (license license:expat))) + +(define-public r-htmltable + (package + (name "r-htmltable") + (version "1.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "htmlTable" version)) + (sha256 + (base32 + "1n5136vb7mi4rxl5jgwdmdhn4mwv2pcqyw2mrj406ih4hy6hpxa2")))) + (properties `((upstream-name . "htmlTable"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-rstudioapi" ,r-rstudioapi) + ("r-stringr" ,r-stringr))) + (home-page "http://gforge.se/packages/") + (synopsis "Advanced tables for Markdown/HTML") + (description + "This package provides functions to build tables with advanced layout +elements such as row spanners, column spanners, table spanners, zebra +striping, and more. While allowing advanced layout, the underlying +CSS-structure is simple in order to maximize compatibility with word +processors such as LibreOffice. The package also contains a few text +formatting functions that help outputting text compatible with HTML or +LaTeX.") + (license license:gpl3+))) + +(define-public r-curl + (package + (name "r-curl") + (version "3.2") + (source (origin + (method url-fetch) + (uri (cran-uri "curl" version)) + (sha256 + (base32 + "15hmy71310hnf9yqvz0icx4cq939gv6iqaifzlfdh2ia8akawdhn")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; The environment variable CURL_CA_BUNDLE is only respected when + ;; running Windows, so we disable the platform checks. + ;; This can be removed once the libcurl has been patched. + (add-after 'unpack 'allow-CURL_CA_BUNDLE + (lambda _ + (substitute* "R/onload.R" + (("if \\(!grepl\\(\"mingw\".*") + "if (FALSE)\n")) + (substitute* "src/handle.c" + (("#ifdef _WIN32") "#if 1")) + #t))))) + (inputs + `(("libcurl" ,curl))) + (home-page "https://github.com/jeroenooms/curl") + (synopsis "HTTP client for R") + (description + "The @code{curl()} and @code{curl_download()} functions provide highly +configurable drop-in replacements for base @code{url()} and +@code{download.file()} with better performance, support for encryption, gzip +compression, authentication, and other @code{libcurl} goodies. The core of +the package implements a framework for performing fully customized requests +where data can be processed either in memory, on disk, or streaming via the +callback or connection interfaces.") + (license license:expat))) + +(define-public r-hwriter + (package + (name "r-hwriter") + (version "1.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "hwriter" version)) + (sha256 + (base32 + "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/hwriter") + (synopsis "Output R objects in HTML format") + (description + "This package provides easy-to-use and versatile functions to output R +objects in HTML format.") + (license license:lgpl2.1+))) + +(define-public r-rjson + (package + (name "r-rjson") + (version "0.2.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "rjson" version)) + (sha256 + (base32 + "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/rjson") + (synopsis "JSON library for R") + (description + "This package provides functions to convert R objects into JSON objects +and vice-versa.") + (license license:gpl2+))) + +(define-public r-shiny + (package + (name "r-shiny") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rstudio/shiny.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "041q2gzvzs13syfhbirmkik96asdji8dxnnbs63j7v1ks97hrvvz")))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules (,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + (modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'replace-bundled-minified-JavaScript + (lambda* (#:key inputs #:allow-other-keys) + (let ((replace-file (lambda (old new) + (format #t "replacing ~a with ~a\n" old new) + (delete-file old) + (symlink new old)))) + ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ + ;; contain just data. They are not minified code, so we don't + ;; replace them. + (with-directory-excursion "inst/www/shared" + (replace-file "bootstrap/shim/respond.min.js" + (string-append (assoc-ref inputs "js-respond") + "/share/javascript/respond.min.js")) + (replace-file "bootstrap/shim/html5shiv.min.js" + (string-append (assoc-ref inputs "js-html5shiv") + "/share/javascript/html5shiv.min.js")) + (replace-file "json2-min.js" + (string-append (assoc-ref inputs "js-json2") + "/share/javascript/json2.min.js")) + (replace-file "strftime/strftime-min.js" + (string-append (assoc-ref inputs "js-strftime") + "/share/javascript/strftime.min.js")) + (replace-file "highlight/highlight.pack.js" + (string-append (assoc-ref inputs "js-highlight") + "/share/javascript/highlight.min.js")) + (replace-file "datatables/js/jquery.dataTables.min.js" + (string-append (assoc-ref inputs "js-datatables") + "/share/javascript/jquery.dataTables.min.js")) + (replace-file "selectize/js/selectize.min.js" + (string-append (assoc-ref inputs "js-selectize") + "/share/javascript/selectize.min.js")) + (replace-file "selectize/js/es5-shim.min.js" + (string-append (assoc-ref inputs "js-es5-shim") + "/share/javascript/es5-shim.min.js")) + (for-each (match-lambda + ((source . target) + (delete-file target) + (minify source #:target target))) + '(("jqueryui/jquery-ui.js" . + "jqueryui/jquery-ui.min.js") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js") + ("datepicker/js/bootstrap-datepicker.js" . + "datepicker/js/bootstrap-datepicker.min.js") + ("ionrangeslider/js/ion.rangeSlider.js" . + "ionrangeslider/js/ion.rangeSlider.min.js") + ("bootstrap/js/bootstrap.js" . + "bootstrap/js/bootstrap.min.js") + ("shiny.js" . + "shiny.min.js") + ("jquery.js" . + "jquery.min.js"))))) + #t))))) + (propagated-inputs + `(("r-crayon" ,r-crayon) + ("r-httpuv" ,r-httpuv) + ("r-mime" ,r-mime) + ("r-jsonlite" ,r-jsonlite) + ("r-xtable" ,r-xtable) + ("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-r6" ,r-r6) + ("r-sourcetools" ,r-sourcetools))) + (inputs + `(("js-datatables" ,js-datatables) + ("js-html5shiv" ,js-html5shiv) + ("js-json2" ,js-json2) + ("js-respond" ,js-respond) + ("js-selectize" ,js-selectize) + ("js-strftime" ,js-strftime) + ("js-highlight" ,js-highlight) + ("js-es5-shim" ,js-es5-shim))) + (home-page "http://shiny.rstudio.com") + (synopsis "Easy interactive web applications with R") + (description + "Makes it incredibly easy to build interactive web applications +with R. Automatic \"reactive\" binding between inputs and outputs and +extensive prebuilt widgets make it possible to build beautiful, +responsive, and powerful applications with minimal effort.") + (license license:artistic2.0))) + +(define-public r-shinydashboard + (package + (name "r-shinydashboard") + (version "0.7.1") + (source (origin + (method url-fetch) + (uri (cran-uri "shinydashboard" version)) + (sha256 + (base32 + "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) + (build-system r-build-system) + ;; The directory inst/AdminLTE/ contains a minified JavaScript file. + ;; Regenerate it from the included sources. + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'generate-minified-javascript + (lambda _ + (with-directory-excursion "inst/AdminLTE" + (delete-file "app.min.js") + (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js"))) + (call-with-output-file "app.min.js" + (lambda (port) + (dump-port minified port)))))))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-promises" ,r-promises) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("uglify-js" ,uglify-js))) + (home-page "http://rstudio.github.io/shinydashboard/") + (synopsis "Create dashboards with shiny") + (description "This package provides an extension to the Shiny web +application framework for R, making it easy to create attractive dashboards.") + ;; This package includes software that was released under the Expat + ;; license, but the whole package is released under GPL version 2 or + ;; later. + (license license:gpl2+))) + +(define-public r-shinyfiles + (package + (name "r-shinyfiles") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyFiles" version)) + (sha256 + (base32 + "0dlcjrw96x72grg6j915070x8x98l7629pn86gf148iknflm7gd5")))) + (properties `((upstream-name . "shinyFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fs" ,r-fs) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/thomasp85/shinyFiles") + (synopsis "Server-side file system viewer for Shiny") + (description + "This package provides functionality for client-side navigation of the +server side file system in shiny apps. In case the app is running locally +this gives the user direct access to the file system without the need to +\"download\" files to a temporary location. Both file and folder selection as +well as file saving is available.") + (license license:gpl2+))) + +(define-public r-crosstalk + (package + (name "r-crosstalk") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "crosstalk" version)) + (sha256 + (base32 + "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-lazyeval" ,r-lazyeval) + ("r-r6" ,r-r6) + ("r-shiny" ,r-shiny))) + (home-page "https://rstudio.github.io/crosstalk/") + (synopsis "Inter-widget interactivity for HTML widgets") + (description + "This package provides building blocks for allowing HTML widgets to +communicate with each other, with Shiny or without (i.e. static @code{.html} +files). It currently supports linked brushing and filtering.") + (license