diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 2258 |
1 files changed, 1862 insertions, 396 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1fe90619cd..61de48e08e 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> @@ -26,13 +26,14 @@ ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es> -;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org> +;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org> ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net> ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com> ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com> +;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -91,6 +92,7 @@ #:use-module (gnu packages networking) #:use-module (gnu packages node) #:use-module (gnu packages pcre) + #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile @@ -99,6 +101,7 @@ #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) + #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) #:use-module (gnu packages web) @@ -129,14 +132,14 @@ files and provide more explicit control over line endings.") (define-public r-cachem (package (name "r-cachem") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "cachem" version)) (sha256 (base32 - "0y3jb96lyn3vc3nq8gs9x669w3xp69vdg5xc69qy0l356r39gp3r")))) + "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh")))) (properties `((upstream-name . "cachem"))) (build-system r-build-system) (propagated-inputs @@ -153,14 +156,14 @@ automatically pruning objects to maintain the constraints.") (define-public r-diffobj (package (name "r-diffobj") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 - "1x3d5sk8mk0s2d7dq8wxi1zv6krlx33n22ls2jwnb58b8xrmakj1")))) + "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon))) @@ -175,14 +178,14 @@ visualization of their differences.") (define-public r-waldo (package (name "r-waldo") - (version "0.2.3") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "waldo" version)) (sha256 (base32 - "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz")))) + "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr")))) (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs @@ -205,14 +208,14 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.18") + (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1srczjy9dqw06glrv95798xsg462kfbbwm3yk1fv1zhpz9jhakwv")))) + "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -341,13 +344,13 @@ the system clipboards.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-8") + (version "1.8-9") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f")))) + "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -390,13 +393,13 @@ variables.") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.3.8-1") + (version "0.3.9") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf")))) + "0nb0lpwqph9334s9sq77mk3nd22icy9d9hywz4awhf6nvp5rcc2v")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -498,14 +501,14 @@ higher.") (define-public r-oenb (package (name "r-oenb") - (version "0.0.1") + (version "0.0.2") (source (origin (method url-fetch) (uri (cran-uri "oenb" version)) (sha256 (base32 - "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz")))) + "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5")))) (properties `((upstream-name . "oenb"))) (build-system r-build-system) (propagated-inputs @@ -871,18 +874,21 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "0.3.6") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka")))) + (base32 "04spcv6nxlmx5bxncq0vybfqrs8jgjamzyrn6wmkdcwii8jvyn53")))) (build-system r-build-system) (propagated-inputs `(("r-httr" ,r-httr) + ("r-lifecycle" ,r-lifecycle) ("r-magrittr" ,r-magrittr) + ("r-rlang" ,r-rlang) ("r-selectr" ,r-selectr) + ("r-tibble" ,r-tibble) ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -921,14 +927,14 @@ package is a port of the Python package @code{cssselect}.") (define-public r-reprex (package (name "r-reprex") - (version "1.0.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "reprex" version)) (sha256 (base32 - "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx")))) + "1lcnxczy28n4g3rvph09va7svcznfyqa7zdggklqb924qvy7flwh")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -939,6 +945,7 @@ package is a port of the Python package @code{cssselect}.") ("r-knitr" ,r-knitr) ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) + ("r-rstudioapi" ,r-rstudioapi) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -977,14 +984,14 @@ same time tries to group instances from the same class together.") (define-public r-callr (package (name "r-callr") - (version "3.5.1") + (version "3.6.0") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf")))) + "050s7l1ipi6snbj6xnk052l6acycnxjyzv84026adw5x8kki0yz6")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -1344,10 +1351,230 @@ are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.") (license license:expat))) +(define-public r-fastghquad + (package + (name "r-fastghquad") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fastGHQuad" version)) + (sha256 + (base32 + "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj")))) + (properties `((upstream-name . "fastGHQuad"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/awblocker/fastGHQuad") + (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature") + (description + "This package implements numerically-stable Gauss-Hermite quadrature +rules and utility functions for adaptive GH quadrature.") + (license license:expat))) + +(define-public r-rstpm2 + (package + (name "r-rstpm2") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rstpm2" version)) + (sha256 + (base32 + "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4")))) + (properties `((upstream-name . "rstpm2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbmle" ,r-bbmle) + ("r-bh" ,r-bh) + ("r-desolve" ,r-desolve) + ("r-fastghquad" ,r-fastghquad) + ("r-mgcv" ,r-mgcv) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-survival" ,r-survival))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://github.com/mclements/rstpm2") + (synopsis "Link-based survival models") + (description + "This package provides R implementations of @dfn{generalized survival +models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov +multi-state models.") + ;; One of these licenses + (license (list license:gpl2 license:gpl3)))) + +;; 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 +1584,23 @@ 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 +1615,11 @@ 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 +1632,10 @@ 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 +1643,32 @@ 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 +1678,21 @@ 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 +2016,29 @@ 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 +2394,25 @@ 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 @@ -2273,6 +2553,30 @@ inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) +(define-public r-palmerpenguins + (package + (name "r-palmerpenguins") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "palmerpenguins" version)) + (sha256 + (base32 + "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x")))) + (properties + `((upstream-name . "palmerpenguins"))) + (build-system r-build-system) + (home-page "https://allisonhorst.github.io/palmerpenguins/") + (synopsis "Palmer Archipelago (Antarctica) penguin data") + (description + "This package includes size measurements, clutch observations, and blood +isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins +observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. +Data were collected and made available by Dr. Kristen Gorman and the Palmer +Station Long Term Ecological Research (LTER) Program.") + (license license:cc0))) + (define-public r-pastecs (package (name "r-pastecs") @@ -2286,7 +2590,7 @@ 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 @@ -2297,13 +2601,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-12") + (version "1.2-13") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "15d5g89winndv8cy8jjjxy87fliafp5zyb8b58czrijwcmagg50l")))) + "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4")))) (build-system r-build-system) (propagated-inputs `(("r-formula" ,r-formula) @@ -2377,13 +2681,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl")))) + (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -2423,14 +2727,14 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q")))) + "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2473,6 +2777,27 @@ 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") @@ -2515,31 +2840,6 @@ where the bound function accepts additional arguments.") bindings that call a C++ function.") (license license:expat))) -(define-public r-bisquerna - (package - (name "r-bisquerna") - (version "1.0.4") - (source (origin - (method url-fetch) - (uri (cran-uri "BisqueRNA" version)) - (sha256 - (base32 - "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) - (properties `((upstream-name . "BisqueRNA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) - (home-page "https://www.biorxiv.org/content/10.1101/669911v1") - (synopsis "Decomposition of bulk expression with single-cell sequencing") - (description "This package provides tools to accurately estimate cell type -abundances from heterogeneous bulk expression. A reference-based method -utilizes single-cell information to generate a signature matrix and -transformation of bulk expression for accurate regression based estimates. -A marker-based method utilizes known cell-specific marker genes to measure -relative abundances across samples.") - (license license:gpl3))) - (define-public r-auc (package (name "r-auc") @@ -2808,14 +3108,14 @@ in main memory.") (define-public r-ffbase (package (name "r-ffbase") - (version "0.13.1") + (version "0.13.3") (source (origin (method url-fetch) (uri (cran-uri "ffbase" version)) (sha256 (base32 - "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x")))) + "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit) @@ -2928,14 +3228,14 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "0lvcvlc8p2cii7rqx7m81f7cv3kk9mlf7cbbgv7l75g7ljw8dyvz")))) + "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs @@ -2967,14 +3267,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-24") + (version "0.4-25") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc")))) + "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") @@ -3050,13 +3350,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-9") + (version "0.6-9.1") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj")))) + "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments @@ -3432,17 +3732,18 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-7") + (version "1.7-8") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37")))) + "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) + ("r-gsl" ,r-gsl) ("r-rcpp" ,r-rcpp))) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") @@ -3468,7 +3769,7 @@ statistics/methods are implemented.") (uri (cran-uri "SuppDists" version)) (sha256 (base32 - "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak")))) + "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") @@ -3567,14 +3868,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.8.1") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d")))) + "07difbrz8zmvdyns63958v0zw4hyv48956mcww8zh7064a564k83")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -3895,14 +4196,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-9") + (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d")))) + "04hfg27c72v0fz4091w3rgbc2vd7g6yl78y9plvsvh0vjlx8ymmp")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -3922,19 +4223,21 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.0.12") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca")))) + "1ibh1ivr280wpmk3qjgm715dk79wx0ikjl9jjjcqs03q6vz4wmdx")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-mnormt" ,r-mnormt) ("r-nlme" ,r-nlme))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description @@ -3975,14 +4278,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.4") + (version "0.7.6") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1zwdgv59a5c4mdcfn3anvsf83ymi11ij6k9nssw3aqzirp6fwg3w")))) + "1ljcl8mh0yqxw3qxzar482qwbxbcaim1x6y1wm82ws12pfdw0j8n")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -4465,14 +4768,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v")))) + "15vmrm9gwdhfg8mnq8rsg7m59kzc9h53cv96am4ds1dkm56w4n6p")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) @@ -4748,18 +5051,17 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "128bx3bds0dnkixc4frbky11rz1ilnvdfzz9mggajj690i11b62q")))) + "0l1s9yv23bc7mm0hfdlamgz4wjfrisv8aylr65ihjs98jsynrkg3")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-glue" ,r-glue))) + `(("r-glue" ,r-glue))) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build @@ -4770,14 +5072,14 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (define-public r-argparser (package (name "r-argparser") - (version "0.6") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "argparser" version)) (sha256 (base32 - "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x")))) + "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6")))) (build-system r-build-system) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") @@ -4811,13 +5113,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.5") + (version "3.5.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73")))) + (base32 "1z7zag7g041xlhzhkdfl33y2phc877h1pwj9k69p69b967qi6p6k")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -4958,13 +5260,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4")))) + (base32 "0ix3p0iw2c60whn5mvsflh0vhm4yixhw4s9d9v4023qhp077nw9y")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -4980,15 +5282,17 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.1.4") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn")))) + "1yw7vjn3gpkqddc91rbfh4kk0zmn2kp0jycrd3066sissh01jhdk")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -5021,18 +5325,17 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz")))) + "03hyxk3x635xfdn2x707gygdb2xk0cayl1nl44zib9bwqyyb7nas")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-ellipsis" ,r-ellipsis) + `(("r-ellipsis" ,r-ellipsis) ("r-glue" ,r-glue) ("r-rlang" ,r-rlang))) (native-inputs @@ -5060,14 +5363,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.7") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd")))) + "0wp68cg95895aybi7yjqy0sidvc68lmfqndinpd63dysci9x3r8c")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -5078,6 +5381,8 @@ to variables on the left-hand side of the assignment.") ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8) ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description @@ -5108,14 +5413,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.29") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0my1412vn5zri01w2myzn268lfwinbhfgdj4bbcib3s48i9djw0n")))) + "04a3ncaxix30n9m73slpsn1idxv7j1f7fy3nhxpvkk514x9rgg0p")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -5423,14 +5728,14 @@ sapa R packages.") (define-public r-sapa (package (name "r-sapa") - (version "2.0-2") + (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "sapa" version)) (sha256 (base32 - "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) + "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc")))) (build-system r-build-system) (propagated-inputs `(("r-ifultools" ,r-ifultools) @@ -6402,14 +6707,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-6") + (version "1.6-7") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm")))) + "0m80kndfbannw8h53nqdd5wl8h33q2z259aa1cp1nwadaxf9fc1q")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -6547,14 +6852,14 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.16") + (version "0.5.26") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk")))) + "1k6zxjb2bb0z6rv7zmkbaz85cbvs84mj602ikkwk60alh8kpdw2d")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -6564,6 +6869,8 @@ dependency on Java.") ("r-openxlsx" ,r-openxlsx) ("r-readxl" ,r-readxl) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description @@ -6581,14 +6888,14 @@ simple method for converting between file types.") (define-public r-maptools (package (name "r-maptools") - (version "1.0-2") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "maptools" version)) (sha256 (base32 - "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s")))) + "0pn4gwh2rl6pfh2vbc7ln86kzlg22cfpd02z95j7zpjidz2mva8l")))) (build-system r-build-system) (propagated-inputs `(("r-foreign" ,r-foreign) @@ -6634,14 +6941,14 @@ time after the current time, after the R execution stack has emptied.") (define-public r-promises (package (name "r-promises") - (version "1.1.1") + (version "1.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "promises" version)) (sha256 (base32 - "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p")))) + "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld")))) (build-system r-build-system) (propagated-inputs `(("r-later" ,r-later) @@ -6841,7 +7148,7 @@ 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 @@ -6925,14 +7232,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.49") + (version "0.50.1") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk")))) + "1fkmyllydnmk3j2cmgf86r91wyxf2kh573x8bkck7wgkfniw4h7w")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs @@ -6942,6 +7249,7 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") ("r-raster" ,r-raster) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-sp" ,r-sp) + ("r-terra" ,r-terra) ("r-viridislite" ,r-viridislite) ("r-zoo" ,r-zoo))) (home-page "https://oscarperpinan.github.io/rastervis/") @@ -6983,14 +7291,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.12.5") + (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh")))) + "0jlsf6vfvqhr4i35xy3xf1ixkfillivzy3wbpl6ca9vyjpnhiwj1")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -7173,14 +7481,14 @@ movies, and TV shows.") (define-public r-ggsignif (package (name "r-ggsignif") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 - "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg")))) + "0rjy9wqsq67jjm1jz3j7hm599x0rshrrhw2w01iaqb9kf506hvjh")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7200,14 +7508,14 @@ and adds the annotation to the plot.") (define-public r-rstatix (package (name "r-rstatix") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 - "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb")))) + "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs @@ -7554,14 +7862,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83")))) + "13phw0dk3p3s1z45ff7dbqnn27zws1209mp3d4763zh7xnsdsl44")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -7576,19 +7884,18 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16")))) + "11psw5yiamq0g7jc6fqn2wis565i60qgda4a5d09qi8fyzd6mnfb")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs - `(("r-rbibutils" ,r-rbibutils) - ("r-gbrd" ,r-gbrd))) + `(("r-rbibutils" ,r-rbibutils))) (home-page "https://github.com/GeoBosh/Rdpack") (synopsis "Update and manipulate Rd documentation objects") (description @@ -7603,14 +7910,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.16") + (version "0.3.18") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1ls5kp70jfxrzxxb3xrg8sn2fyk6qd7rmx23n5jxi7z7850avjrj")))) + "1j3bv4j8x5ijj0j447vpdsk4p8pl3ncwdwnns6n3plfrqgsf3vsg")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -7864,14 +8171,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.12.0") + (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0gkvcw9d729ql1gfrpxzgrag4xafd0hchrdww215qz11ma1rzy7s")))) + "03b7kd17h25mi1si40ibcp3jpasyqpj51mr8js0ywywyfw7909j1")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -8000,14 +8307,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg")))) + "1ykjfnqhn8nd9f3l4jj8hf1bbjjckkna3p7fdsg0a73c05a17yma")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -8226,14 +8533,14 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "4.1.2") + (version "4.1.3") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "1j9sh1w9lsnnhlh59g4ghykyfx46rxh380s8imvm7pzna7rw7c64")))) + "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") @@ -8248,14 +8555,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.8") + (version "4.6.9") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg")))) + "02f545md5yhbpp3wb3q2c8zabqwgf02555r5c6g7znab5zjbyr00")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -8270,7 +8577,7 @@ 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: @@ -8334,14 +8641,14 @@ procedures to speed up calculations in R.") (define-public r-blockfest (package (name "r-blockfest") - (version "1.8") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "BlockFeST" version)) (sha256 (base32 - "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5")))) + "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) (propagated-inputs `(("r-basix" ,r-basix))) @@ -8682,22 +8989,22 @@ and coverage methods to tune the choice of threshold.") (define-public r-labelled (package (name "r-labelled") - (version "2.7.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 - "1nsb0mh0jg7gggc41b6v55nmfq07g0qn9fy55x4jws5dscs6pdmi")))) + "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-haven" ,r-haven) ("r-lifecycle" ,r-lifecycle) - ("r-pillar" ,r-pillar) ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) ("r-tidyr" ,r-tidyr) ("r-vctrs" ,r-vctrs))) (native-inputs @@ -9361,14 +9668,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.6.0") + (version "2.7.1") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36")))) + "16svy84dq25g69axqgympsrh8dzssa1w3zz08zc8m6nprr3jqwqf")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -9803,14 +10110,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.5.4") + (version "1.5.5-1") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361")))) + "0l5dd71ihhs7zy6ygniy07iisgy7a1ai1w41hqf84swb0j3cl6iz")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -10093,14 +10400,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy")))) + "0qh8x8yi8gkb5x7zfxmb1c689k7bhc1f5947yymny34j7xdsb9s8")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -10123,14 +10430,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.3") + (version "0.4.4-1") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2")))) + "02rwf3lxnzgc8yh0wridsc6lqr9s6v0cqzbk4biwnr494rvs46zb")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -10240,14 +10547,14 @@ repositories.") (define-public r-gh (package (name "r-gh") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 - "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219")))) + "16xa1qb1r28f8yc6ybjrxiq2zigxj886dp9k29jpsn5091xbzkq0")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -10351,14 +10658,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.1.