diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 324 |
1 files changed, 287 insertions, 37 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1fe90619cd..0943a8972b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com> ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net> ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> -;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2020, 2021 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> @@ -1344,10 +1344,175 @@ are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.") (license license:expat))) +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-jquerylib + (package + (name "r-jquerylib") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "jquerylib" version)) + (sha256 + (base32 + "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq")) + (snippet + '(for-each delete-file + '("inst/lib/jquery-1.12.4.min.js" + "inst/lib/jquery-2.2.4.min.js" + "inst/lib/jquery-3.5.1.min.js"))))) + (properties `((upstream-name . "jquerylib"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/lib/" + (call-with-values + (lambda () + (unzip2 + `(("jquery-1.12.4.js" + "jquery-1.12.4.min.js") + ("jquery-2.2.4.js" + "jquery-2.2.4.min.js") + ("jquery-3.5.1.js" + "jquery-3.5.1.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools))) + (native-inputs + `(("esbuild" ,esbuild))) + (home-page "https://cran.r-project.org/package=jquerylib") + (synopsis "Obtain jQuery as an HTML dependency object") + (description + "Obtain any major version of jQuery and use it in any webpage generated +by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't +need to use this package directly, but other R packages (e.g. shiny, +rmarkdown, etc.) depend on this package to avoid bundling redundant copies of +jQuery.") + (license license:expat))) + +(define-public r-sass + (package + (name "r-sass") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sass" version)) + (sha256 + (base32 + "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s")))) + (properties `((upstream-name . "sass"))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-fs" ,r-fs) + ("r-htmltools" ,r-htmltools) + ("r-r6" ,r-r6) + ("r-rappdirs" ,r-rappdirs) + ("r-rlang" ,r-rlang))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/rstudio/sass") + (synopsis "Syntactically Awesome Style Sheets (SASS)") + (description + "This package provides an SCSS compiler, powered by the libsass library. +With this, R developers can use variables, inheritance, and functions to +generate dynamic style sheets. The package uses the Sass CSS extension +language, which is stable, powerful, and CSS compatible.") + (license license:expat))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. +(define-public r-bslib + (package + (name "r-bslib") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "bslib" version)) + (sha256 + (base32 + "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac")) + (snippet + '(for-each delete-file + '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" + "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js" + "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js" + "inst/lib/bs/dist/js/bootstrap.bundle.min.js"))))) + (properties `((upstream-name . "bslib"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/lib/" + (call-with-values + (lambda () + (unzip2 + `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js" + "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js") + ("bs-colorpicker/js/bootstrap-colorpicker.js" + "bs-colorpicker/js/bootstrap-colorpicker.min.js") + ("bs-sass/assets/javascripts/bootstrap.js" + "bs-sass/assets/javascripts/bootstrap.min.js") + (,(assoc-ref inputs "js-bootstrap-bundle") + "bs/dist/js/bootstrap.bundle.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-jquerylib" ,r-jquerylib) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) + ("r-sass" ,r-sass))) + (native-inputs + `(("esbuild" ,esbuild) + ("js-bootstrap-bundle" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js") + (sha256 + (base32 + "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak")))))) + (home-page "https://rstudio.github.io/bslib/") + (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown") + (description + "This package simplifies custom CSS styling of both shiny and rmarkdown +via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their +various Bootswatch themes. An interactive widget is also provided for +previewing themes in real time.") + (license license:expat))) + +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. (define-public r-shiny (package (name "r-shiny") - (version "1.4.0.2") + (version "1.6.0") (source (origin (method git-fetch) @@ -1357,7 +1522,23 @@ data structures in C++.") (file-name (git-file-name name version)) (sha256 (base32 - "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs")))) + "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9")) + (snippet + '(for-each delete-file + '("inst/www/shared/bootstrap/js/bootstrap.min.js" + "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO + "inst/www/shared/datatables/js/jquery.dataTables.min.js" + "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js" + "inst/www/shared/highlight/highlight.pack.js" + "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js" + "inst/www/shared/jquery.min.js" + "inst/www/shared/jqueryui/jquery-ui.min.js" + "inst/www/shared/legacy/jquery.min.js" + "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js" + "inst/www/shared/selectize/js/selectize.min.js" + "inst/www/shared/shiny.min.js" + "inst/www/shared/showdown/compressed/showdown.js" + "inst/www/shared/strftime/strftime-min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -1372,21 +1553,11 @@ data structures in C++.") (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")) @@ -1399,14 +1570,10 @@ data structures in C++.") (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.js" . "jqueryui/jquery-ui.min.js") ("datepicker/js/bootstrap-datepicker.js" . "datepicker/js/bootstrap-datepicker.min.js") @@ -1414,23 +1581,32 @@ data structures in C++.") "ionrangeslider/js/ion.rangeSlider.min.js") ("bootstrap/js/bootstrap.js" . "bootstrap/js/bootstrap.min.js") + (,(assoc-ref