license: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 "https://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 license:gpl2))) + +(define-public r-miniui + (package + (name "r-miniui") + (version "0.1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "miniUI" version)) + (sha256 + (base32 + "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5")))) + (properties `((upstream-name . "miniUI"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-shiny" ,r-shiny))) + (home-page "https://cran.r-project.org/web/packages/miniUI/") + (synopsis "Shiny UI widgets for small screens") + (description + "This package provides UI widget and layout functions for writing Shiny apps that +work well on small screens.") + (license license:gpl3))) + +(define-public r-feather + (package + (name "r-feather") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "feather" version)) + (sha256 + (base32 + "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-hms" ,r-hms) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/wesm/feather") + (synopsis "R Bindings to the Feather API") + (description "Read and write feather files, a lightweight binary columnar +data store designed for maximum speed.") + (license license:asl2.0))) + +(define-public r-maps + (package + (name "r-maps") + (version "3.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "maps" version)) + (sha256 + (base32 + "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/maps") + (synopsis "Draw geographical maps") + (description "This package provides an R module for display of maps. +Projection code and larger maps are in separate packages ('mapproj' and +'mapdata').") + (license license:gpl2))) + +(define-public r-mapproj + (package + (name "r-mapproj") + (version "1.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "mapproj" version)) + (sha256 + (base32 + "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2")))) + (build-system r-build-system) + (propagated-inputs `(("r-maps" ,r-maps))) + (home-page "https://cran.r-project.org/web/packages/mapproj") + (synopsis "Map projection in R") + (description "This package converts latitude/longitude into projected +coordinates.") + (license (list license:gpl2 ; The R interface + (license:non-copyleft ; The C code + "https://www.gnu.org/licenses/license-list.en.html#lucent102" + "Lucent Public License Version 1.02"))))) + +(define-public r-rgooglemaps + (package + (name "r-rgooglemaps") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "RgoogleMaps" version)) + (sha256 + (base32 + "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4")))) + (properties `((upstream-name . "RgoogleMaps"))) + (build-system r-build-system) + (propagated-inputs `(("r-png" ,r-png))) + (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") + (synopsis "Use Google Maps in R") + (description "This package serves two purposes: +@enumerate +@item Provide a comfortable R interface to query the Google server for static + maps, and +@item Use the map as a background image to overlay plots within R. This + requires proper coordinate scaling. +@end enumerate\n") + (license license:gpl2+))) + +(define-public r-geosphere + (package + (name "r-geosphere") + (version "1.5-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "geosphere" version)) + (sha256 + (base32 + "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx")))) + (build-system r-build-system) + (propagated-inputs `(("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/web/packages/geosphere") + (synopsis "Spherical trigonometry") + (description "This package computes spherical trigonometry for geographic +applications. That is, compute distances and related measures for angular +(longitude/latitude) locations.") + (license license:gpl3+))) + +(define-public r-ggmap + (package + (name "r-ggmap") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggmap" version)) + (sha256 + (base32 + "0mssb09w818jv58h7mly9y181pzv22sgcd4a079cfpq04bs0wigw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-geosphere" ,r-geosphere) + ("r-ggplot2" ,r-ggplot2) + ("r-jpeg" ,r-jpeg) + ("r-mapproj" ,r-mapproj) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-proto" ,r-proto) + ("r-reshape2" ,r-reshape2) + ("r-rgooglemaps" ,r-rgooglemaps) + ("r-rjson" ,r-rjson) + ("r-scales" ,r-scales))) + (home-page "https://github.com/dkahle/ggmap") + (synopsis "Spatial visualization with ggplot2") + (description "This package provides a collection of functions to visualize +spatial data and models on top of static maps from various online sources (e.g +Google Maps and Stamen Maps). It includes tools common to those tasks, +including functions for