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8")))) + "1fh72p92wj83yv1ch77jms6k1gjqfji8cmgw23vpxd0p8l9jj4h7")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -10451,14 +10758,14 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj")))) + "0f35648bdxhvplcfj80r4hfj5w21f1s01kcz6b29d098c1mnfzb7")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -10577,14 +10884,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.8") + (version "0.9.9") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j")))) + "0ig7vgjvldbndwhky1bsi38zifr9ji8xvvfqbfffplac08llvrbr")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -10729,14 +11036,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.1.6") + (version "4.1.9") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "0aisvax9d7bk6aykrcdcn1ji618r520mcrkr1i3jnck1qs31z41f")))) + "19kyg0agjk7gxipa5kmklz4cqh97xrdbibmmy1g99r1gp3s9ml30")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -10918,14 +11225,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.0.2") + (version "5.0.3") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc")))) + "0ihcirny4al2ydymxhdfacwmybmrgrz5nm0lbf49gk2zy8w124ki")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") @@ -10968,15 +11275,17 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.10") + (version "1.30.12") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk")))) + (base32 "0c2anza01pc36manj3cvycbq8p57qpq18dsimk3y3gpks70hhqf3")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description @@ -10987,14 +11296,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.104.16") + (version "0.105.22") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "169a8riiam8445nl7rcwn0x92dlwyzh5xldvap6dcxjyjqmjwbdq")))) + "1y69phym8pkdh1k808y3rp1030xmhjpc8vig9035v9n1r7v7a1kz")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -11089,7 +11398,7 @@ 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 +11425,7 @@ 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 @@ -11182,14 +11491,14 @@ Scientific.") (define-public r-activity (package (name "r-activity") - (version "1.3") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 - "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92")))) + "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5")))) (build-system r-build-system) (propagated-inputs `(("r-circular" ,r-circular) @@ -11208,14 +11517,14 @@ circular variables).") (define-public r-ouch (package (name "r-ouch") - (version "2.14-1") + (version "2.15-1") (source (origin (method url-fetch) (uri (cran-uri "ouch" version)) (sha256 (base32 - "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) + "0myddn3b28pswyk42kvwhyvkj30q41f677vpxclxacdfkhgvrj6q")))) (build-system r-build-system) (propagated-inputs `(("r-subplex" ,r-subplex))) (home-page "https://kingaa.github.io/ouch/") @@ -11366,16 +11675,18 @@ components).") (define-public r-fftwtools (package (name "r-fftwtools") - (version "0.9-9") + (version "0.9-11") (source (origin (method url-fetch) (uri (cran-uri "fftwtools" version)) (sha256 (base32 - "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9")))) + "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) (inputs `(("fftw" ,fftw))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description @@ -11391,19 +11702,21 @@ redundant complex conjugate when the input is real data.") (define-public r-tiff (package (name "r-tiff") - (version "0.1-6") + (version "0.1-8") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 - "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2")))) + "18m17g5q3nz4v4wrqxnb129b1j02873g2vknddczkklf1pvq4x2b")))) (build-system r-build-system) (inputs `(("libtiff" ,libtiff) ("libjpeg" ,libjpeg-turbo) ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description @@ -12305,21 +12618,24 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "0.5.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n")))) + "03y29dzz54bw9px5k8a72vmc000lcyrkc5l0izkqcciyi9ijkr3w")))) (build-system r-build-system) (propagated-inputs - `(("r-fs" ,r-fs) + `(("r-cli" ,r-cli) + ("r-fs" ,r-fs) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) + ("r-rappdirs" ,r-rappdirs) ("r-rlang" ,r-rlang) + ("r-rstudioapi" ,r-rstudioapi) ("r-withr" ,r-withr))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -12394,14 +12710,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-2") + (version "0.8-3") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl")))) + "1m9wwwch9wg886147brr2zfih65yfdfs3vmfvim1w6jykycasc9a")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs @@ -12839,14 +13155,14 @@ to throw errors if they aren't in the right form.") (define-public r-dotcall64 (package (name "r-dotcall64") - (version "1.0-0") + (version "1.0-1") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 - "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9")))) + "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -13185,14 +13501,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.43") + (version "2.44") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089")))) + "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -13369,14 +13685,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.23.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p")))) + "1x04pxcyyzmg1rl9mcd7mmxglzmxgy40fmbwpy7vf5y7z15rzrp6")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -13643,14 +13959,14 @@ several common set, element and attribute related tasks.") (define-public r-shinyjqui (package (name "r-shinyjqui") - (version "0.3.3") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjqui" version)) (sha256 (base32 - "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x")) + "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah")) (snippet '(begin (delete-file "inst/www/shinyjqui.min.js"))))) @@ -13860,13 +14176,13 @@ such software by imputing dropout events.") (define-public r-gamlss-dist (package (name "r-gamlss-dist") - (version "5.1-7") + (version "5.3-2") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 - (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq")))) + (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -14117,21 +14433,21 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-7") + (version "0.6-8") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk")))) + "18l49f1v7nrngwra4v983ic8w1d4w23ws8xf36337dq0j6809qj0")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("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, @@ -14819,14 +15135,14 @@ utilities for sequence data management under the ACNUC system.") (define-public r-units (package (name "r-units") - (version "0.6-7") + (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "units" version)) (sha256 (base32 - "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz")))) + "0wwndzjjgqj795xvx1jwa86nwd8adfiwj0pn15yyzzk9baky2axw")))) (build-system r-build-system) (inputs `(("udunits" ,udunits))) @@ -14948,14 +15264,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.2-9") + (version "0.2-10") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "0jfwff5kk0zraspsvbk26lphl3fnrc6xmhl4690hr0a5k177ildm")))) + "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -14972,14 +15288,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-7") + (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja")))) + "096gg2hbynn6mv3w8n69x987fklg5rrgd0d4nbqaw7vhg1jhlmqi")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -15009,14 +15325,14 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-5") + (version "1.1-7") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7")))) + "0sg417d95paww625663lgmk6jwhs88djqzc96gbs1hxazlf77qb1")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -15137,14 +15453,14 @@ genetics of complex population dynamics.") (define-public r-genetics (package (name "r-genetics") - (version "1.3.8.1.2") + (version "1.3.8.1.3") (source (origin (method url-fetch) (uri (cran-uri "genetics" version)) (sha256 (base32 - "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh")))) + "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs `(("r-combinat" ,r-combinat) @@ -15212,13 +15528,13 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.1-1") + (version "6.2-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli")))) + (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) @@ -15258,14 +15574,14 @@ generalized linear models, and quantile regression.") (define-public r-arsenal (package (name "r-arsenal") - (version "3.6.1") + (version "3.6.2") (source (origin (method url-fetch) (uri (cran-uri "arsenal" version)) (sha256 (base32 - "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy")))) + "0spm0s23xs5bm88slkz6a65mbs663qhnravwxp7rkdkr378vb5fn")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs `(("r-knitr" ,r-knitr))) @@ -15881,14 +16197,14 @@ consists of @code{grid} grobs and viewports that can then be manipulated with (define-public r-farver (package (name "r-farver") - (version "2.0.3") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "farver" version)) (sha256 (base32 - "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f")))) + "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75")))) (build-system r-build-system) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") @@ -15956,14 +16272,14 @@ packages with Rcpp.") (define-public r-tweenr (package (name "r-tweenr") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "tweenr" version)) (sha256 (base32 - "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg")))) + "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q")))) (build-system r-build-system) (propagated-inputs `(("r-farver" ,r-farver) @@ -16034,14 +16350,14 @@ sets of URLs.") (define-public r-ggforce (package (name "r-ggforce") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 - "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc")))) + "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -16107,14 +16423,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.") (define-public r-ggraph (package (name "r-ggraph") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "ggraph" version)) (sha256 (base32 - "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w")))) + "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -16144,6 +16460,32 @@ visualizations and provides the same flexible approach to building up plots layer by layer.") (license license:gpl3))) +(define-public r-gkmsvm + (package + (name "r-gkmsvm") + (version "0.81.