diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 501 |
1 files changed, 500 insertions, 1 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 423bb5b54f..68c4431a68 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> @@ -30,10 +30,12 @@ #: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 base) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages gl) @@ -41,6 +43,8 @@ #: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 +280,501 @@ 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-haven (package (name "r-haven") |