geolocation and routing.") + (license license:gpl2))) + (define-public r-haven (package (name "r-haven") @@ -1656,6 +2300,35 @@ a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.") (license license:gpl2))) +(define-public r-rmysql + (package + (name "r-rmysql") + (version "0.10.15") + (source + (origin + (method url-fetch) + (uri (cran-uri "RMySQL" version)) + (sha256 + (base32 + "0bmc7w5fnkjaf333sgc0hskiy332m9gmfaxg0yzkjxscpizdw43n")))) + (properties `((upstream-name . "RMySQL"))) + (build-system r-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("mariadb" ,mariadb) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-dbi" ,r-dbi))) + (home-page "https://github.com/r-dbi/RMySQL") + (synopsis "Database interface and MySQL driver for R") + (description + "This package provides a DBI interface to MySQL / MariaDB. The RMySQL +package contains an old implementation based on legacy code from S-PLUS which +is being phased out. A modern MySQL client based on Rcpp is available from +the RMariaDB package.") + (license license:gpl2))) + (define-public r-geometry (package (name "r-geometry") @@ -7775,3 +8448,429 @@ for evolution along a phylogenetic tree.") Japan, 2007) with Japanese demographic data and some demographic analysis related functions.") (license license:gpl2+))) + +(define-public r-stabledist + (package + (name "r-stabledist") + (version "0.7-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "stabledist" version)) + (sha256 + (base32 + "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86")))) + (build-system r-build-system) + (home-page "http://www.rmetrics.org") + (synopsis "Stable distribution functions") + (description + "This package provides density, probability and quantile functions, and +random number generation for (skew) stable distributions, using the +parametrizations of Nolan.") + (license license:gpl2+))) + +(define-public r-gsl + (package + (name "r-gsl") + (version "1.9-10.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "gsl" version)) + (sha256 + (base32 + "00isw2iha5af4s7rr8svqka9mkl9l26l8h2rnk4r7fkhh7fc97sg")))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (home-page "https://cran.r-project.org/web/packages/gsl") + (synopsis "Wrapper for the GNU Scientific Library") + (description + "This package provides an R wrapper for the special functions and quasi +random number generators of the GNU Scientific Library.") + (license license:gpl2+))) + +(define-public r-adgoftest + (package + (name "r-adgoftest") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "ADGofTest" version)) + (sha256 + (base32 + "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw")))) + (properties `((upstream-name . "ADGofTest"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ADGofTest") + (synopsis "Anderson-Darling GoF test") + (description + "This package provides an implementation of the Anderson-Darling GoF test +with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the +Anderson-Darling Distribution\".") + ;; Any version of the GPL. + (license license:gpl3+))) + +(define-public r-softimpute + (package + (name "r-softimpute") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "softImpute" version)) + (sha256 + (base32 + "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq")))) + (properties `((upstream-name . "softImpute"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/softImpute") + (synopsis "Matrix completion via iterative soft-thresholded SVD") + (description + "This package provides iterative methods for matrix completion that use +nuclear-norm regularization. The package includes procedures for centering +and scaling rows, columns or both, and for computing low-rank @dfn{single +value decompositions} (SVDs) on large sparse centered matrices (i.e. principal +components).") + (license license:gpl2))) + +(define-public r-fftwtools + (package + (name "r-fftwtools") + (version "0.9-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "fftwtools" version)) + (sha256 + (base32 + "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6")))) + (build-system r-build-system) + (inputs `(("fftw" ,fftw))) + (home-page "https://github.com/krahim/fftwtools") + (synopsis "Wrapper for FFTW3") + (description + "This package provides a wrapper for several FFTW functions. It provides +access to the two-dimensional FFT, the multivariate FFT, and the +one-dimensional real to complex FFT using the FFTW3 library. The package +includes the functions @code{fftw()} and @code{mvfftw()} which are designed to +mimic the functionality of the R functions @code{fft()} and @code{mvfft()}. +The FFT functions have a parameter that allows them to not return the +redundant complex conjugate when the input is real data.") + (license license:gpl2+))) + +(define-public r-tiff + (package + (name "r-tiff") + (version "0.