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gkmSVM" version)) + (sha256 + (base32 + "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) + (properties `((upstream-name . "gkmSVM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernlab" ,r-kernlab) + ("r-rcpp" ,r-rcpp) + ("r-rocr" ,r-rocr) + ("r-seqinr" ,r-seqinr))) + (home-page "https://cran.r-project.org/web/packages/gkmSVM") + (synopsis "Gapped-kmer support vector machine") + (description + "This R package provides tools for training gapped-kmer SVM classifiers +for DNA and protein sequences. This package supports several sequence +kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") + (license license:gpl2+))) + (define-public r-varselrf (package (name "r-varselrf") @@ -16429,6 +16771,64 @@ matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.") (license license:gpl2))) +(define-public r-gridtext + (package + (name "r-gridtext") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "gridtext" version)) + (sha256 + (base32 + "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61")))) + (properties `((upstream-name . "gridtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-jpeg" ,r-jpeg) + ("r-markdown" ,r-markdown) + ("r-png" ,r-png) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rlang" ,r-rlang) + ("r-stringr" ,r-stringr) + ("r-xml2" ,r-xml2))) + (home-page "https://wilkelab.org/gridtext/") + (synopsis "Improved text rendering support for Grid graphics") + (description + "This package provides support for rendering of formatted text using Grid +graphics. Text can be formatted via a minimal subset of Markdown, HTML, and +inline CSS directives, and it can be rendered both with and without word +wrap.") + (license license:expat))) + +(define-public r-ggtext + (package + (name "r-ggtext") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggtext" version)) + (sha256 + (base32 + "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b")))) + (properties `((upstream-name . "ggtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gridtext" ,r-gridtext) + ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://wilkelab.org/ggtext/") + (synopsis "Improved text rendering support for ggplot2") + (description + "This package provides a ggplot2 extension that enables the rendering of +complex formatted plot labels (titles, subtitles, facet labels, axis labels, +etc.). Text boxes with automatic word wrap are also supported.") + (license license:gpl2))) + ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-flexdashboard @@ -16671,14 +17071,14 @@ regular expressions from human readable expressions") (define-public r-xmlparsedata (package (name "r-xmlparsedata") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "xmlparsedata" version)) (sha256 (base32 - "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq")))) + "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n")))) (properties `((upstream-name . "xmlparsedata"))) (build-system r-build-system) (home-page "https://github.com/r-lib/xmlparsedata#readme") @@ -16786,14 +17186,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.3.2") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz")))) + "10fj4cnazicb2z9djbv5pszcmrf7wbzagbjvksffqpdc5vbbbw5x")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -16807,6 +17207,8 @@ batch correction, and data correction.") ("r-tibble" ,r-tibble) ("r-withr" ,r-withr) ("r-xfun" ,r-xfun))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description @@ -17060,14 +17462,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.1-32") + (version "3.1-37") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi")))) + "102fgbdpn7yvm1zj180cv4sr1096sz35d4gndsv7w9kriqyi1c1l")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -17099,14 +17501,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.0.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98")))) + "1qnjbhilv4jfmwqxfi9xc5ysrh8gr84a2a5imjfci7d1n3zcnryn")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -17363,14 +17765,14 @@ LargeVis method of Tang et al. (2016) is also provided.") (define-public r-kableextra (package (name "r-kableextra") - (version "1.3.1") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "kableExtra" version)) (sha256 (base32 - "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf")))) + "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9")))) (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs @@ -17384,6 +17786,7 @@ LargeVis method of Tang et al. (2016) is also provided.") ("r-rvest" ,r-rvest) ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) + ("r-svglite" ,r-svglite) ("r-viridislite" ,r-viridislite) ("r-webshot" ,r-webshot) ("r-xml2" ,r-xml2))) @@ -17751,6 +18154,41 @@ stress majorization by Gansner et al. (2004) emphasize hidden group structures in networks or focus on specific nodes.") (license license:expat))) +(define-public r-terra + (package + (name "r-terra") + (version "1.1-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "terra" version)) + (sha256 + (base32 + "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg")))) + (properties `((upstream-name . "terra"))) + (build-system r-build-system) + (inputs + `(("gdal" ,gdal) + ("geos" ,geos) + ("proj" ,proj) + ("sqlite" ,sqlite) ; needed for proj + ("zlib" ,zlib))) + (propagated-inputs + `(("r-raster" ,r-raster) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://rspatial.org/terra") + (synopsis "Spatial data analysis") + (description + "This package provides methods for spatial data analysis, especially +raster data. The included methods allow for low-level data manipulation as +well as high-level global, local, zonal, and focal computation. The predict +and interpolate methods facilitate the use of regression type (interpolation, +machine learning) models for spatial prediction. Processing of very large +files is supported.") + (license license:gpl3+))) + (define-public r-tidygraph (package (name "r-tidygraph") @@ -17844,14 +18282,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.11.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "020k3vxnp0vjrlkcxx5vj30vag474hw48zxzw9315whsq4hhhbqc")))) + "0dfqn4l4qmlpwmdva2ahyhlngkzdm0sgiirbdrf3mbbw52bhlmpm")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -17929,14 +18367,14 @@ atmospheric physics.") (define-public r-lifecycle (package (name "r-lifecycle") - (version "0.2.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "lifecycle" version)) (sha256 (base32 - "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19")))) + "13hgxk93q9387s8dnqpm8dfx610y0pr76khqksj4kbgj2fr4lcq3")))) (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs @@ -19143,14 +19581,14 @@ discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (define-public r-gamlss-data (package (name "r-gamlss-data") - (version "5.1-4") + (version "6.0-1") (source (origin (method url-fetch) (uri (cran-uri "gamlss.data" version)) (sha256 (base32 - "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd")))) + "1cjb2n5i5mnhmb5qbqycdbfg65j7nxb9s74yihqs9kpa39byrzcq")))) (properties `((upstream-name . "gamlss.data"))) (build-system r-build-system) (home-page "http://www.gamlss.org/") @@ -19164,14 +19602,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.2-0") + (version "5.3-4") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk")))) + "06mh00jjxnqwknbv777hawjk0zm81ixrp35fg59mrlqz8y3p2w3j")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -20375,14 +20813,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-1") + (version "3.1-2") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9")))) + "0gaqm8bkjly2b1jkr1nqnxlp5vqvfpj0a4jd70jv4f9ndlif676y")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) @@ -20452,14 +20890,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.3") + (version "0.42.8") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg")))) + "1kzl93l6k9i4528bbycbqxdn28mj7hnx0fbxisva859xl1wys5c5")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -20601,14 +21039,14 @@ functions.") (define-public r-univoutl (package (name "r-univoutl") - (version "0.2") + (version "0.3") (source (origin (method url-fetch) (uri (cran-uri "univOutl" version)) (sha256 (base32 - "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v")))) + "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp")))) (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs @@ -20816,14 +21254,14 @@ different conceptual parts of the algorithm.") (define-public r-shapes (package (name "r-shapes") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "shapes" version)) (sha256 (base32 - "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s")))) + "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66")))) (properties `((upstream-name . "shapes"))) (build-system r-build-system) (propagated-inputs @@ -21440,14 +21878,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.13") + (version "8.14") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9")))) + "12bfw029xb1dndcjyn2r7a51i7hnkkbdilp69k97sz2v8b7v1y3s")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -21526,14 +21964,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2020.12.04") + (version "2021.02.24") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx")))) + "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") @@ -21616,32 +22054,23 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "2.1.2") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy")))) + "0b1jfkdhpsg5jhjz4p0nf4cmi9p8w40wv3i2f17jf2x1n1y2hjj8")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-extrafont" ,r-extrafont) - ("r-fastmatch" ,r-fastmatch) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-jsonlite" ,r-jsonlite) + `(("r-fastmatch" ,r-fastmatch) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) - ("r-network" ,r-network) - ("r-proxyc" ,r-proxyc) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) - ("r-sna" ,r-sna) ("r-snowballc" ,r-snowballc) ("r-stopwords" ,r-stopwords) ("r-stringi" ,r-stringi) @@ -22002,14 +22431,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.18.1") + (version "2.19.1") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm")))) + "0fbndmwb3krypsavgm3blqkhh8blmi3p186yxmvgv3a9m6r154rj")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -22308,14 +22737,14 @@ Latent regression models and plausible value imputation are also supported.") (define-public r-erm (package (name "r-erm") - (version "1.0-1") + (version "1.0-2") (source (origin (method url-fetch) (uri (cran-uri "eRm" version)) (sha256 (base32 - "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9")))) + "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk")))) (properties `((upstream-name . "eRm"))) (build-system r-build-system) (propagated-inputs @@ -22410,14 +22839,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n")))) + "01cn2vf95nc8bh0hh8imkn030yra3hx64q1fb8jwsr52p9s397fr")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") @@ -22946,18 +23375,16 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr")))) + "0z1qpxcl8b6fi691fbdr3vrb19mn4pas1iff62zl1bafzbdvpmcn")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) - (propagated-inputs - `(("r-testthat" ,r-testthat))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/wilkelab/isoband") @@ -23058,7 +23485,7 @@ 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 @@ -23088,17 +23515,19 @@ appropriate dog and cat images for many status codes.") (define-public r-latex2exp (package (name "r-latex2exp") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "latex2exp" version)) (sha256 (base32 - "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw")))) + "0qknpw7zwwbzsbry94j8fn48mq7kq5rc5448g9hybbisain3wfvg")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr) ("r-magrittr" ,r-magrittr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to @@ -23538,6 +23967,17 @@ 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) @@ -23657,14 +24097,14 @@ vignette for more information and examples.") (define-public r-brms (package (name "r-brms") - (version "2.14.4") + (version "2.15.