inputs "js-bootstrap-accessibility") . + "bootstrap/accessibility/js/bootstrap-accessibility.min.js") ("shiny.js" . "shiny.min.js") ("jquery.js" . "jquery.min.js") ("legacy/jquery.js" . "legacy/jquery.min.js") + ("selectize/accessibility/js/selectize-plugin-a11y.js" . + "selectize/accessibility/js/selectize-plugin-a11y.min.js") ("showdown/src/showdown.js" . - "showdown/compressed/showdown.js"))))) - #t))))) + "showdown/compressed/showdown.js")))))))))) (propagated-inputs - `(("r-crayon" ,r-crayon) + `(("r-bslib" ,r-bslib) + ("r-cachem" ,r-cachem) + ("r-commonmark" ,r-commonmark) + ("r-crayon" ,r-crayon) ("r-digest" ,r-digest) + ("r-ellipsis" ,r-ellipsis) ("r-fastmap" ,r-fastmap) + ("r-glue" ,r-glue) ("r-htmltools" ,r-htmltools) ("r-httpuv" ,r-httpuv) ("r-jsonlite" ,r-jsonlite) ("r-later" ,r-later) + ("r-lifecycle" ,r-lifecycle) ("r-mime" ,r-mime) ("r-promises" ,r-promises) ("r-r6" ,r-r6) @@ -1440,17 +1616,21 @@ data structures in C++.") ("r-xtable" ,r-xtable))) (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))) + ("js-highlight" ,js-highlight))) (native-inputs `(("uglify-js" ,uglify-js) - ("gfortran" ,gfortran))) - (home-page "http://shiny.rstudio.com") + ("gfortran" ,gfortran) + ("js-bootstrap-accessibility" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\ +v1.0.7/_site/plugins/js/bootstrap-accessibility.js") + (sha256 + (base32 + "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))))) + (home-page "https://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description "Makes it incredibly easy to build interactive web applications @@ -1774,6 +1954,29 @@ in R and Shiny via the D3 visualization library.") from Wes Anderson movies.") (license license:expat))) +(define-public r-gg-gap + (package + (name "r-gg-gap") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "gg.gap" version)) + (sha256 + (base32 + "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h")))) + (properties `((upstream-name . "gg.gap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") + (synopsis "Define segments on the y-axis for ggplot2") + (description + "The @code{gg.gap} function enables you to define segments for the y-axis +in a ggplot2 plot.") + (license license:gpl3))) + (define-public r-tablerdash (package (name "r-tablerdash") @@ -2129,10 +2332,25 @@ including functions for geolocation and routing.") (uri (cran-uri "haven" version)) (sha256 (base32 - "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf")))) + "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor readstat + (delete-file-recursively "src/readstat") + #t)))) (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'unbundle-readstat + (lambda _ + ;; Not required, since we’re not building readstat. + (substitute* "src/Makevars" + (("-lz") "-lreadstat")) + #t))))) (inputs - `(("zlib" ,zlib))) + `(("readstat" ,readstat))) (native-inputs `(("r-knitr" ,r-knitr))) (propagated-inputs @@ -2286,7 +2504,7 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot))) - (home-page "http://www.sciviews.org/pastecs") + (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description "This package provides functions for regulation, decomposition and analysis @@ -2473,6 +2691,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppthread + (package + (name "r-rcppthread") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppThread" version)) + (sha256 + (base32 + "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl")))) + (properties `((upstream-name . "RcppThread"))) + (build-system r-build-system) + (home-page + "https://github.com/tnagler/RcppThread") + (synopsis "R threading in C++") + (description + "This package provides a C++11-style thread class and thread pool that can +safely be interrupted from R.") + (license license:expat))) + (define-public r-bindr (package (name "r-bindr") @@ -6841,7 +7080,7 @@ JavaScript library) and interact with the igraph package.") ("r-stringi" ,r-stringi))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://github.com/gluc/data.tree") + (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description "Create tree structures from hierarchical data, and traverse the tree in @@ -8270,7 +8509,7 @@ the work.") ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://people.math.aau.dk/~sorenh/software/doBy/") + (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description "This package contains: @@ -11089,7 +11328,7 @@ isosurfaces.") ("r-multicool" ,r-multicool) ("r-mvtnorm" ,r-mvtnorm) ("r-plot3d" ,r-plot3d))) - (home-page "http://www.mvstat.net/tduong/") + (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description "This package provides kernel smoothers for univariate and multivariate @@ -11116,7 +11355,7 @@ hypothesis testing.") ("r-plot3d" ,r-plot3d))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://www.mvstat.net/tduong/") + (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description "The feature package contains functions to display and compute kernel @@ -14131,7 +14370,7 @@ probabilities from a standard bivariate normal CDF.") ("r-mnormt" ,r-mnormt) ("r-numderiv" ,r-numderiv) ("r-pbivnorm" ,r-pbivnorm))) - (home-page "http://lavaan.ugent.be") + (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description "This package provides tools to fit a variety of latent variable models, @@ -23058,7 +23297,7 @@ as possible (with tests to prove it).") "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp")))) (properties `((upstream-name . "boa"))) (build-system r-build-system) - (home-page "http://www.jstatsoft.org/v21/i11") + (home-page "https://www.jstatsoft.org/v21/i11") (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC") (description "This package provides a menu-driven program and library of functions for @@ -23538,6 +23777,17 @@ download images.") (base32 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'install-server-binary + ;; Makevars tries to install to R's store directory. + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (substitute* "src/Makevars.in" + (("\\$\\(R_HOME\\)") out)) + (mkdir-p bin))))))) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-mime" ,r-mime) |