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "tiff" version)) + (sha256 + (base32 + "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m")))) + (build-system r-build-system) + (inputs + `(("libtiff" ,libtiff) + ("libjpeg" ,libjpeg) + ("zlib" ,zlib))) + (home-page "http://www.rforge.net/tiff/") + (synopsis "Read and write TIFF images") + (description + "This package provides an easy and simple way to read, write and display +bitmap images stored in the TIFF format. It can read and write both files and +in-memory raw vectors.") + ;; Either of these two license versions. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-waveslim + (package + (name "r-waveslim") + (version "1.7.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "waveslim" version)) + (sha256 + (base32 + "0lqslkihgrd7rbihqhhk57m9vkbnfsznkvk8430cvbcsn7vridii")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://waveslim.blogspot.com") + (synopsis "Basic wavelet routines for signal processing") + (description + "This package provides basic wavelet routines for time series (1D), +image (2D) and array (3D) analysis. The code provided here is based on +wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk +and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from +Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet +pairs (Selesnick 2001, 2002).") + (license license:bsd-3))) + +(define-public r-wordcloud + (package + (name "r-wordcloud") + (version "2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "wordcloud" version)) + (sha256 + (base32 + "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp))) + (home-page "https://cran.r-project.org/web/packages/wordcloud") + (synopsis "Word clouds") + (description + "This package provides functionality to create pretty word clouds, +visualize differences and similarity between documents, and avoid +over-plotting in scatter plots with text.") + (license license:lgpl2.1))) + +(define-public r-colorramps + (package + (name "r-colorramps") + (version "2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "colorRamps" version)) + (sha256 + (base32 + "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z")))) + (properties `((upstream-name . "colorRamps"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/colorRamps") + (synopsis "Build color tables") + (description "This package provides features to build gradient color +maps.") + ;; Any version of the GPL + (license license:gpl3+))) + +(define-public r-tidytree + (package + (name "r-tidytree") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tidytree" version)) + (sha256 + (base32 + "1sx69wvlp7k761cmglrzq2jxkm2iq27x6bhhdcisj62wryj96wb2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-dplyr" ,r-dplyr) + ("r-lazyeval" ,r-lazyeval) + ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/GuangchuangYu/tidytree") + (synopsis "Tidy tool for phylogenetic tree data manipulation") + (description + "Phylogenetic trees generally contain multiple components including nodes, +edges, branches and associated data. This package provides an approach to +convert tree objects to tidy data frames. It also provides tidy interfaces to +manipulate tree data.") + (license license:artistic2.0))) + +(define-public r-rvcheck + (package + (name "r-rvcheck") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rvcheck" version)) + (sha256 + (base32 + "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rlang" ,r-rlang))) + (home-page "https://cran.r-project.org/web/packages/rvcheck") + (synopsis "R package version check") + (description + "This package provides tools to check the latest release version of R and +R packages (on CRAN, Bioconductor or Github).") + (license license:artistic2.0))) + +(define-public r-docopt + (package + (name "r-docopt") + (version "0.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "docopt" version)) + (sha256 + (base32 + "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) + (build-system r-build-system) + (home-page "https://github.com/docopt/docopt.R") + (synopsis "Command-line interface specification language") + (description + "This package enables you to define a command-line interface by just +giving it a description in the specific format.") + (license license:expat))) + +(define-public r-sparsesvd + (package + (name "r-sparsesvd") + (version "0.