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j")))) + "0byc3fyvf9qbvvgwf55ih5d4br1nnxlbaidq9fvr11bmv38h25y1")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -23947,14 +24387,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.1.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555")))) + "0aw1zcrg7nhddfaif9544hn8g8qcylv6vzpkf8d3kl07nzvgxkvj")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -23983,14 +24423,14 @@ designed to be distributed and efficient with the following goals: (define-public r-shapforxgboost (package (name "r-shapforxgboost") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 - "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly")))) + "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5")))) (properties `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) @@ -24001,9 +24441,10 @@ designed to be distributed and efficient with the following goals: ("r-ggforce" ,r-ggforce) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) - ("r-lightgbm" ,r-lightgbm) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-xgboost" ,r-xgboost))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/liuyanguu/SHAPforxgboost") (synopsis "SHAP Plots for XGBoost") (description @@ -24335,14 +24776,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "2.0-0") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d")))) + "18gqsc1a85pk69aifi10wprv1c0lci3zxp4wqjb27dlmlbz6jdgd")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -24353,17 +24794,44 @@ diagonals. This package allows you to compute the tensor product of arrays.") which may also be useful for other purposes.") (license license:gpl2+))) +(define-public r-spatstat-sparse + (package + (name "r-spatstat-sparse") + (version "2.0-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.sparse" version)) + (sha256 + (base32 + "1iqrpazb88s4w208adf2qgm4ajwz3kwqck65k9g5l28zw9jcxyr7")))) + (properties + `((upstream-name . "spatstat.sparse"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-matrix" ,r-matrix) + ("r-spatstat-utils" ,r-spatstat-utils) + ("r-tensor" ,r-tensor))) + (home-page "http://spatstat.org/") + (synopsis "Sparse three-dimensional arrays and linear algebra utilities") + (description + "This package defines sparse three-dimensional arrays and supports +standard operations on them. The package also includes utility functions for +matrix calculations that are common in statistics, such as quadratic forms.") + (license license:gpl2+))) + (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "2.0-0") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7")))) + "0csmz5vjaxnznkbsfah8qd3v8p0y56jvis01ialxzvf71snl160v")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -24376,31 +24844,110 @@ which may also be useful for other purposes.") package.") (license license:gpl2+))) -(define-public r-spatstat +(define-public r-spatstat-geom (package - (name "r-spatstat") - (version "1.64-1") + (name "r-spatstat-geom") + (version "2.0-1") (source (origin (method url-fetch) - (uri (cran-uri "spatstat" version)) + (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya")))) - (properties `((upstream-name . "spatstat"))) + "1r7nlgh62apchidg28fxq1a22iv1b29y5xmsg1kjwfvkbq8zxsvh")))) + (properties `((upstream-name . "spatstat.geom"))) + (build-system r-build-system) + (propagated-inputs + `(("r-deldir" ,r-deldir) + ("r-polyclip" ,r-polyclip) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://spatstat.org/") + (synopsis "Geometrical functionality of the spatstat package") + (description + "This is a subset of the original spatstat package, containing the +user-level code from spatstat which performs geometrical operations, except +for the geometry of linear networks.") + (license license:gpl2+))) + +(define-public r-spatstat-core + (package + (name "r-spatstat-core") + (version "2.0-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.core" version)) + (sha256 + (base32 + "19wv27nfx48xkqa1amys4jf93k0d8xns20p84n5kqyibscdsksgx")))) + (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) - ("r-deldir" ,r-deldir) ("r-goftest" ,r-goftest) ("r-matrix" ,r-matrix) ("r-mgcv" ,r-mgcv) ("r-nlme" ,r-nlme) - ("r-polyclip" ,r-polyclip) ("r-rpart" ,r-rpart) ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-sparse" ,r-spatstat-sparse) ("r-spatstat-utils" ,r-spatstat-utils) ("r-tensor" ,r-tensor))) + (home-page "http://spatstat.org/") + (synopsis "Core functionality of the spatstat package") + (description + "This is a subset of the original spatstat package, containing all of the +user-level code from spatstat, except for the code for linear networks.") + (license license:gpl2+))) + +(define-public r-spatstat-linnet + (package + (name "r-spatstat-linnet") + (version "2.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat.linnet" version)) + (sha256 + (base32 + "1ia0qgggddiwhhyd3q516f3p6by0p4xnq26wqz7410n2ja60bbb4")))) + (properties + `((upstream-name . "spatstat.linnet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-utils" ,r-spatstat-utils))) + (home-page "http://spatstat.org/") + (synopsis "Linear networks functionality of the spatstat package") + (description + "This is a subset of the spatstat package, containing its functionality +for spatial data on a linear network.") + (license license:gpl2+))) + +(define-public r-spatstat + (package + (name "r-spatstat") + (version "2.1-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatstat" version)) + (sha256 + (base32 + "0vr5md53247v6crvjvg9m82vc6h914zzvkzfkga8x79hv35ii4as")))) + (properties `((upstream-name . "spatstat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-data" ,r-spatstat-data) + ("r-spatstat-geom" ,r-spatstat-geom) + ("r-spatstat-linnet" ,r-spatstat-linnet) + ("r-spatstat-utils" ,r-spatstat-utils))) (home-page "http://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description @@ -24446,14 +24993,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.2.6") + (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz")))) + "1m31yq3kn5wqvm0ahj08kb4bszbbhfybx3l2x975cjzgv3058h8x")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -24631,14 +25178,14 @@ to speed up repeated queries of the same set of target points.") (define-public r-muhaz (package (name "r-muhaz") - (version "1.2.6.1") + (version "1.2.6.3") (source (origin (method url-fetch) (uri (cran-uri "muhaz" version)) (sha256 (base32 - "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk")))) + "1lzc8arbpcxgfap3dfsgq8crpp1cxd9qlbrhvyvl79zgpxjqx4q2")))) (properties `((upstream-name . "muhaz"))) (build-system r-build-system) (propagated-inputs @@ -24656,26 +25203,36 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "1.1.1") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr")))) + "0vshsijqlzsz0xh426vsswpai1v5c990ggyniqqzsjbg3mn8dbl9")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs - `(("r-desolve" ,r-desolve) + `(("r-assertthat" ,r-assertthat) + ("r-desolve" ,r-desolve) + ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) ("r-mstate" ,r-mstate) ("r-muhaz" ,r-muhaz) ("r-mvtnorm" ,r-mvtnorm) + ("r-numderiv" ,r-numderiv) + ("r-purrr" ,r-purrr) ("r-quadprog" ,r-quadprog) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) + ("r-rstpm2" ,r-rstpm2) ("r-survival" ,r-survival) ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-tidyselect" ,r-tidyselect))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/chjackson/flexsurv-dev") @@ -24841,14 +25398,14 @@ p-value approximations.") (define-public r-survminer (package (name "r-survminer") - (version "0.4.8") + (version "0.4.9") (source (origin (method url-fetch) (uri (cran-uri "survminer" version)) (sha256 (base32 - "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff")))) + "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz")))) (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs @@ -24856,6 +25413,7 @@ p-value approximations.") ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) + ("r-ggtext" ,r-ggtext) ("r-gridextra" ,r-gridextra) ("r-magrittr" ,r-magrittr) ("r-maxstat" ,r-maxstat) @@ -25024,14 +25582,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9")))) + "19ipcxx4qfz28cjkgr1vny03yhmbd3m2v64v30gk5pf73nazvmaz")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs @@ -25042,7 +25600,8 @@ more.") ("r-hardhat" ,r-hardhat) ("r-parsnip" ,r-parsnip) ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidymodels/workflows") @@ -25091,14 +25650,14 @@ workflow. The advantages are: (define-public r-yardstick (package (name "r-yardstick") - (version "0.0.7") + (version "0.0.8") (source (origin (method url-fetch) (uri (cran-uri "yardstick" version)) (sha256 (base32 - "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq")))) + "13b0lyj2k0r568mwlyz9yvp9156rzlj4jqnjazaffh9vwqh4whir")))) (properties `((upstream-name . "yardstick"))) (build-system r-build-system) (propagated-inputs @@ -25106,7 +25665,8 @@ workflow. The advantages are: ("r-generics" ,r-generics) ("r-proc" ,r-proc) ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect))) + ("r-tidyselect" ,r-tidyselect) + ("r-vctrs" ,r-vctrs))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tidymodels/yardstick") @@ -25145,18 +25705,19 @@ observations.") (define-public r-slider (package (name "r-slider") - (version "0.1.5") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "slider" version)) (sha256 (base32 - "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck")))) + "1jijh8f3qcn8fa677sqvgl2fb4r5vca1cw4l2vbcqscxb2hr4bqw")))) (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue) + `(("r-ellipsis" ,r-ellipsis) + ("r-glue" ,r-glue) ("r-rlang" ,r-rlang) ("r-vctrs" ,r-vctrs) ("r-warp" ,r-warp))) @@ -25173,14 +25734,14 @@ sliding windows are to be created.") (define-public r-rsample (package (name "r-rsample") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i")))) + "03qwsvylgmj2a2h764mzy0x57pgzmvjvl0ypmbn4lcf912bvrd2c")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs @@ -25188,7 +25749,6 @@ sliding windows are to be created.") ("r-ellipsis" ,r-ellipsis) ("r-furrr" ,r-furrr) ("r-generics" ,r-generics) - ("r-modeldata" ,r-modeldata) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-slider" ,r-slider) @@ -25208,14 +25768,14 @@ different types of resampling objects (e.g. bootstrap, cross-validation).") (define-public r-dicedesign (package (name "r-dicedesign") - (version "1.8-1") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "DiceDesign" version)) (sha256 (base32 - "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp")))) + "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk")))) (properties `((upstream-name . "DiceDesign"))) (build-system r-build-system) (home-page "http://dice.emse.fr/") @@ -25260,14 +25820,14 @@ for creating, simulating, or validating values for such parameters.") (define-public r-tune (package (name "r-tune") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "tune" version)) (sha256 (base32 - "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37")))) + "05r5jzg96g2z10a2w4w8wq1ysfaxr91acwrvn75pmcy4rmixf293")))) (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs @@ -25279,7 +25839,6 @@ for creating, simulating, or validating values for such parameters.") ("r-ggplot2" ,r-ggplot2) ("r-glue" ,r-glue) ("r-gpfit" ,r-gpfit) - ("r-hardhat" ,r-hardhat) ("r-parsnip" ,r-parsnip) ("r-purrr" ,r-purrr) ("r-recipes" ,r-recipes) @@ -25299,31 +25858,71 @@ for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.") (license license:expat))) +(define-public r-workflowsets + (package + (name "r-workflowsets") + (version "0.