diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1552 |
1 files changed, 1309 insertions, 243 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0483af3d6b..1db2e1c27a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> @@ -55,6 +55,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix utils) + #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages algebra) @@ -63,6 +64,7 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) @@ -126,14 +128,14 @@ files and provide more explicit control over line endings.") (define-public r-diffobj (package (name "r-diffobj") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 - "0v18zz14g8ppzmj1d997rdmsfh327ml4wvpmfx168lravdsk5ym2")))) + "1x3d5sk8mk0s2d7dq8wxi1zv6krlx33n22ls2jwnb58b8xrmakj1")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) (propagated-inputs `(("r-crayon" ,r-crayon))) @@ -178,14 +180,14 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.17") + (version "0.18") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "1wbwva5n88dw3vvhcrlzkr58cv03hyx0dqgfmxj7d0dgf4ichr3c")))) + "1srczjy9dqw06glrv95798xsg462kfbbwm3yk1fv1zhpz9jhakwv")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs @@ -639,13 +641,13 @@ objects.") (define-public r-mboost (package (name "r-mboost") - (version "2.9-3") + (version "2.9-4") (source (origin (method url-fetch) (uri (cran-uri "mboost" version)) (sha256 (base32 - "1qp5c43kc0939sss5w3hhn794lbi69wgfsa31sq4c8vzh35pjqmf")))) + "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -1024,19 +1026,17 @@ into a pipeline of data manipulation and visualisation.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.5.4") + (version "1.5.5") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm")) + "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. - (patches (search-patches "r-httpuv-1.5.4-unvendor-libuv.patch")) - (modules '((guix build utils) - (ice-9 ftw) - (srfi srfi-1))) + (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch")) + (modules '((guix build utils))) (snippet `(begin (delete-file-recursively "src/libuv") @@ -1080,13 +1080,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1wygpnycmyf339x92hwapqk7nc1gs9cadx890b809a9spjhah41a")))) + "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -1106,13 +1106,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.20") + (version "0.21") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0px75vkc6q4iwbirr27bbrbpv0v9ial7zijnbd6dhjccwxl3x1l3")))) + "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) @@ -1130,13 +1130,13 @@ directory.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz")))) + "01v33zcs9rv16r6v8ckqh92k5axj6skmk9hyakmqqmgra522xj3a")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -1151,13 +1151,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.5.2") + (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "0072wlkl58lav3qszzqw6pmx8qra4784r0yb6rx4lg7rbrik6335")))) + "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -1725,17 +1725,142 @@ in R and Shiny via the D3 visualization library.") ;; 3-clause BSD license. (license (list license:gpl3+ license:bsd-3))))) +(define-public r-wesanderson + (package + (name "r-wesanderson") + (version "0.3.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "wesanderson" version)) + (sha256 + (base32 + "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2")))) + (properties `((upstream-name . "wesanderson"))) + (build-system r-build-system) + (home-page "https://github.com/karthik/wesanderson") + (synopsis "Wes Anderson color palette generator") + (description + "This package provides color palettes that have been generated mostly +from Wes Anderson movies.") + (license license:expat))) + +(define-public r-tablerdash + (package + (name "r-tablerdash") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tablerDash" version)) + (sha256 + (base32 + "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm")) + (snippet + '(begin + ;; Delete minified JavaScript + (for-each delete-file + '("inst/tablerDash-0.1.0/require.min.js" + "inst/bootstrap-4.0.0/bootstrap.bundle.min.js")) + #true)))) + (properties `((upstream-name . "tablerDash"))) + (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" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-requirejs") + "tablerDash-0.1.0/require.min.js") + (,(assoc-ref inputs "js-bootstrap") + "bootstrap-4.0.0/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)))) + #t))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("esbuild" ,esbuild) + ("js-requirejs" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js") + (sha256 + (base32 + "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds")))) + ("js-bootstrap" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/twbs/bootstrap/\ +v4.0.0/dist/js/bootstrap.bundle.js") + (sha256 + (base32 + "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj")))))) + (home-page "https://rinterface.github.io/tablerDash/") + (synopsis "Tabler API for Shiny") + (description + "This package provides an R interface to the +@url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap +4 dashboard template. There are different layouts available such as a one +page dashboard or a multi-page template, where the navigation menu is +contained in the navigation bar.") + (license license:gpl2+))) + +(define-public r-spelling + (package + (name "r-spelling") + (version "2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "spelling" version)) + (sha256 + (base32 + "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl")))) + (properties `((upstream-name . "spelling"))) + (build-system r-build-system) + (propagated-inputs + `(("r-commonmark" ,r-commonmark) + ("r-hunspell" ,r-hunspell) + ("r-knitr" ,r-knitr) + ("r-xml2" ,r-xml2))) + (home-page "https://docs.ropensci.org/spelling/") + (synopsis "Tools for spell checking in R") + (description + "This is an R package for spell checking common document formats +including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes +utilities to automate checking of documentation and vignettes as a unit test +during @code{R CMD check}. Both British and American English are supported +out of the box and other languages can be added. In addition, packages may +define a wordlist to allow custom terminology without having to abuse +punctuation.") + (license license:expat))) + (define-public r-crosstalk (package (name "r-crosstalk") - (version "1.1.0.1") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 - "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn")))) + "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -2143,13 +2268,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-10") + (version "1.2-11") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "1jg68rqhk2r0h2hk50xl99zp56b1nfdcam06kfvssqrkgkavkswf")))) + "00n6a74x257m2jk7jadjfxaclihxqpqwh356bgxmq8rag0nk70rs")))) (build-system r-build-system) (propagated-inputs `(("r-formula" ,r-formula) @@ -2241,13 +2366,13 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "1gdbrjq4kiwm45c6pb23mp327qyjvslhyf72ca4zhlzwc5vgp6xk")))) + (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -2298,13 +2423,13 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq")))) + (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -2473,14 +2598,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.11") + (version "0.4.12") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "1s84xl7kv3qc1261xxaq4aqh64gwywhacsf5nh6yf8djw0d1w42d")))) + "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) @@ -2581,14 +2706,14 @@ compare different dendrograms to one another.") (define-public r-getoptlong (package (name "r-getoptlong") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 - "0l9pa9dx8pcg3j7jn4b9k98g7r5vdsvnmf6apnifzm57mc0vlkg6")))) + "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs @@ -2718,13 +2843,13 @@ quantities.") (define-public r-restrserve (package (name "r-restrserve") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "RestRserve" version)) (sha256 - (base32 "07mm65yxzpwlg6x3lsggj41v8nl4m6v9mszhqjpgj19v3yxvwgi0")))) + (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) @@ -2774,20 +2899,22 @@ package also provides a C++ API, that works with or without Rcpp.") (define-public r-ggally (package (name "r-ggally") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "GGally" version)) (sha256 (base32 - "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s")))) + "0lvcvlc8p2cii7rqx7m81f7cv3kk9mlf7cbbgv7l75g7ljw8dyvz")))) (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs - `(("libressl" ,libressl))) + `(("openssl" ,openssl))) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) + `(("r-dplyr" ,r-dplyr) + ("r-forcats" ,r-forcats) + ("r-ggplot2" ,r-ggplot2) ("r-gtable" ,r-gtable) ("r-lifecycle" ,r-lifecycle) ("r-plyr" ,r-plyr) @@ -2795,7 +2922,8 @@ package also provides a C++ API, that works with or without Rcpp.") ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape" ,r-reshape) ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + ("r-scales" ,r-scales) + ("r-tidyr" ,r-tidyr))) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description @@ -2830,13 +2958,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.4-4") + (version "1.4-5") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "0zzw1gfic5b311vrbkmmmaap3yllgd192af067l5ymm885jqm1zs")))) + (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -3387,14 +3515,14 @@ contexts.") (define-public r-squarem (package (name "r-squarem") - (version "2020.5") + (version "2021.1") (source (origin (method url-fetch) (uri (cran-uri "SQUAREM" version)) (sha256 (base32 - "1f0j5pbsz2wi7dfl8h8gvdl991bjywiwkd2f6z0xgkh87kl5y0b4")))) + "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6")))) (properties `((upstream-name . "SQUAREM"))) (build-system r-build-system) (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html") @@ -3552,14 +3680,14 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.20") + (version "0.10.21") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i")))) + "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs @@ -3765,14 +3893,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.0.9") + (version "2.0.12") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0wdh580a0psbdil28n0d85hnp42wmn11hcbnihjq8r7h54drgzpn")))) + "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -3818,14 +3946,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.2") + (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "18qkgw5f46cfr8sc7r9a261ivn3s4w88sdj653gaa20723179300")))) + "0bxwmqj37m06ci378xqlf7kar7pg5g903i1vnrv4i256dkj50mny")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -3922,18 +4050,19 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.8.2") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d")))) + "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -4228,14 +4357,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.6.9") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0l93r1hkr483hp4yd7rm7mdkgl5lp0nkvv0inahj3r1cplgfxpvs")))) + "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -4539,20 +4668,22 @@ plotting. a three dimensional point cloud.") (define-public r-ggridges (package (name "r-ggridges") - (version "0.5.2") + (version "0.5.3") (source (origin (method url-fetch) (uri (cran-uri "ggridges" version)) (sha256 (base32 - "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh")))) + "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-plyr" ,r-plyr) ("r-scales" ,r-scales) ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description @@ -4798,13 +4929,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.19") + (version "0.20") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "15yyigkl1g9w9d7097hrm94dxn1af333ywr5xdw78qqrw6npn0iv")))) + (base32 "043wv9qihs3r29810mf8ajpn2iks1bxq44wbxz8sfpix5b8kjhi8")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -4861,14 +4992,14 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "1k1mcq7jkpc55dsm0wb4k8asc1irvmi5884v3ap4sabf22c5sq0i")))) + "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -4948,14 +5079,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.27") + (version "0.28") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "10hbc9h1fsw91w5f4fjcaqy68b3n1wr6pml01fnkf3pdjiri5sj0")))) + "11pa1q7gl17ala74lz10qbghk2yqanl9pylwvi9b4kmhx856b83n")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4969,6 +5100,41 @@ functions to compile LaTeX documents, and install missing LaTeX packages automatically.") (license license:expat))) +(define-public r-tinytest + (package + (name "r-tinytest") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "tinytest" version)) + (sha256 + (base32 + "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45")))) + (properties `((upstream-name . "tinytest"))) + (build-system r-build-system) + (home-page "https://github.com/markvanderloo/tinytest") + (synopsis "Lightweight unit testing framework") + (description + "This package provides a lightweight unit testing framework. Main +features: + +@enumerate +@item install tests with the package; +@item test results are treated as data that can be stored and manipulated; +@item test files are R scripts interspersed with test commands, that can be + programmed over; +@item fully automated build-install-test sequence for packages; +@item skip tests when not run locally (e.g. on CRAN); +@item flexible and configurable output printing; +@item compare computed output with output stored with the package; +@item run tests in parallel; +@item extensible by other packages; +@item report side effects. +@end enumerate +") + (license license:gpl3))) + (define-public r-network (package (name "r-network") @@ -5496,14 +5662,14 @@ sample Robust Rank-Order Distributional Test.") (define-public r-expm (package (name "r-expm") - (version "0.999-5") + (version "0.999-6") (source (origin (method url-fetch) (uri (cran-uri "expm" version)) (sha256 (base32 - "0y98ya8rhy891nysjlzzy7kcm13dsz8gvxwzvbkmcp1xx0vicxc7")))) + "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) @@ -6042,14 +6208,14 @@ specific S3-method.") (define-public r-vim (package (name "r-vim") - (version "6.0.0") + (version "6.1.0") (source (origin (method url-fetch) (uri (cran-uri "VIM" version)) (sha256 (base32 - "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv")))) + "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz")))) (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs @@ -6485,6 +6651,31 @@ promises, but with a syntax that is idiomatic R.") using the @code{snow} package.") (license license:gpl2))) +(define-public r-fst + (package + (name "r-fst") + (version "0.9.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "fst" version)) + (sha256 + (base32 + "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr")))) + (properties `((upstream-name . "fst"))) + (build-system r-build-system) + (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (home-page "http://www.fstpackage.org") + (synopsis "Fast serialization of data frames") + (description + "The fst package for R provides a fast, easy and flexible way to +serialize data frames. With access speeds of multiple GB/s, fst is +specifically designed to unlock the potential of high speed solid state disks. +Data frames stored in the fst format have full random access, both in column +and rows. The fst format allows for random access of stored data and +compression with the LZ4 and ZSTD compressors.") + (license license:agpl3))) + (define-public r-snowfall (package (name "r-snowfall") @@ -6507,6 +6698,176 @@ to the cluster management tool @code{sfCluster}, but can also used without it.") (license license:gpl2+))) +(define-public r-rgexf + (package + (name "r-rgexf") + (version "0.16.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rgexf" version)) + (sha256 + (base32 + "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra")) + (snippet + '(begin + ;; Delete minified JavaScript files + (for-each delete-file + '("inst/gexf-js/js/jquery-2.0.2.min.js" + "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js" + "inst/gexf-js/js/jquery.mousewheel.min.js")) + #true)))) + (properties `((upstream-name . "rgexf"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1) + (ice-9 popen)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui")) + (with-directory-excursion "inst/gexf-js/js/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery") + "jquery-2.0.2.min.js") + ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js" + "jquery-ui-1.10.3.custom.min.js") + (,(assoc-ref inputs "js-jquery-mousewheel") + "jquery.mousewheel.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets)))) + #t))))) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-servr" ,r-servr) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("esbuild" ,esbuild) + ("unzip" ,unzip) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-2.0.2.js") + (sha256 + (base32 + "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj")))) + ("js-jquery-ui" + ,(origin + (method url-fetch) + (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip") + (sha256 + (base32 + "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx")))) + ("js-jquery-mousewheel" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\ +3.0.6/jquery.mousewheel.js") + (sha256 + (base32 + "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v")))))) + (home-page "https://gvegayon.github.io/rgexf") + (synopsis "Build, import and export GEXF graph files") + (description + "Create, read and write GEXF (Graph Exchange XML Format) graph +files (used in Gephi and others). It allows the user to easily build/read +graph files including attributes, GEXF visual attributes (such as color, size, +and position), network dynamics (for both edges and nodes) and edge weighting. +Users can build/handle graphs element-by-element or massively through +data-frames, visualize the graph on a web browser through gexf-js (a +JavaScript library) and interact with the igraph package.") + (license license:expat))) + +(define-public r-data-tree + (package + (name "r-data-tree") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "data.tree" version)) + (sha256 + (base32 + "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0")))) + (properties `((upstream-name . "data.tree"))) + (build-system r-build-system) + (propagated-inputs + `(("r-r6" ,r-r6) + ("r-stringi" ,r-stringi))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://github.com/gluc/data.tree") + (synopsis "General purpose hierarchical data structure") + (description + "Create tree structures from hierarchical data, and traverse the tree in +various orders. Aggregate, cumulate, print, plot, convert to and from +data.frame and more. This is useful for decision trees, machine learning, +finance, conversion from and to JSON, and many other applications.") + (license license:gpl2+))) + +(define-public r-collapsibletree + (package + (name "r-collapsibletree") + (version "0.1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "collapsibleTree" version)) + (sha256 + (base32 + "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343")) + (snippet + '(begin + ;; Delete minified JavaScript file + (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js") + #true)))) + (properties + `((upstream-name . "collapsibleTree"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/" + (let ((source (assoc-ref inputs "d3.v4.js")) + (target "d3.min.js")) + (format #t "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) + (propagated-inputs + `(("r-data-tree" ,r-data-tree) + ("r-htmlwidgets" ,r-htmlwidgets))) + (native-inputs + `(("esbuild" ,esbuild) + ("d3.v4.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) + (home-page "https://github.com/AdeelK93/collapsibleTree") + (synopsis "Interactive collapsible tree diagrams using D3.js") + (description + "This is a package for interactive Reingold-Tilford tree diagrams created +using D3.js, where every node can be expanded and collapsed by clicking on it. +Tooltips and color gradients can be mapped to nodes using a numeric column in +the source data frame.") + (license license:gpl3+))) + (define-public r-rappdirs (package (name "r-rappdirs") @@ -6527,17 +6888,75 @@ user's computer should be used to save data, caches and logs. It is a port of Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (license license:expat))) +(define-public r-rastervis + (package + (name "r-rastervis") + (version "0.49") + (source + (origin + (method url-fetch) + (uri (cran-uri "rasterVis" version)) + (sha256 + (base32 + "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk")))) + (properties `((upstream-name . "rasterVis"))) + (build-system r-build-system) + (propagated-inputs + `(("r-hexbin" ,r-hexbin) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-raster" ,r-raster) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-sp" ,r-sp) + ("r-viridislite" ,r-viridislite) + ("r-zoo" ,r-zoo))) + (home-page "https://oscarperpinan.github.io/rastervis/") + (synopsis "Visualization methods for raster data") + (description + "This package provides methods for enhanced visualization and interaction +with raster data. It implements visualization methods for quantitative data +and categorical data, both for univariate and multivariate rasters. It also +provides methods to display spatiotemporal rasters, and vector fields.") + (license license:gpl3))) + +(define-public r-rentrez + (package + (name "r-rentrez") + (version "1.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rentrez" version)) + (sha256 + (base32 + "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv")))) + (properties `((upstream-name . "rentrez"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/rentrez/") + (synopsis "Entrez in R") + (description + "This package provides an R interface to the NCBI's EUtils API, +allowing users to search databases like GenBank PubMed, process the results of +those searches and pull data into their R sessions.") + (license license:expat))) + (define-public r-renv (package (name "r-renv") - (version "0.12.3") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0k31x19gzpffb701c76p840cip10c0dh8yv3wcs30gqi0ag1g77l")))) + "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -6867,19 +7286,20 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.3") + (version "2.4") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6")))) + "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) ("r-cluster" ,r-cluster) + ("r-dt" ,r-dt) ("r-ellipse" ,r-ellipse) ("r-flashclust" ,r-flashclust) ("r-ggplot2" ,r-ggplot2) @@ -6888,6 +7308,8 @@ clustering.") ("r-leaps" ,r-leaps) ("r-mass" ,r-mass) ("r-scatterplot3d" ,r-scatterplot3d))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://factominer.free.fr") (synopsis "Multivariate exploratory data analysis and data mining") (description @@ -6938,14 +7360,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w")))) + "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -7147,18 +7569,17 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.15") + (version "0.3.16") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1s9hrkdx105c1plpxywv68bmp8hvvxbdizhwx81fxr79fhj62x5j")))) + "1ls5kp70jfxrzxxb3xrg8sn2fyk6qd7rmx23n5jxi7z7850avjrj")))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) + `(("r-r6" ,r-r6) ("r-uuid" ,r-uuid) ("r-xml2" ,r-xml2) ("r-zip" ,r-zip))) @@ -7180,14 +7601,14 @@ to help insert or delete content at a specific location in the document.") (define-public r-profilemodel (package (name "r-profilemodel") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "profileModel" version)) (sha256 (base32 - "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8")))) + "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i")))) (properties `((upstream-name . "profileModel"))) (build-system r-build-system) (home-page "https://github.com/ikosmidis/profileModel") @@ -7409,14 +7830,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.11.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1m95xfvai1kbzqxdggjvdbk6ax2dg4v2lrfpqn7v607g2n77n2k0")))) + "0gkvcw9d729ql1gfrpxzgrag4xafd0hchrdww215qz11ma1rzy7s")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7463,14 +7884,14 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.8.5") + (version "2.8.6") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk")))) + "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -7514,23 +7935,25 @@ hypothesis of normality.") (define-public r-moonbook (package (name "r-moonbook") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "moonBook" version)) (sha256 (base32 - "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6")))) + "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry")))) (properties `((upstream-name . "moonBook"))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) ("r-nortest" ,r-nortest) - ("r-purrr" ,r-purrr) ("r-sjmisc" ,r-sjmisc) ("r-stringr" ,r-stringr) - ("r-survival" ,r-survival))) + ("r-survival" ,r-survival) + ("r-ztable" ,r-ztable))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/cardiomoon/moonBook") (synopsis "Functions and datasets for the book by Keon-Woong Moon") (description @@ -7769,14 +8192,14 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "4.1.1") + (version "4.1.2") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "1fzchsignpb7cpizbf6l8v9k1nkmaf4r4j3mnxz0csl2g2npi1xc")))) + "1j9sh1w9lsnnhlh59g4ghykyfx46rxh380s8imvm7pzna7rw7c64")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/Deriv") @@ -7901,14 +8324,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.16.2") + (version "1.17.0.1") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn")))) + "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -8176,13 +8599,13 @@ and coverage methods to tune the choice of threshold.") (define-public r-ggstance (package (name "r-ggstance") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "ggstance" version)) (sha256 - (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1")))) + (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -8202,13 +8625,13 @@ and coverage methods to tune the choice of threshold.") (define-public r-mosaiccore (package (name "r-mosaiccore") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "mosaicCore" version)) (sha256 - (base32 "00va6x1i8d3wkm1bgsms9dsjfn5a1l43prpl9pqirgq3zm85hrqj")))) + (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs @@ -8222,26 +8645,62 @@ and coverage methods to tune the choice of threshold.") "Common utilities used in other Mosaic family packages are collected here.") (license license:gpl2+))) +(define-public r-labelled + (package + (name "r-labelled") + (version "2.