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sparsesvd" version)) + (sha256 + (base32 + "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam")))) + (build-system r-build-system) + (propagated-inputs `(("r-matrix" ,r-matrix))) + (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") + (synopsis "Sparse truncated singular value decomposition") + (description + "This package provides a Wrapper around the SVDLIBC library +for (truncated) singular value decomposition of a sparse matrix. Currently, +only sparse real matrices in Matrix package format are supported.") + ;; SVDLIBC is released under BSD-2. The R interface is released under + ;; BSD-3. + (license (list license:bsd-3 license:bsd-2)))) + +(define-public r-densityclust + (package + (name "r-densityclust") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "densityClust" version)) + (sha256 + (base32 + "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13")))) + (properties `((upstream-name . "densityClust"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fnn" ,r-fnn) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gridextra" ,r-gridextra) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rtsne" ,r-rtsne))) + (home-page "https://cran.r-project.org/web/packages/densityClust") + (synopsis "Clustering by fast search and find of density peaks") + (description + "This package provides an improved implementation (based on k-nearest +neighbors) of the density peak clustering algorithm, originally described by +Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle +large datasets (> 100,000 samples) very efficiently.") + (license license:gpl2+))) + +(define-public r-combinat + (package + (name "r-combinat") + (version "0.0-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "combinat" version)) + (sha256 + (base32 + "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/combinat") + (synopsis "Combinatorics utilities") + (description "This package provides assorted routines for combinatorics.") + (license license:gpl2))) + +(define-public r-qlcmatrix + (package + (name "r-qlcmatrix") + (version "0.9.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "qlcMatrix" version)) + (sha256 + (base32 + "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y")))) + (properties `((upstream-name . "qlcMatrix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-docopt" ,r-docopt) + ("r-matrix" ,r-matrix) + ("r-slam" ,r-slam) + ("r-sparsesvd" ,r-sparsesvd))) + (home-page "https://cran.r-project.org/web/packages/qlcMatrix") + (synopsis "Sparse matrix functions for quantitative language comparison") + (description + "This package provides an extension of the functionality of the Matrix +package for using sparse matrices. Some of the functions are very general, +while other are highly specific for the special data format used for +@dfn{quantitative language comparison} (QLC).") + (license license:gpl3))) + +(define-public r-ddrtree + (package + (name "r-ddrtree") + (version "0.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "DDRTree" version)) + (sha256 + (base32 + "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk")))) + (properties `((upstream-name . "DDRTree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-irlba" ,r-irlba) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen))) + (home-page "https://cran.r-project.org/web/packages/DDRTree") + (synopsis "Learning principal graphs with DDRTree") + (description + "This package provides an implementation of the framework of +@dfn{reversed graph embedding} (RGE) which projects data into a reduced +dimensional space while constructs a principal tree which passes through the +middle of the data simultaneously. DDRTree shows superiority to +alternatives (Wishbone, DPT) for inferring the ordering as well as the +intrinsic structure of single cell genomics data. In general, it could be +used to reconstruct the temporal progression as well as the bifurcation +structure of any data type.") + (license license:asl2.0))) + +(define-public r-corpcor + (package + (name "r-corpcor") + (version "1.6.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "corpcor" version)) + (sha256 + (base32 + "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf")))) + (build-system r-build-system) + (home-page "http://strimmerlab.org/software/corpcor/") + (synopsis "Efficient estimation of covariance and (partial) correlation") + (description + "This package implements a James-Stein-type shrinkage estimator for the +covariance matrix, with separate shrinkage for variances and correlations. +Furthermore, functions are available for fast singular value decomposition, +for computing the pseudoinverse, and for checking the rank and positive +definiteness of a matrix.") + (license license:gpl3+))) |