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "workflowsets" version)) + (sha256 + (base32 + "1q41isvj7hhbkx3y8k6kazpiygig92xannsz8dpklh0k3j9l3c2p")))) + (properties `((upstream-name . "workflowsets"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cli" ,r-cli) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-prettyunits" ,r-prettyunits) + ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) + ("r-rsample" ,r-rsample) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-tune" ,r-tune) + ("r-vctrs" ,r-vctrs) + ("r-withr" ,r-withr) + ("r-workflows" ,r-workflows))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tidymodels/workflowsets") + (synopsis "Create a collection of tidymodels workflows") + (description + "A workflow is a combination of a model and preprocessors (e.g, a +formula, recipe, etc.). In order to try different combinations of these, an +object can be created that contains many workflows. There are functions to +create workflows en masse as well as training them and visualizing the +results.") + (license license:expat))) + (define-public r-tidyposterior (package (name "r-tidyposterior") - (version "0.0.3") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "tidyposterior" version)) (sha256 (base32 - "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg")))) + "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah")))) (properties `((upstream-name . "tidyposterior"))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) ("r-generics" ,r-generics) ("r-ggplot2" ,r-ggplot2) - ("r-lifecycle" ,r-lifecycle) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-rsample" ,r-rsample) ("r-rstanarm" ,r-rstanarm) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs))) + ("r-tune" ,r-tune) + ("r-vctrs" ,r-vctrs) + ("r-workflowsets" ,r-workflowsets))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://tidyposterior.tidymodels.org") @@ -25626,6 +26225,32 @@ statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse.") (license license:gpl3))) +(define-public r-lsa + (package + (name "r-lsa") + (version "0.73.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "lsa" version)) + (sha256 + (base32 + "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b")))) + (properties `((upstream-name . "lsa"))) + (build-system r-build-system) + (propagated-inputs + `(("r-snowballc" ,r-snowballc))) + (home-page "https://cran.r-project.org/package=lsa") + (synopsis "Latent semantic analysis") + (description + "The basic idea of latent semantic analysis (LSA) is, that text do have a +higher order (=latent semantic) structure which, however, is obscured by word +usage (e.g. through the use of synonyms or polysemy). By using conceptual +indices that are derived statistically via a truncated singular value +decomposition (a two-mode factor analysis) over a given document-term matrix, +this variability problem can be overcome.") + (license license:gpl2+))) + (define-public r-mlecens (package (name "r-mlecens") @@ -25693,14 +26318,14 @@ phylogenetic relatedness) can also be conducted.") (define-public r-altmeta (package (name "r-altmeta") - (version "3.2") + (version "3.3") (source (origin (method url-fetch) (uri (cran-uri "altmeta" version)) (sha256 (base32 - "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0")))) + "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm")))) (properties `((upstream-name . "altmeta"))) (build-system r-build-system) (propagated-inputs @@ -25755,14 +26380,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.47-9") + (version "1.48-1") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b")))) + "098mgmfj8ndi8yipr9b3f6gbbh78cgp9j7y561nlnhrnyc8bsih9")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -25904,13 +26529,13 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn")))) + "17cmp9mimvykb8ny796dn1zwmvg0pwwjw1zcixyamc5q1lwnxi3p")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -25953,7 +26578,8 @@ other R users.") ("r-sctransform" ,r-sctransform) ("r-seuratobject" ,r-seuratobject) ("r-shiny" ,r-shiny) - ("r-spatstat" ,r-spatstat) + ("r-spatstat-core" ,r-spatstat-core) + ("r-spatstat-geom" ,r-spatstat-geom) ("r-tibble" ,r-tibble) ("r-uwot" ,r-uwot))) (home-page "http://www.satijalab.org/seurat") @@ -25970,14 +26596,14 @@ discovery of differentially expressed genes and markers.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.5.5") + (version "2.6.3") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) + "08yqz8qlw960x4b52wzrm22f242xnpc8695pjkhy7bi1nzm303ga")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -25987,6 +26613,8 @@ discovery of differentially expressed genes and markers.") ("r-matrix" ,r-matrix) ("r-quadprog" ,r-quadprog) ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description @@ -26026,33 +26654,6 @@ include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) -(define-public r-absfiltergsea - (package - (name "r-absfiltergsea") - (version "1.5.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "AbsFilterGSEA" version)) - (sha256 - (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) - (properties `((upstream-name . "AbsFilterGSEA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") - (synopsis "Improved false positive control of gene-permuting with absolute filtering") - (description - "This package provides a function that performs gene-permuting of a gene-set -enrichment analysis (GSEA) calculation with or without the absolute filtering. - Without filtering, users can perform (original) two-tailed or one-tailed -absolute GSEA.") - (license license:gpl2))) - (define-public r-calculus (package (name "r-calculus") @@ -26273,13 +26874,13 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3")))) + "0mzicqs8rhzppyd7v3ljqs35k8pp7p2jg5cs7hx21mxr831bwsys")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -26298,13 +26899,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-paradox (package (name "r-paradox") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 - "1fz6sdwvvifm4qbmwgm27dil278mswvcfw8bbsvli5v4l1ghw8kj")))) + "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -26323,13 +26924,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "1arqijbbmhv57mj8kyq30zxykah83ab1d1c7gs0cxs0xhfwln66g")))) + "0qh9vdac1als2123wf51bwa7spdqk33iydlawi5n5dpci892iahl")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -26342,7 +26943,9 @@ implemented as @code{R6} classes.") ("r-mlbench" ,r-mlbench) ("r-mlr3measures" ,r-mlr3measures) ("r-mlr3misc" ,r-mlr3misc) + ("r-palmerpenguins" ,r-palmerpenguins) ("r-paradox" ,r-paradox) + ("r-parallelly" ,r-parallelly) ("r-uuid" ,r-uuid))) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") @@ -26357,13 +26960,13 @@ computational operations, add-on packages provide additional functionality.") (define-public r-mlr3learners (package (name "r-mlr3learners") - (version "0.4.3") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 - "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri")))) + "02v4y32yn1m0akkqzhfg65ib21rgy9iz8db4kdcrvi949clkxnfk")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -26383,14 +26986,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.3.0") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0")))) + "0bd9nxfgsj4ixpgky1mj6knb8l8nivvxpqpyw8vgpkj0za7gp4gr")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -26413,13 +27016,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.6.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "0kxf9wl1jnwyrj2zfmiz12w2594407y44m0xxwp9b2lrwxk31wm7")))) + "16rvsf0jf06yvalydbs7zzn2994hvvyfw975ydiyv3wy1qzgr8bv")))) (build-system r-build-system) (propagated-inputs `(("r-bbotk" ,r-bbotk) @@ -26712,14 +27315,14 @@ clusterings as resolution increases.") (define-public r-textshaping (package (name "r-textshaping") - (version "0.3.0") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 - "053pbw45by96q62kjfnyc3d0ssar9svssrdqy6a09kdmdh75xdar")))) + "0yl3cv6r8k27h4lzbrsikjydhz94skdjmxx4zqzihvb7h3jfnlpn")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs @@ -26745,14 +27348,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "0.4.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "0443dhfi7bjfpap041vrnslw3ql3vpsxx18raz2w9nfdb7id8lsc")))) + "0q28bwjdxpxm1wlkd8sxdf1m1q8wp4mmzp83d3m09nyy90ydkd8w")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -26851,3 +27454,866 @@ from a source package. @code{pkgdown} converts your documentation, vignettes, README file, and more to HTML making it easy to share information about your package online.") (license license:expat))) + +(define-public r-prereg + (package + (name "r-prereg") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "prereg" version)) + (sha256 + (base32 + "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi")))) + (properties `((upstream-name . "prereg"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rmarkdown" ,r-rmarkdown))) + (home-page "https://github.com/crsh/prereg") + (synopsis + "R Markdown Templates to preregister Scientific Studies") + (description + "This package provides a collection of templates to author +preregistration documents for scientific studies in PDF format.") + (license license:gpl3))) + +(define-public r-ez + (package + (name "r-ez") + (version "4.