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "labelled" version)) + (sha256 + (base32 + "1nsb0mh0jg7gggc41b6v55nmfq07g0qn9fy55x4jws5dscs6pdmi")))) + (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-tidyr" ,r-tidyr) + ("r-vctrs" ,r-vctrs))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://larmarange.github.io/labelled/") + (synopsis "Manipulating labelled data") + (description + "This package provides useful functions to deal with the +@code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the +haven package. ") + (license license:gpl3))) + (define-public r-ggformula (package (name "r-ggformula") - (version "0.9.4") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "ggformula" version)) (sha256 - (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f")))) + (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp")))) (build-system r-build-system) (propagated-inputs `(("r-ggforce" ,r-ggforce) ("r-ggplot2" ,r-ggplot2) + ("r-ggridges" ,r-ggridges) ("r-ggstance" ,r-ggstance) + ("r-labelled" ,r-labelled) ("r-magrittr" ,r-magrittr) ("r-mosaiccore" ,r-mosaiccore) ("r-rlang" ,r-rlang) + ("r-scales" ,r-scales) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ProjectMOSAIC/ggformula/") (synopsis "Formula interface for the @code{r-ggplot2}") (description @@ -8254,13 +8713,13 @@ while providing the intuitive capabilities of @code{r-ggplot2}.") (define-public r-mosaicdata (package (name "r-mosaicdata") - (version "0.20.1") + (version "0.20.2") (source (origin (method url-fetch) (uri (cran-uri "mosaicData" version)) (sha256 - (base32 "05mrwvs7awhpv2gvk0jjva74gndfgh2cl17slxcjhwlpga8nmxji")))) + (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4")))) (properties `((upstream-name . "mosaicData"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/mosaicData/") @@ -8868,14 +9327,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.5.2") + (version "2.6.0") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "0myvryya7b4bbw0hs4jqflrbdffmg78kz28gbybw3yc7zwc7sqxx")))) + "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -9310,14 +9769,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.5.2-1") + (version "1.5.3") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0ndbjhglycdycppz9lbj3vhiqv2mp0z6h4w8fbyjziqx15ai5h59")))) + "11x7bn260v91gb7qri1pq54l339zm4msa5frc8saqb9ykbg4dby5")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -9361,13 +9820,13 @@ Cohen (1988).") (define-public r-libcoin (package (name "r-libcoin") - (version "1.0-6") + (version "1.0-7") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 - (base32 "0njfdbz4mkyasxm80p0fb0qibvzz7kdzddn8ybj2k6y8bx0w3bs8")))) + (base32 "1vb21pw3vpv2pdnfcddw2bax13v0dg656r28j0p8njcyhwk89xln")))) (build-system r-build-system) (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) (home-page "https://cran.r-project.org/web/packages/libcoin") @@ -9380,14 +9839,14 @@ and permutation inference in the framework of Strasser and Weber (1999).") (define-public r-coin (package (name "r-coin") - (version "1.3-1") + (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 - "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx")))) + "1n2ad4m3zw8px6yc0h750k59pci3fqpnr742hhvsqirrwcdzp6zv")))) (build-system r-build-system) (propagated-inputs `(("r-libcoin" ,r-libcoin) @@ -9407,14 +9866,14 @@ correlation, censored, ordered and multivariate problems.") (define-public r-bayesplot (package (name "r-bayesplot") - (version "1.7.2") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "bayesplot" version)) (sha256 (base32 - "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl")))) + "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6")))) (build-system r-build-system) (inputs `(("pandoc" ,pandoc) @@ -9471,13 +9930,13 @@ detection, parallelism through BLAS and parallel user templates.") (define-public r-sjstats (package (name "r-sjstats") - (version "0.18.0") + (version "0.18.1") (source (origin (method url-fetch) (uri (cran-uri "sjstats" version)) (sha256 - (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0")))) + (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -9573,14 +10032,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0ai1pp6k0pmmjgpj7hc53s0h258c4mljln8lv3nd9r7kzrmic0gc")))) + "0wz2zc98r99pg6r4l09qxxzv1fwxwp1md6wmhay401568kd8h5zn")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -9600,14 +10059,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "18diwssc5vij5g7zh9mv0ppcv3xgfi2jqzfx9srxfahg05sr1xdq")))) + "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -9630,14 +10089,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.1") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1rbl63b1c7z9llznnwvclqrcgdd4hfmc7y66v7raqqf2a4nadqa5")))) + "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -9657,13 +10116,13 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.6") + (version "2.8.7") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "1dn9nvvp4jd45kwr4rpp2abf7xdpdmiv41rr3fkdb32a136bzx4b")))) + (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -9811,17 +10270,96 @@ when building command line applications. They fall back to alternatives on terminals that do not support Unicode.") (license license:expat))) +(define-public r-credentials + (package + (name "r-credentials") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "credentials" version)) + (sha256 + (base32 + "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1")))) + (properties `((upstream-name . "credentials"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'setenv-HOME + (lambda _ + ;; This is necessary because git looks for $HOME/.gitconfig + (setenv "HOME" "/tmp") + #t))))) + (inputs + `(("git" ,git-minimal))) + (propagated-inputs + `(("r-askpass" ,r-askpass) + ("r-curl" ,r-curl) + ("r-jsonlite" ,r-jsonlite) + ("r-openssl" ,r-openssl) + ("r-sys" ,r-sys))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/credentials/") + (synopsis "Tools for managing SSH and Git credentials") + (description + "This package assists you in setting up and retrieving of HTTPS and SSH +credentials for use with git and other services. For HTTPS remotes the +package interfaces the @command{git-credential} utility which @command{git} +uses to store HTTP usernames and passwords. For SSH remotes this package +provides convenient functions to find or generate appropriate SSH keys. The +package both helps the user to setup a local git installation, and also +provides a back-end for git/ssh client libraries to authenticate with existing +user credentials.") + (license license:expat))) + +(define-public r-gert + (package + (name "r-gert") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "gert" version)) + (sha256 + (base32 + "1lq4hgv2727lwcv8vha5af26nslj99rjxjrgflshmmcihawpls1n")))) + (properties `((upstream-name . "gert"))) + (build-system r-build-system) + (inputs + `(("libgit2" ,libgit2) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-askpass" ,r-askpass) + ("r-credentials" ,r-credentials) + ("r-openssl" ,r-openssl) + ("r-rstudioapi" ,r-rstudioapi) + ("r-zip" ,r-zip))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/gert/") + (synopsis "Simple Git client for R") + (description + "This package provides a simple git client for R based on libgit2 with +support for SSH and HTTPS remotes. All functions in gert use basic R data +types (such as vectors and data-frames) for their arguments and return values. +User credentials are shared with command line git through the +@code{git-credential} store and SSH keys stored on disk or ssh-agent.") + (license license:expat))) + (define-public r-usethis (package (name "r-usethis") - (version "1.6.3") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "09lk04kycvf5x9ggrb6pwc7bx5mzqxwialm2w9vn1a0w0gh2gcfc")))) + "0m4qnnkdiizsdvq33x502zwkn98hw2qcfm45cjj031vaydcjpai2")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -9830,11 +10368,13 @@ terminals that do not support Unicode.") ("r-curl" ,r-curl) ("r-desc" ,r-desc) ("r-fs" ,r-fs) + ("r-gert" ,r-gert) ("r-gh" ,r-gh) - ("r-git2r" ,r-git2r) ("r-glue" ,r-glue) + ("r-jsonlite" ,r-jsonlite) + ("r-lifecycle" ,r-lifecycle) ("r-purrr" ,r-purrr) - ("r-rematch2" ,r-rematch2) + ("r-rappdirs" ,r-rappdirs) ("r-rlang" ,r-rlang) ("r-rprojroot" ,r-rprojroot) ("r-rstudioapi" ,r-rstudioapi) @@ -10002,14 +10542,14 @@ ways.") (define-public r-summarytools (package (name "r-summarytools") - (version "0.9.6") + (version "0.9.8") (source (origin (method url-fetch) (uri (cran-uri "summarytools" version)) (sha256 (base32 - "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2")))) + "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -10024,6 +10564,8 @@ ways.") ("r-rapportools" ,r-rapportools) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") (description @@ -10152,14 +10694,14 @@ the interfaces between R and C++.") (define-public r-mvabund (package (name "r-mvabund") - (version "4.1.3") + (version "4.1.6") (source (origin (method url-fetch) (uri (cran-uri "mvabund" version)) (sha256 (base32 - "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b")))) + "0aisvax9d7bk6aykrcdcn1ji618r520mcrkr1i3jnck1qs31z41f")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -10177,14 +10719,14 @@ analysing multivariate abundance data in community ecology.") (define-public r-afex (package (name "r-afex") - (version "0.28-0") + (version "0.28-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 - "0c47bq2llzw2b4avhkxyhmf1m2zjh9jsjiw2kww9n1bhwqsyr4ci")))) + "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) @@ -10294,14 +10836,14 @@ address a bug.") (define-public r-rcppannoy (package (name "r-rcppannoy") - (version "0.0.17") + (version "0.0.18") (source (origin (method url-fetch) (uri (cran-uri "RcppAnnoy" version)) (sha256 (base32 - "0z4dpvk2hmh817709l70jdl1vvnzn0vb9wlr5m8jza24sn9w14ac")))) + "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4")))) (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs @@ -10410,17 +10952,18 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.100.54") + (version "0.104.16") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp")))) + "169a8riiam8445nl7rcwn0x92dlwyzh5xldvap6dcxjyjqmjwbdq")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (inputs `(("freetype" ,freetype) ("libpng" ,libpng) @@ -10729,6 +11272,33 @@ Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) +(define-public r-sodium + (package + (name "r-sodium") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "sodium" version)) + (sha256 + (base32 + "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w")))) + (properties `((upstream-name . "sodium"))) + (build-system r-build-system) + (inputs + `(("libsodium" ,libsodium))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/jeroen/sodium") + (synopsis "R bindings to the libsodium crypto library") + (description + "This package provides bindings to libsodium: a library for encryption, +decryption, signatures, password hashing and more. Sodium uses curve25519, a +Diffie-Hellman function by Daniel Bernstein, which has become very popular +after it was discovered that the NSA had backdoored Dual EC DRBG.") + (license license:expat))) + (define-public r-softimpute (package (name "r-softimpute") @@ -11017,14 +11587,14 @@ only sparse real matrices in Matrix package format are supported.") (define-public r-speedglm (package (name "r-speedglm") - (version "0.3-2") + (version "0.3-3") (source (origin (method url-fetch) (uri (cran-uri "speedglm" version)) (sha256 (base32 - "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz")))) + "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -11401,14 +11971,14 @@ conditional reporting based on the current \"output level\".") (define-public r-tractor-base (package (name "r-tractor-base") - (version "3.3.2") + (version "3.3.3.1") (source (origin (method url-fetch) (uri (cran-uri "tractor.base" version)) (sha256 (base32 - "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i")))) + "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p")))) (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs @@ -11758,14 +12328,14 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.6-1") + (version "0.6-2") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "11rl7qmfrpp1974f0vzsi3zjyx147wlb82ydxak2b60khfvhrn90")))) + "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b")))) (build-system r-build-system) (arguments '(#:phases @@ -12254,17 +12824,19 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.5-1") + (version "2.6-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi")))) + (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3")))) (build-system r-build-system) (propagated-inputs `(("r-dotcall64" ,r-dotcall64))) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description @@ -12757,14 +13329,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.21.0") + (version "1.23.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "1hlr81khr7z4x9gprymdh19mdq3nw6wm8d2795sd2pa3ya6phnb0")))) + "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -12785,14 +13357,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.20.1") + (version "1.21.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "14k00g8c9zgf77d6q7x2vibvlivzk2rzj7lwn7v7d9nr6prqzlb6")))) + "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -12818,14 +13390,14 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.6.0") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms")))) + "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (propagated-inputs @@ -13028,6 +13600,49 @@ several common set, element and attribute related tasks.") "This package adds additional Twitter Bootstrap components to Shiny.") (license license:gpl3))) +(define-public r-shinyjqui + (package + (name "r-shinyjqui") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyjqui" version)) + (sha256 + (base32 + "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x")) + (snippet + '(begin + (delete-file "inst/www/shinyjqui.min.js"))))) + (properties `((upstream-name . "shinyjqui"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/www/" + (let ((source "shinyjqui.js") + (target "shinyjqui.min.js")) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("esbuild" ,esbuild))) + (home-page "https://github.com/yang-tang/shinyjqui") + (synopsis "jQuery UI interactions and effects for Shiny") + (description + "This is an extension to Shiny that brings interactions and animation +effects from the jQuery UI library.") + (license license:expat))) + (define-public r-outliers (package (name "r-outliers") @@ -13131,14 +13746,14 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "2.0-0") + (version "2.0-1") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "0xsx4n699q2r4pk2jrvifi3wi49lih7d1j3j6qgqqd31brg53jqr")))) + "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4")))) (build-system r-build-system) (propagated-inputs `(("r-bayesm" ,r-bayesm) @@ -13419,17 +14034,19 @@ them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") (define-public r-msir (package (name "r-msir") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "msir" version)) (sha256 (base32 - "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb")))) + "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84")))) (build-system r-build-system) (propagated-inputs `(("r-mclust" ,r-mclust))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/msir") (synopsis "Model-based sliced inverse regression") (description @@ -13611,14 +14228,14 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-3.1") + (version "0.3-4") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "08qmrzazadkyxlqc8830r0pckaq10l3fgj1f198xy6wwrm2lf0wy")))) + "0adiac53yq305ymhrds1gas4jm0rn1ddv7c7df5ky2cfhpb4ny87")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs @@ -14137,14 +14754,14 @@ barplots or heatmaps.") (define-public r-seqinr (package (name "r-seqinr") - (version "4.2-4") + (version "4.2-5") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "0pw035h17dmic8m0pb73fbyf6p4jbwggxjk5vpjlybn8dwd0rk93")))) + "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -14270,14 +14887,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.2-3") + (version "0.2-9") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "0kin1hsd6dj36kkg7n328mzp21wwn9jm69lvgg2rvbf6bq7q091d")))) + "0jfwff5kk0zraspsvbk26lphl3fnrc6xmhl4690hr0a5k177ildm")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -14294,14 +14911,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.9-6") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "01yqlnx9v7lzb6g4ywjlncz67cnkizszarnf2dmd4fi8abhw4zs9")))) + "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -14907,14 +15524,14 @@ handle missing genotypes at some SNPs.") (define-public r-sampling (package (name "r-sampling") - (version "2.8") + (version "2.9") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 - "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m")))) + "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz")))) (build-system r-build-system) (propagated-inputs `(("r-lpsolve" ,r-lpsolve) @@ -15180,14 +15797,14 @@ yeast.") (define-public r-gridgraphics (package (name "r-gridgraphics") - (version "0.5-0") + (version "0.5-1") (source (origin (method url-fetch) (uri (cran-uri "gridGraphics" version)) (sha256 (base32 - "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r")))) + "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219")))) (properties `((upstream-name . "gridGraphics"))) (build-system r-build-system) (home-page "https://github.com/pmur002/gridgraphics") @@ -16075,14 +16692,14 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sctransform (package (name "r-sctransform") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "0b8ni8dzlcikjm2bx5w8yi9vygx0qqxjrmnsy4kf7d1h03n2sxwa")))) + "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx")))) (build-system r-build-system) (propagated-inputs `(("r-future" ,r-future) @@ -16179,14 +16796,14 @@ parallel versions of vectorized R functions of the @code{mc*apply} family.") (define-public r-blme (package (name "r-blme") - (version "1.0-4") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "blme" version)) (sha256 (base32 - "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2")))) + "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4))) (home-page "https://github.com/vdorie/blme") @@ -16200,14 +16817,14 @@ extends the lme4 package.") (define-public r-batchtools (package (name "r-batchtools") - (version "0.9.14") + (version "0.9.15") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 - "1b78r70gm4a0wzjr367hqx2rfphfkbppp14d0l5zs2fvyz166lsx")))) + "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -16593,20 +17210,19 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "1.2.0.1") + (version "1.3.2.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "16hpvv2hwdzcyg90z7c1g5d2hj011qk8mivy4l2nqd2g7rkjwis4")))) + "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-stringi" ,r-stringi))) + ("r-matrix" ,r-matrix))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/dmlc/xgboost") @@ -16652,14 +17268,14 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.9") + (version "0.1.10") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "1iqvircvlxyd68n5279a0cwn5rc3pshxs7w1gqrns9c602xd6mhy")))) + "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf")))) (build-system r-build-system) (propagated-inputs `(("r-dqrng" ,r-dqrng) @@ -16839,14 +17455,14 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (define-public r-patchwork (package (name "r-patchwork") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 - "13vswvcfmadmjz7pw0qdqdr6x85zbza4gljx2nx3a39hldj71yck")))) + "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -17164,14 +17780,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.10.1") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "1xvjvsdd0hql209f7v2l1nw7gy8jkj5qp0699p5m2h55a01jl778")))) + "020k3vxnp0vjrlkcxx5vj30vag474hw48zxzw9315whsq4hhhbqc")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -17193,13 +17809,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-18") + (version "1.5-19") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "1pr267sh0v6cympdg12yny51cmn4r20s5sjq2hqymn4kphcpqijk")))) + (base32 "1cii2azm3zv5l6fn33xzwahp8349z3pb2769vpdxkf7734dxggvg")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -17811,14 +18427,14 @@ server-side.") (define-public r-sysfonts (package (name "r-sysfonts") - (version "0.8.2") + (version "0.8.3") (source (origin (method url-fetch) (uri (cran-uri "sysfonts" version)) (sha256 (base32 - "1gapsiva0vjd2myxgm1avav6my5x00rmy2hx0qll7dm7v1isznbv")))) + "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5")))) (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs @@ -17859,14 +18475,14 @@ package.") (define-public r-showtext (package (name "r-showtext") - (version "0.9-1") + (version "0.9-2") (source (origin (method url-fetch) (uri (cran-uri "showtext" version)) (sha256 (base32 - "1hq346k2lm7rv49hw7srn3ab5gcp6b0r4zc1kgsdmswyh3q1asra")))) + "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z")))) (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs @@ -18563,6 +19179,26 @@ the align-and-count method.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-filelock + (package + (name "r-filelock") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "filelock" version)) + (sha256 + (base32 + "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc")))) + (properties `((upstream-name . "filelock"))) + (build-system r-build-system) + (home-page "https://github.com/r-lib/filelock") + (synopsis "Portable file locking") + (description + "This library lets you place an exclusive or shared lock on a file using +the appropriate system call provided by the underlying operating system.") + (license license:expat))) + (define-public r-filematrix (package (name "r-filematrix") @@ -18706,14 +19342,14 @@ identify file sets and individual files.") (define-public r-r-devices (package (name "r-r-devices") - (version "2.16.1") + (version "2.17.0") (source (origin (method url-fetch) (uri (cran-uri "R.devices" version)) (sha256 (base32 - "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd")))) + "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62")))) (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs @@ -19351,14 +19987,14 @@ R.") (define-public r-hdrcde (package (name "r-hdrcde") - (version "3.3") + (version "3.4") (source (origin (method url-fetch) (uri (cran-uri "hdrcde" version)) (sha256 (base32 - "0c2qbw4c3mq1cb068kjs72rxlbibz8svwcrx853jyr8ybs23z7ab")))) + "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3")))) (properties `((upstream-name . "hdrcde"))) (build-system r-build-system) (propagated-inputs @@ -19432,14 +20068,14 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "5.1.7") + (version "5.1.9") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "1r8hfi6x1maw5zz8k95wfcr7v69lg4zl3mcj69cvvq2mkg4y3158")))) + "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs @@ -19539,20 +20175,22 @@ data for different accelerometer brands.") (define-public r-activityindex (package (name "r-activityindex") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "ActivityIndex" version)) (sha256 (base32 - "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk")))) + "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5")))) (properties `((upstream-name . "ActivityIndex"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-matrixstats" ,r-matrixstats) ("r-r-utils" ,r-r-utils))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description @@ -19671,14 +20309,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.0-0") + (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz")))) + "15a8axb2ym46j8vlm7icwnsc950p8m66hp0armha7drk0725y77k")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs `(("r-expint" ,r-expint))) @@ -21176,14 +21814,14 @@ least squares.") (define-public r-semtools (package (name "r-semtools") - (version "0.5-3") + (version "0.5-4") (source (origin (method url-fetch) (uri (cran-uri "semTools" version)) (sha256 (base32 - "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d")))) + "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq")))) (properties `((upstream-name . "semTools"))) (build-system r-build-system) (propagated-inputs @@ -21227,14 +21865,14 @@ perform @dfn{exploratory mediation} (XMed).") (define-public r-stanheaders (package (name "r-stanheaders") - (version "2.21.0-6") + (version "2.21.0-7") (source (origin (method url-fetch) (uri (cran-uri "StanHeaders" version)) (sha256 (base32 - "1wwcrss4y6xbi81cg6ldhm57wz5paflzzp3yxh8b6shf9l2jla50")))) + "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) (inputs `(("pandoc" ,pandoc))) @@ -21912,13 +22550,13 @@ recommendations for developers.") (define-public r-loo (package (name "r-loo") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (cran-uri "loo" version)) (sha256 - (base32 "01a15ikfnyxhjhrgvy3ag929rg45dxp3wji1j38r4hg4q1yz4ma9")))) + (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw")))) (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs @@ -22065,6 +22703,39 @@ a formula and @code{data.frame} plus some additional arguments for priors.") trend test.") (license license:gpl2+))) +(define-public r-keyring + (package + (name "r-keyring") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "keyring" version)) + (sha256 + (base32 + "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq")))) + (properties `((upstream-name . "keyring"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-filelock" ,r-filelock) + ("r-getpass" ,r-getpass) + ("r-openssl" ,r-openssl) + ("r-r6" ,r-r6) + ("r-rappdirs" ,r-rappdirs) + ("r-sodium" ,r-sodium) + ("r-yaml" ,r-yaml))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/r-lib/keyring") + (synopsis "Access the system credential store from R") + (description + "This package provides a platform-independent API to access the operating +system's credential store. It currently supports Keychain on macOS, +Credential Store on Windows, the Secret Service API on GNU/Linux, and a +simple, platform independent store implemented with environment variables. +Additional storage back-ends can be added easily.") + (license license:expat))) + (define-public r-zyp (package (name "r-zyp") @@ -22603,14 +23274,14 @@ is also implemented here.") (define-public r-aws (package (name "r-aws") - (version "2.5") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "aws" version)) (sha256 (base32 - "1mwg1q7l4a07g5aa9c6kh3fpl9lakk01pbzlk7ixbpy12yfvj9nm")))) + "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8")))) (properties `((upstream-name . "aws"))) (build-system r-build-system) @@ -22978,19 +23649,26 @@ with posterior predictive checks and leave-one-out cross-validation.") (define-public r-mstate (package (name "r-mstate") - (version "0.2.12") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "mstate" version)) (sha256 (base32 - "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv")))) + "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i")))) (properties `((upstream-name . "mstate"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-survival" ,r-survival))) + `(("r-data-table" ,r-data-table) + ("r-lattice" ,r-lattice) + ("r-magrittr" ,r-magrittr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-survival" ,r-survival) + ("r-viridis" ,r-viridis))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/") (synopsis @@ -23029,6 +23707,31 @@ multi-state