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ez" version)) + (sha256 + (base32 + "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq")))) + (properties `((upstream-name . "ez"))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/mike-lawrence/ez") + (synopsis "Easy Analysis and Visualization of Factorial Experiments") + (description + "Facilitates easy analysis of factorial experiments, including purely +within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs, +and mixed within-and-between-Ss designs. The functions in this package aim to +provide simple, intuitive and consistent specification of data analysis and +visualization. Visualization functions also include design visualization for +pre-analysis data auditing, and correlation matrix visualization. Finally, +this package includes functions for non-parametric analysis, including +permutation tests and bootstrap resampling. The bootstrap function obtains +predictions either by cell means or by more advanced/powerful mixed effects +models, yielding predictions and confidence intervals that may be easily +visualized at any level of the experiment's design.") + (license license:gpl2+))) + +(define-public r-qdapregex + (package + (name "r-qdapregex") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "qdapRegex" version)) + (sha256 + (base32 + "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p")))) + (properties `((upstream-name . "qdapRegex"))) + (build-system r-build-system) + (propagated-inputs `(("r-stringi" ,r-stringi))) + (home-page + "https://trinker.github.com/qdapRegex/") + (synopsis + "Regular Expression Removal, Extraction, and Replacement Tools") + (description + "This package provides a collection of regular expression tools +associated with the @code{qdap} package that may be useful outside of the +context of discourse analysis. Tools include removal/extraction/replacement of +abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, +percentages, citations, person tags, phone numbers, times, and zip codes.") + (license license:gpl2))) + +(define-public r-mgsub + (package + (name "r-mgsub") + (version "1.7.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "mgsub" version)) + (sha256 + (base32 + "02l1b96zv36ia0c97wgcwfhi037mbn3wy9c64hcw0n0w67yj77rr")))) + (properties `((upstream-name . "mgsub"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=mgsub") + (synopsis + "Safe, Multiple, Simultaneous String Substitution") + (description + "Designed to enable simultaneous substitution in strings in a safe +fashion. Safe means it does not rely on placeholders (which can cause errors +in same length matches).") + (license license:expat))) + +(define-public r-textshape + (package + (name "r-textshape") + (version "1.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "textshape" version)) + (sha256 + (base32 + "02111kj3kka84mpx7s19bjna9cas8diw5fxz51v5ggz0ldswa5pa")))) + (properties `((upstream-name . "textshape"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-slam" ,r-slam) + ("r-stringi" ,r-stringi))) + (home-page "https://github.com/trinker/textshape") + (synopsis "Tools for Reshaping Text") + (description + "Tools that can be used to reshape and restructure text data.") + (license license:gpl2))) + +(define-public r-syuzhet + (package + (name "r-syuzhet") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "syuzhet" version)) + (sha256 + (base32 + "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv")))) + (properties `((upstream-name . "syuzhet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dplyr" ,r-dplyr) + ("r-dtt" ,r-dtt) + ("r-nlp" ,r-nlp) + ("r-rlang" ,r-rlang) + ("r-textshape" ,r-textshape) + ("r-tidyr" ,r-tidyr) + ("r-zoo" ,r-zoo))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mjockers/syuzhet") + (synopsis + "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") + (description + "Extracts sentiment and sentiment-derived plot arcs from text using a +variety of sentiment dictionaries conveniently packaged for consumption by R +users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the +Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing} +developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif +M. and Turney, Peter D. Applicable references are available in +@file{README.md} and in the documentation for the @code{get_sentiment} +function. The package also provides a hack for implementing Stanford's coreNLP +sentiment parser. The package provides several methods for plot arc +normalization.") + (license license:gpl3))) + +(define-public r-lexicon + (package + (name "r-lexicon") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lexicon" version)) + (sha256 + (base32 + "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c")))) + (properties `((upstream-name . "lexicon"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-syuzhet" ,r-syuzhet))) + (home-page "https://github.com/trinker/lexicon") + (synopsis "Lexicons for Text Analysis") + (description + "This package provides a collection of lexical hash tables, dictionaries, +and word lists.") + (license license:gpl3))) + +(define-public r-english + (package + (name "r-english") + (version "1.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "english" version)) + (sha256 + (base32 + "0d6rin40wy2y6k75x8d5qvf03rfy139f309wrl8xwbdb1h8fjkd1")))) + (properties `((upstream-name . "english"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=english") + (synopsis "Translate Integers into English") + (description + "Allow numbers to be presented in an English language version, one, two, +three, ... Ordinals are also available, first, second, third, ... and +indefinite article choice, \"a\" or \"an\".") + (license license:gpl2))) + +(define-public r-textclean + (package + (name "r-textclean") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "textclean" version)) + (sha256 + (base32 + "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz")))) + (properties `((upstream-name . "textclean"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-english" ,r-english) + ("r-glue" ,r-glue) + ("r-lexicon" ,r-lexicon) + ("r-mgsub" ,r-mgsub) + ("r-qdapregex" ,r-qdapregex) + ("r-stringi" ,r-stringi) + ("r-textshape" ,r-textshape))) + (home-page + "https://github.com/trinker/textclean") + (synopsis "Text Cleaning Tools") + (description + "Tools to clean and process text. Tools are geared at checking for +substrings that are not optimal for analysis and replacing or removing them +(normalizing) with more analysis friendly substrings (see Sproat, Black, Chen, +Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or +extracting them into new variables. For example, emoticons are often used in +text but not always easily handled by analysis algorithms. The +@code{replace_emoticon()} function replaces emoticons with word equivalents.") + (license license:gpl2))) + +(define-public r-striprtf + (package + (name "r-striprtf") + (version "0.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "striprtf" version)) + (sha256 + (base32 + "1ra6aalalig6drsj26z9s24lmb10zssagqrvgqqi4358zbm8gwcd")))) + (properties `((upstream-name . "striprtf"))) + (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/kota7/striprtf") + (synopsis "Extract Text from RTF File") + (description + "Extracts plain text from @dfn{Rich Text Format} (RTF) file.") + (license license:expat))) + +(define-public r-ndjson + (package + (name "r-ndjson") + (version "0.8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ndjson" version)) + (sha256 + (base32 + "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor gzstream + (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h")) + #t)))) + (properties `((upstream-name . "ndjson"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-gzstream + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Makevars" + (("PKG_LIBS = " all) + (string-append all "-lgzstream "))) + #t))))) + (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream))) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://gitlab.com/hrbrmstr/ndjson") + (synopsis + "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") + (description + "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many +modern ndjson files contain large numbers of records. These constructs may not +be columnar in nature, but it is often useful to read in these files and +\"flatten\" the structure out to enable working with the data in an R +@code{data.frame}-like context. Functions are provided that make it possible +to read in plain ndjson files or compressed (@code{gz}) ndjson files and either +validate the format of the records or create \"flat\" @code{data.table} +structures from them.") + (license license:expat))) + +(define-public r-streamr + (package + (name "r-streamr") + (version "0.4.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "streamR" version)) + (sha256 + (base32 + "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix")))) + (properties `((upstream-name . "streamR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ndjson" ,r-ndjson) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson))) + (home-page + "https://cran.r-project.org/package=streamR") + (synopsis + "Access to Twitter Streaming API via R") + (description + "This package provides functions to access Twitter's filter, sample, and +user streams, and to parse the output into data frames.") + (license license:gpl2))) + +(define-public r-readods + (package + (name "r-readods") + (version "1.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "readODS" version)) + (sha256 + (base32 + "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n")))) + (properties `((upstream-name . "readODS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cellranger" ,r-cellranger) + ("r-readr" ,r-readr) + ("r-stringi" ,r-stringi) + ("r-xml2" ,r-xml2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/package=readODS") + (synopsis "Read and Write ODS Files") + (description + "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. +Also support writing data frame into ODS file.") + (license license:gpl3))) + +(define-public r-qpdf + (package + (name "r-qpdf") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "qpdf" version)) + (sha256 + (base32 + "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor libqpdf + (delete-file-recursively "src/libqpdf") + (delete-file-recursively "src/include/qpdf") + #t)))) + (properties `((upstream-name . "qpdf"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'configure + (lambda _ + (setenv "EXTERNAL_QPDF" "1") + #t))))) + (inputs + `(("zlib" ,zlib) + ("qpdf" ,qpdf))) + (propagated-inputs + `(("r-askpass" ,r-askpass) + ("r-curl" ,r-curl) + ("r-rcpp" ,r-rcpp))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/ropensci/qpdf") + (synopsis + "Split, Combine and Compress PDF Files") + (description + "Content-preserving transformations transformations of PDF files such as +split, combine, and compress. This package interfaces directly to the +@code{qpdf} C++ API and does not require any command line utilities. Note that +@code{qpdf} does not read actual content from PDF files: to extract text and +data you need the @code{pdftools} package.") + (license license:asl2.0))) + +(define-public r-pdftools + (package + (name "r-pdftools") + (version "2.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "pdftools" version)) + (sha256 + (base32 + "01i5g2mjkshis0zlm7lrvi7kkzl4dn3if1hzwkgzf9n2mi33ndsx")))) + (properties `((upstream-name . "pdftools"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib) + ("poppler" ,poppler))) + (propagated-inputs + `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page + "https://docs.ropensci.org/pdftools/") + (synopsis + "Text Extraction, Rendering and Converting of PDF Documents") + (description + "Utilities based on @code{libpoppler} for extracting text, fonts, +attachments and metadata from a PDF file. Also supports high quality rendering +of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for +further processing in R.") + (license license:expat))) + +(define-public r-antiword + (package + (name "r-antiword") + (version "1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "antiword" version)) + (sha256 + (base32 + "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j")) + (modules '((guix build utils))) + (snippet + '(begin + ;; unvendor libantiword + (delete-file-recursively "src") + #t)))) + (properties `((upstream-name . "antiword"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-antiword + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "R/antiword.R" + (("system.file\\(\"bin\", package = \"antiword\"\\)") + (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) + #t))))) + (inputs `(("antiword" ,antiword))) + (propagated-inputs `(("r-sys" ,r-sys))) + (home-page + "https://github.com/ropensci/antiword#readme") + (synopsis + "Extract Text from Microsoft Word Documents") + (description + "Wraps the @code{AntiWord} utility to extract text from Microsoft Word +documents. The utility only supports the old @code{doc} format, not the new +xml based @code{docx} format. Use the @code{xml2} package to read the +latter.") + (license license:gpl2))) + +(define-public r-readtext + (package + (name "r-readtext") + (version "0.80") + (source + (origin + (method url-fetch) + (uri (cran-uri "readtext" version)) + (sha256 + (base32 + "0q8ajnp99fwvh14ppkm2z3gqwdwmjrvxvsfb4q7ad0dhkqric05y")))) + (properties `((upstream-name . "readtext"))) + (build-system r-build-system) + (propagated-inputs + `(("r-antiword" ,r-antiword) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-pdftools" ,r-pdftools) + ("r-readods" ,r-readods) + ("r-readxl" ,r-readxl) + ("r-streamr" ,r-streamr) + ("r-stringi" ,r-stringi) + ("r-striprtf" ,r-striprtf) + ("r-tibble" ,r-tibble) + ("r-xml2" ,r-xml2))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/quanteda/readtext") + (synopsis + "Import and Handling for Plain and Formatted Text Files") + (description + "This package provides functions for importing and handling text files +and formatted text files with additional meta-data, such including @code{.csv}, +@code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc}, +@code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.") + (license license:gpl3))) + +(define-public r-packcircles + (package + (name "r-packcircles") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "packcircles" version)) + (sha256 + (base32 + "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) + (properties `((upstream-name . "packcircles"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/mbedward/packcircles") + (synopsis "Circle Packing") + (description + "Algorithms to find arrangements of non-overlapping circles.") + (license license:expat))) + +;; Cannot unbundle liblwgeom, because PostGIS does not support building it on +;; its own. +(define-public r-lwgeom + (package + (name "r-lwgeom") + (version "0.2-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "lwgeom" version)) + (sha256 + (base32 + "1733iwinn426bcmgjxp4j0scvbz35rvqkanmw7g7f47l6j7w14vn")))) + (properties `((upstream-name . "lwgeom"))) + (build-system r-build-system) + (inputs + `(("geos" ,geos) + ("proj" ,proj) + ("sqlite" ,sqlite) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-sf" ,r-sf) + ("r-units" ,r-units))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/r-spatial/lwgeom/") + (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") + (description + "Access to selected functions found in +@url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the +light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") + (license license:gpl2))) + +(define-public r-stars + (package + (name "r-stars") + (version "0.5-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "stars" version)) + (sha256 + (base32 + "0w2svw02ywvclq0nsnjns1n0rfr54q7x30y64y14n7zfr969ly1n")))) + (properties `((upstream-name . "stars"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-classint" ,r-classint) + ("r-lwgeom" ,r-lwgeom) + ("r-rlang" ,r-rlang) + ("r-sf" ,r-sf) + ("r-units" ,r-units))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://r-spatial.github.io/stars/") + (synopsis + "Spatiotemporal Arrays, Raster and Vector Data Cubes") + (description + "Reading, manipulating, writing and plotting spatiotemporal arrays +(raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided +by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.") + (license license:asl2.0))) + +(define-public r-tmaptools + (package + (name "r-tmaptools") + (version "3.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "tmaptools" version)) + (sha256 + (base32 + "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx")))) + (properties `((upstream-name . "tmaptools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dichromat" ,r-dichromat) + ("r-lwgeom" ,r-lwgeom) + ("r-magrittr" ,r-magrittr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-sf" ,r-sf) + ("r-stars" ,r-stars) + ("r-units" ,r-units) + ("r-viridislite" ,r-viridislite) + ("r-xml" ,r-xml))) + (home-page + "https://github.com/mtennekes/tmaptools") + (synopsis "Thematic Map Tools") + (description + "Set of tools for reading and processing spatial data. The aim is to +supply the workflow to create thematic maps. This package also facilitates +@code{tmap}, the package for visualizing thematic maps.") + (license license:gpl3))) + +(define-public r-rworldmap + (package + (name "r-rworldmap") + (version "1.3-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "rworldmap" version)) + (sha256 + (base32 + "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk")))) + (properties `((upstream-name . "rworldmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fields" ,r-fields) + ("r-maptools" ,r-maptools) + ("r-sp" ,r-sp))) + (home-page + "https://github.com/AndySouth/rworldmap/") + (synopsis "Mapping Global Data") + (description + "Enables mapping of country level and gridded user datasets.") + (license license:gpl2+))) + +(define-public r-rtweet + (package + (name "r-rtweet") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rtweet" version)) + (sha256 + (base32 + "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n")))) + (properties `((upstream-name . "rtweet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httpuv" ,r-httpuv) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr) + ("r-progress" ,r-progress) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://docs.ropensci.org/rtweet/") + (synopsis "Collecting Twitter Data") + (description + "An implementation of calls designed to collect and organize Twitter data +via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream +Application Program Interfaces (API)}.") + (license license:expat))) + +(define-public r-intervals + (package + (name "r-intervals") + (version "0.15.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "intervals" version)) + (sha256 + (base32 + "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb")))) + (properties `((upstream-name . "intervals"))) + (build-system r-build-system) + (home-page "https://github.com/edzer/intervals") + (synopsis + "Tools for Working with Points and Intervals") + (description + "Tools for working with and comparing sets of points and intervals.") + (license license:artistic2.0))) + +(define-public r-eyelinker + (package + (name "r-eyelinker") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "eyelinker" version)) + (sha256 + (base32 + "14rfcdxad9iazwd46q6bm8gg1ryh6s8kf7arj00hhb7xz3gvk9c2")))) + (properties `((upstream-name . "eyelinker"))) + (build-system r-build-system) + (propagated-inputs + `(("r-intervals" ,r-intervals) + ("r-readr" ,r-readr) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/a-hurst/eyelinker") + (synopsis + "Import ASC Files from EyeLink Eye Trackers") + (description + "Imports plain-text ASC data files from EyeLink eye trackers into +(relatively) tidy data frames for analysis and visualization.") + (license license:gpl3))) + +(define-public r-btm + (package + (name "r-btm") + (version "0.3.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "BTM" version)) + (sha256 + (base32 + "1x6bncb7r97z8bdyxnn2frdi9kyawfy6c2041mv9f42zdrfzm6jb")))) + (properties `((upstream-name . "BTM"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bnosac/BTM") + (synopsis "Biterm Topic Models for Short Text") + (description + "Biterm Topic Models find topics in collections of short texts. It is a +word co-occurrence based topic model that learns topics by modeling word-word +co-occurrences patterns which are called biterms. This in contrast to +traditional topic models like Latent Dirichlet Allocation and Probabilistic +Latent Semantic Analysis which are word-document co-occurrence topic models. A +biterm consists of two words co-occurring in the same short text window. This +context window can for example be a twitter message, a short answer on a +survey, a sentence of a text or a document identifier. The techniques are +explained in detail in the paper 'A Biterm Topic Model For Short Text' by +Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) +@url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\ +BTM-WWW13.pdf}.") + (license license:asl2.0))) + +(define-public r-textplot + (package + (name "r-textplot") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "textplot" version)) + (sha256 + (base32 + "1sgkndy2cxk8c76h8hwajn6f78w5jj2n8vsmaxh9kj931crzn8cy")))) + (properties `((upstream-name . "textplot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/bnosac/textplot") + (synopsis "Text Plots") + (description + "Visualise complex relations in texts. This is done by providing +functionalities for displaying text co-occurrence networks, text correlation +networks, dependency relationships as well as text clustering. Feel free to +join the effort of providing interesting text visualisations.") + (license license:gpl2))) + +(define-public r-gsa + (package + (name "r-gsa") + (version "1.03.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "GSA" version)) + (sha256 + (base32 + "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1")))) + (properties `((upstream-name . "GSA"))) + (build-system r-build-system) + (home-page "https://statweb.stanford.edu/~tibs/GSA/") + (synopsis "Gene set analysis") + (description "This package lets you determine the significance of +pre-defined sets of genes with respect to an outcome variable, such as a group +indicator, a quantitative variable or a survival time.") + ;; Any version of the LGPL + (license license:lgpl3+))) + +(define-public r-samr + (package + (name "r-samr") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "samr" version)) + (sha256 + (base32 + "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) + (properties `((upstream-name . "samr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gsa" ,r-gsa) + ("r-impute" ,r-impute) + ("r-matrixstats" ,r-matrixstats) + ("r-openxlsx" ,r-openxlsx) + ("r-shiny" ,r-shiny) + ("r-shinyfiles" ,r-shinyfiles))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://statweb.stanford.edu/~tibs/SAM/") + (synopsis "Significance analysis of Microarrays") + (description + "This is a package for significance analysis of Microarrays for +differential expression analysis, RNAseq data and related problems.") + ;; Any version of the LGPL + (license license:lgpl3+))) |