models.") pies on a map.") (license license:artistic2.0))) +(define-public r-scrypt + (package + (name "r-scrypt") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "scrypt" version)) + (sha256 + (base32 + "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm")))) + (properties `((upstream-name . "scrypt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/rstudio/rscrypt") + (synopsis "Key derivation functions for R based on Scrypt") + (description + "This package provides functions for working with the scrypt key +derivation functions. Scrypt is a password-based key derivation function +created by Colin Percival. The algorithm was specifically designed to make it +costly to perform large-scale custom hardware attacks by requiring large +amounts of memory.") + (license license:bsd-2))) + (define-public r-boruta (package (name "r-boruta") @@ -23055,14 +23758,14 @@ permuted copies (shadows).") (define-public r-directlabels (package (name "r-directlabels") - (version "2020.6.17") + (version "2021.1.13") (source (origin (method url-fetch) (uri (cran-uri "directlabels" version)) (sha256 (base32 - "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f")))) + "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog))) @@ -23180,17 +23883,53 @@ by providing functionality for preprocessing, predicting, and validating input.") (license license:expat))) +(define-public r-lightgbm + (package + (name "r-lightgbm") + (version "3.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lightgbm" version)) + (sha256 + (base32 + "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555")))) + (properties `((upstream-name . "lightgbm"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-jsonlite" ,r-jsonlite) + ("r-matrix" ,r-matrix) + ("r-r6" ,r-r6))) + (home-page "https://github.com/Microsoft/LightGBM") + (synopsis "Light gradient boosting machine") + (description + "Tree based algorithms can be improved by introducing boosting +frameworks. LightGBM is one such framework, based on Ke, Guolin et +al. (2017). This package offers an R interface to work with it. It is +designed to be distributed and efficient with the following goals: + +@enumerate +@item Faster training speed and higher efficiency; +@item lower memory usage; +@item better accuracy; +@item parallel learning supported; and +@item capable of handling large-scale data. +@end enumerate +") + (license license:expat))) + (define-public r-shapforxgboost (package (name "r-shapforxgboost") - (version "0.0.4") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "SHAPforxgboost" version)) (sha256 (base32 - "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq")))) + "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly")))) (properties `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) @@ -23201,6 +23940,7 @@ input.") ("r-ggforce" ,r-ggforce) ("r-ggplot2" ,r-ggplot2) ("r-ggpubr" ,r-ggpubr) + ("r-lightgbm" ,r-lightgbm) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-xgboost" ,r-xgboost))) (home-page "https://github.com/liuyanguu/SHAPforxgboost") @@ -23534,14 +24274,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "1.17-0") + (version "1.20-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "08h9kzkkxvlnngxnv5mdylfali5jj4yhgbr8kvf8l7glswz6ik9r")))) + "066f35017wpbz9plwc14gji3ddq4a1h2lx4mcgxajrcrk0zl3hk2")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -23555,14 +24295,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "1.5-2") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "17vbf48g1mh8iigzzlaa9j4mw087hib7f1kkbl3c50xjcrr5iw6b")))) + "0by10dx72jjn6rvgrdj4xwh4zg6vxi4cp536aq4b6drb7za95hdv")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -23645,14 +24385,14 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "08lrmpfkwh1w290a5ikhs9yn1vn32wbgvbzb4n3zb2indb8s5g69")))) + "081f3b98mcxyilqsxbzzdnj2x6v7xycprrw7r5934163q0397vvg")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -24103,14 +24843,14 @@ coerce and verify the types and shapes of values for input checking.") (define-public r-config (package (name "r-config") - (version "0.3") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "config" version)) (sha256 (base32 - "0l67nfpm42ssnk0bl4jmq6bibz8hawgfgh2s14s5c8mnimv6mpjs")))) + "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l")))) (properties `((upstream-name . "config"))) (build-system r-build-system) (propagated-inputs @@ -24627,14 +25367,14 @@ consistent interface, and the package is built on the @code{stringi} and (define-public r-hunspell (package (name "r-hunspell") - (version "3.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "hunspell" version)) (sha256 (base32 - "0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1")))) + "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z")))) (properties `((upstream-name . "hunspell"))) (build-system r-build-system) (propagated-inputs @@ -24662,14 +25402,14 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.2.6") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "0xmjkab7p13ncfglf3a9hvndf8fh96mmxw3l7hcpbnaq9qkiwk29")))) + "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs @@ -24677,12 +25417,14 @@ vignettes in all common formats.") ("r-generics" ,r-generics) ("r-hunspell" ,r-hunspell) ("r-janeaustenr" ,r-janeaustenr) + ("r-lifecycle" ,r-lifecycle) ("r-matrix" ,r-matrix) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) - ("r-tokenizers" ,r-tokenizers))) + ("r-tokenizers" ,r-tokenizers) + ("r-vctrs" ,r-vctrs))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/juliasilge/tidytext") @@ -24695,14 +25437,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "1134840xisvkkrbkh5kvx24vxp7sx06124svy573a9m4h8c492sr")))) + "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -24730,14 +25472,14 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (define-public r-infer (package (name "r-infer") - (version "0.5.3") + (version "0.5.4") (source (origin (method url-fetch) (uri (cran-uri "infer" version)) (sha256 (base32 - "1q0lnxnv8krv4n9z80sh4b442s89rvnbph5bddy34z83bkncwv2g")))) + "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2")))) (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs @@ -24952,14 +25694,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.46-2") + (version "1.47-9") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) + "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -24975,12 +25717,12 @@ genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.22-11") + (version "0.24") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 - (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) + (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -25046,16 +25788,39 @@ alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.") (license license:gpl3+))) +(define-public r-scattermore + (package + (name "r-scattermore") + (version "0.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "scattermore" version)) + (sha256 + (base32 + "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk")))) + (properties `((upstream-name . "scattermore"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (home-page "https://github.com/exaexa/scattermore") + (synopsis "Scatterplots with more points") + (description + "This package provides C-based tools for converting large scatterplot +data to rasters. It speeds up plotting of data with millions of points.") + (license license:gpl3+))) + (define-public r-seurat (package (name "r-seurat") - (version "3.2.2") + (version "3.2.3") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "048vnj0c3mrwhr6yq3jqhgnkg68w99nj1ccsmgnd8rl694w26spj")))) + "11rzc7h2ad8z8k5r1sbz4d7y4rl3080qp2hh7vibwmipbkvlial3")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -25095,6 +25860,7 @@ as allowing spectra with different resolutions.") ("r-rsvd" ,r-rsvd) ("r-rtsne" ,r-rtsne) ("r-scales" ,r-scales) + ("r-scattermore" ,r-scattermore) ("r-sctransform" ,r-sctransform) ("r-shiny" ,r-shiny) ("r-spatstat" ,r-spatstat) @@ -25200,18 +25966,20 @@ absolute GSEA.") (define-public r-calculus (package (name "r-calculus") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "0hs7hzjl6xjza20v9zx9a1piywxa6w3h2rskr52d1dcbc0vwhinp")))) + "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description @@ -25368,16 +26136,18 @@ Services (AWS) Simple Storage Service (S3) REST API.") (define-public r-lgr (package (name "r-lgr") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "lgr" version)) (sha256 (base32 - "196553hmni1ha9y6494f4g3ds0lwcl81v7k4r8wwap4a6acdrgd9")))) + "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://s-fleck.github.io/lgr/") (synopsis "Fully featured logging framework") (description "This package offers a flexible, feature-rich yet @@ -25390,13 +26160,13 @@ well as email and push notifications.") (define-public r-mlr3measures (package (name "r-mlr3measures") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 - "106lfaxphz0kh96ddq14hic7wvxjqp871zdp9kkkfk1kwfg35abw")))) + "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6")))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) @@ -25413,13 +26183,13 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "1q63i2059bf7cf61kwm0dqnk5vd60i0j4flziswwdk07fjxqh8xr")))) + "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -25493,3 +26263,299 @@ scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While @code{mlr3} focuses on the core computational operations, add-on packages provide additional functionality.") (license license:lgpl3))) + +(define-public r-mlr3learners + (package + (name "r-mlr3learners") + (version "0.4.3") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3learners" version)) + (sha256 + (base32 + "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-mlr3" ,r-mlr3) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-r6" ,r-r6))) + (home-page "https://mlr3learners.mlr-org.com/") + (synopsis "Recommended Learners for @code{mlr3}") + (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} +with interfaces to essential machine learning packages on CRAN. This includes, +but is not limited to: (penalized) linear and logistic regression, linear and +quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support +vector machines, and gradient boosting.") + (license license:lgpl3))) + +(define-public r-bbotk + (package + (name "r-bbotk") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bbotk" version)) + (sha256 + (base32 + "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv")))) + (properties `((upstream-name . "bbotk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-lgr" ,r-lgr) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-r6" ,r-r6))) + (home-page "https://bbotk.mlr-org.com") + (synopsis "Black-Box Optimization Toolkit") + (description "This package provides a common framework for optimization of +black-box functions for other packages, e.g. @code{mlr3}. It offers various +optimization methods e.g. grid search, random search and generalized simulated +annealing.") + (license license:lgpl3))) + +(define-public r-mlr3tuning + (package + (name "r-mlr3tuning") + (version "0.5.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3tuning" version)) + (sha256 + (base32 + "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbotk" ,r-bbotk) + ("r-checkmate" ,r-checkmate) + ("r-data-table" ,r-data-table) + ("r-lgr" ,r-lgr) + ("r-mlr3" ,r-mlr3) + ("r-mlr3misc" ,r-mlr3misc) + ("r-paradox" ,r-paradox) + ("r-r6" ,r-r6))) + (home-page "https://mlr3tuning.mlr-org.com/") + (synopsis "Tuning for @code{mlr3}") + (description "@code{mlr3tuning} implements methods for hyperparameter +tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various +termination criteria can be set and combined. The class @code{AutoTuner} provides a +convenient way to perform nested resampling in combination with @code{mlr3}.") + (license license:lgpl3))) + +(define-public r-fontliberation + (package + (name "r-fontliberation") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fontLiberation" version)) + (sha256 + (base32 + "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc")))) + (properties + `((upstream-name . "fontLiberation"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=fontLiberation") + (synopsis "Liberation fonts") + (description + "This package provides a placeholder for the Liberation fontset intended +for the fontquiver package. This fontset covers the 12 combinations of +families (sans, serif, mono) and faces (plain, bold, italic, bold italic) +supported in R graphics devices.") + (license license:silofl1.1))) + +(define-public r-fontbitstreamvera + (package + (name "r-fontbitstreamvera") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "fontBitstreamVera" version)) + (sha256 + (base32 + "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j")))) + (properties + `((upstream-name . "fontBitstreamVera"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=fontBitstreamVera") + (synopsis "Fonts for fontquiver") + (description + "This package is a placeholder for the Bitstream Vera font. It is +intended for the fontquiver package.") + (license + (license:fsdg-compatible + "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts" + "The Font Software may be sold as part of a larger software package but +no copy of one or more of the Font Software typefaces may be sold by +itself.")))) + +(define-public r-fontquiver + (package + (name "r-fontquiver") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "fontquiver" version)) + (sha256 + (base32 + "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm")))) + (properties `((upstream-name . "fontquiver"))) + (build-system r-build-system) + (propagated-inputs + `(("r-fontbitstreamvera" ,r-fontbitstreamvera) + ("r-fontliberation" ,r-fontliberation))) + (home-page "https://cran.r-project.org/package=fontquiver") + (synopsis "Set of installed fonts") + (description + "This package provides a set of fonts. This is useful when you want to +avoid system fonts to make sure your outputs are reproducible.") + (license license:gpl3))) + +(define-public r-freetypeharfbuzz + (package + (name "r-freetypeharfbuzz") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "freetypeharfbuzz" version)) + (sha256 + (base32 + "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7")))) + (properties + `((upstream-name . "freetypeharfbuzz"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'prepare-static-libraries + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "src/target/include") + (let ((freetype (assoc-ref inputs "static-freetype")) + (harfbuzz (assoc-ref inputs "static-harfbuzz"))) + (substitute* "src/Makevars.in" + (("include @MK_FILE@") "") ; do not build static libs + (("^HB_STATIC_LIB =.*") + (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n")) + (("^FT_STATIC_LIB =.*") + (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n"))) + (copy-recursively (string-append freetype "/include") + "src/target/include") + (copy-recursively (string-append harfbuzz "/include") + "src/target/include"))))))) + (propagated-inputs + `(("r-fontquiver" ,r-fontquiver))) + ;; This may defeat the purpose of this package as our versions of freetype + ;; and harfbuzz obviously differ from the tarballs offered by this + ;; project. On the other hand, Guix arguably does a better job at + ;; "ensur[ing] deterministic computation". + (native-inputs + `(("static-freetype" + ,(package + (inherit (static-package freetype)) + (arguments + `(#:configure-flags + (list "--enable-static=yes" + "--with-pic=yes" + "--without-zlib" + "--without-bzip2" + "--without-png" + "--without-harfbuzz"))))) + ("static-harfbuzz" + ,(package + (inherit (static-package harfbuzz)) + (arguments + `(#:tests? #false ; fail because shared library is disabled + #:configure-flags + (list "--enable-static=yes" + "--enable-shared=no" + "--with-pic=yes" + "--with-freetype=yes" + "--without-icu" + "--without-cairo" + "--without-fontconfig" + "--without-glib"))))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://cran.r-project.org/package=freetypeharfbuzz") + (synopsis "Deterministic computation of text box metrics") + (description + "Unlike other tools that dynamically link to the Cairo stack, +freetypeharfbuzz is statically linked to specific versions of the FreeType and +harfbuzz libraries. This ensures deterministic computation of text box +extents for situations where reproducible results are crucial (for instance +unit tests of graphics).") + (license license:gpl3))) + +(define-public r-vdiffr + (package + (name "r-vdiffr") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "vdiffr" version)) + (sha256 + (base32 + "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc")) + (snippet + '(begin + (delete-file "inst/htmlwidgets/lib/jquery.min.js"))))) + (properties `((upstream-name . "vdiffr"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (let ((source (assoc-ref inputs "js-jquery")) + (target "jquery.min.js")) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) + (inputs + `(("freetype" ,freetype) + ("harfbuzz" ,harfbuzz))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-devtools" ,r-devtools) + ("r-diffobj" ,r-diffobj) + ("r-fontquiver" ,r-fontquiver) + ("r-freetypeharfbuzz" ,r-freetypeharfbuzz) + ("r-gdtools" ,r-gdtools) + ("r-glue" ,r-glue) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-purrr" ,r-purrr) + ("r-r6" ,r-r6) + ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) + ("r-shiny" ,r-shiny) + ("r-testthat" ,r-testthat) + ("r-usethis" ,r-usethis) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("esbuild" ,esbuild) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.12.4.js") + (sha256 + (base32 + "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))))) + (home-page "https://github.com/r-lib/vdiffr") + (synopsis "Visual regression testing and graphical diffing") + (description + "This package is an extension to the testthat package that makes it easy +to add graphical unit tests. It provides a Shiny application to manage the +test cases.") + (license license:gpl3))) |