diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 437 |
1 files changed, 338 insertions, 99 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 459edb0e90..5ede11a4e3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com> ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net> ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com> +;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -822,14 +823,16 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.6.1") + (version "1.7.0") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl")))) + "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq")))) (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") (description @@ -914,14 +917,13 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 - "1a1al4kld7lrapc2i086crr78kbgrskahs221iy9v77x0nhin2q3")))) + (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -1062,7 +1064,7 @@ data structures in C++.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rstudio/shiny.git") + (url "https://github.com/rstudio/shiny") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -1436,7 +1438,7 @@ R objects into the JSON format that the d3.js library expects.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/fbreitwieser/sankeyD3.git") + (url "https://github.com/fbreitwieser/sankeyD3") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -2259,14 +2261,14 @@ compare different dendrograms to one another.") (define-public r-getoptlong (package (name "r-getoptlong") - (version "1.0.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 - "1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j")))) + "1p89v2qzqfxyrmqzkv245716n9i4bllnq77a6gw811mgdhxbd51l")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs @@ -2345,7 +2347,7 @@ in main memory.") `(("r-bit" ,r-bit) ("r-fastmatch" ,r-fastmatch) ("r-ff" ,r-ff))) - (home-page "http://github.com/edwindj/ffbase") + (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description "This package extends the out of memory vectors of @code{ff} with @@ -3409,22 +3411,23 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.5.6") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb")))) + "0bq8w1ckrladzck2g0mgiyjdrzi06kbqalk5q3pfvj1607fdv3d5")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-dplyr" ,r-dplyr) + ("r-ellipsis" ,r-ellipsis) ("r-generics" ,r-generics) - ("r-nlme" ,r-nlme) + ("r-glue" ,r-glue) ("r-purrr" ,r-purrr) - ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) @@ -3527,7 +3530,7 @@ for certain use cases.") ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "http://github.com/slowkow/ggrepel") + (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description "This package provides text and label geometries for ggplot2 that help to @@ -3707,18 +3710,19 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.9.0") + (version "3.10.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "1wycbc2iqp68gfzvqx1gsn5n1k1h4bg79dy8m5msqf226hy83ncn")))) + "0w81shmd2crpdlh66pnm27v4n06aayganq6kkalirln4c0ci2nyi")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-lattice" ,r-lattice) ("r-rcpp" ,r-rcpp) ("r-tidyr" ,r-tidyr))) @@ -4208,14 +4212,13 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.4.2") + (version "3.4.3") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 - (base32 - "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l")))) + (base32 "07dhzijqnj2zkm3qrk4ppsv8wscn8ysdsjbidlg9zrbj1wcg4izj")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -4458,19 +4461,21 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.4") + (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "0viymfp1rkr7ig3m1b016r75hk8qbr9cqsjc6c20ks9pm5svmsp1")))) + "01ck8ziqzjc9ibbj3g88siz1iw263dgl8jx6ryw2v50rjrr3y7fj")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) + ("r-ellipsis" ,r-ellipsis) ("r-fansi" ,r-fansi) + ("r-lifecycle" ,r-lifecycle) ("r-rlang" ,r-rlang) ("r-utf8" ,r-utf8) ("r-vctrs" ,r-vctrs))) @@ -4947,17 +4952,19 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "2.0.4") + (version "2.0.4.1") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r")))) + "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description @@ -6035,14 +6042,14 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-renv (package (name "r-renv") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "0yy24kq60dh9n68my132xhhkbnbs7q91z55b1yd6ymr7rxj32mif")))) + "0dd63jr240pg95a6p058s5kcclfmscihdy89v212msihmwvylwh3")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -6289,14 +6296,14 @@ matrix.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "1dly74cnn8iq7vsgmcz0czszdsmg5cgzm4w3s0v30k4psmmzqbxq")))) + "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -6603,14 +6610,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rdpack (package (name "r-rdpack") - (version "0.11-1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq")))) + "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs @@ -6630,14 +6637,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.3.11") + (version "0.3.12") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "0nwasra2kb5wplcim7n57kynwhyg4vsk3fz42mbpm0hig1lzl9pp")))) + "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x")))) (build-system r-build-system) (propagated-inputs `(("r-magrittr" ,r-magrittr) @@ -6742,14 +6749,14 @@ there are functions for discretizing continuous random variables.") (define-public r-abn (package (name "r-abn") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "11nbg6dwvbj0ac7qvr203vzjnw5zc1a8cibb9l6rzzr7yfg16xzc")))) + "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) @@ -6925,14 +6932,14 @@ information are missing.") (define-public r-sjlabelled (package (name "r-sjlabelled") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "sjlabelled" version)) (sha256 (base32 - "0grskmd7wrw31lkf85z6xz0bv246m6grvqkijvqi4q8zkl6p5vb3")))) + "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight))) @@ -7275,19 +7282,21 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.6") + (version "4.6.7") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "0wz1vmsf1545r1m42q88s675ncwvm8figjn7kzbngjn9aqck9qbq")))) + "16vg1aa272sfzyqxfb63fyis9hv6g5m3nmxxa6mk1gy0irqnl3jk")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-deriv" ,r-deriv) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) @@ -7756,14 +7765,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.1-5") + (version "3.3-7") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv")))) + "144mva2dx7ffkq7z0fixr4z76ci1s4lizlyv5r7v07fd4nzg5hby")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -8768,14 +8777,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.4.7") + (version "1.4.8") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0jh7l1rzsb2ihbnh4r4388kwm629z17rcapvdws1hnkklhr8j74k")))) + "0h884qn4cip03w0h5psrz5y9zkm2wppklrhdz2chm2xk13zqnq5k")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -8973,14 +8982,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "1.0.1") + (version "1.0.2.1") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm")))) + "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -9205,14 +9214,14 @@ back to file after modifications.") (define-public r-fs (package (name "r-fs") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df")))) + "09rpazjba9jy448j6rq989fw3wv3xhng7fn8p8gr22gyx0n0y1zr")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -9772,14 +9781,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.0.1") + (version "5.0.2") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "029yyjnixggqmddazwxh1wqid1h7xpwpi4sgixyhbb4kmvqlwfkd")))) + "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") @@ -12184,14 +12193,14 @@ them in distributed compute environments.") (define-public r-future (package (name "r-future") - (version "1.17.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg")))) + "01fp8kgjf0k6c83q1w3dy9z90g72cc9d0004d1qw6n1j65nwxg4f")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -12216,14 +12225,14 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.5.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll")))) + "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (propagated-inputs @@ -12351,14 +12360,14 @@ chosen parallel environment and associated foreach backend.") (define-public r-blockmodeling (package (name "r-blockmodeling") - (version "0.3.6") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "blockmodeling" version)) (sha256 (base32 - "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz")))) + "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -12600,13 +12609,13 @@ such software by imputing dropout events.") (define-public r-gamlss-dist (package (name "r-gamlss-dist") - (version "5.1-6") + (version "5.1-7") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 - (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z")))) + (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -12877,14 +12886,14 @@ latent growth curve models.") (define-public r-nonnest2 (package (name "r-nonnest2") - (version "0.5-4") + (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 - "07nr54hxdnc4k022nd4a2g9w9l9ym2ikfr978rrnqc71wx750i0z")))) + "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2")))) (build-system r-build-system) (propagated-inputs `(("r-compquadform" ,r-compquadform) @@ -13196,7 +13205,7 @@ plotting functions are available for analyzing clustering results.") ("r-tibble" ,r-tibble))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://github.com/rnabioco/valr") + (home-page "https://github.com/rnabioco/valr") (synopsis "Genome interval arithmetic in R") (description "This package enables you to read and manipulate genome intervals and @@ -13609,14 +13618,14 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "0.3.5") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh")))) + "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs @@ -13722,14 +13731,14 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-3") + (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk")))) + "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -13744,6 +13753,8 @@ datum transformations.") ("r-sf" ,r-sf) ("r-sp" ,r-sp) ("r-spdata" ,r-spdata))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/r-spatial/spdep/") (synopsis "Spatial dependence: weighting schemes, statistics and models") (description @@ -14363,14 +14374,14 @@ the corresponding outputs (tables and graphs).") (define-public r-rjava (package (name "r-rjava") - (version "0.9-12") + (version "0.9-13") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 - "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12")))) + "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments @@ -15157,17 +15168,28 @@ matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.") (license license:gpl2))) +;; This package includes minified JavaScript files. When upgrading please +;; check that there are no new minified JavaScript files. (define-public r-flexdashboard (package (name "r-flexdashboard") - (version "0.5.1.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "flexdashboard" version)) (sha256 (base32 - "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x")))) + "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled minified JavaScript files + (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js") + (delete-file "inst/www/sly/sly.min.js") + (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js") + (delete-file "inst/www/prism/prism.js") + #t)))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) @@ -15210,7 +15232,6 @@ function for computing a matrix of correlation p-values.") (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) - (delete-file target) (let ((minified (open-pipe* OPEN_READ "uglify-js" source))) (call-with-output-file target (lambda (port) @@ -15710,14 +15731,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-ingredients (package (name "r-ingredients") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 - "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967")))) + "1mp1rgi3nnr8mjddpbyi24zvqcbihz0d8np2j13cbjc089n6jci8")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs @@ -15776,14 +15797,14 @@ classification and regression models.") (define-public r-dalex (package (name "r-dalex") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk")))) + "1azbnykaddsfp2qmxmhpjz76zg78msxv6n2jqkq4gwbgqa5vdfd2")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -16222,7 +16243,7 @@ multiple plots.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/MacoskoLab/liger.git") + (url "https://github.com/MacoskoLab/liger") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -16542,13 +16563,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-10") + (version "1.5-12") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "02z7rhpizzmymiqpi90nm15bjdz0411bqlavlk0lhwxb42ilhif6")))) + (base32 "0jvb5ykp539mi0hqs05w4w8wz45blc4nvkhs70aqmzyx27hadfiq")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -17515,14 +17536,14 @@ data.") (define-public r-mda (package (name "r-mda") - (version "0.5") + (version "0.5-2") (source (origin (method url-fetch) (uri (cran-uri "mda" version)) (sha256 (base32 - "01pjrz9xv1rx78ndy0x9dc32ws8brcvwyb500m1f0dqd42375vmx")))) + "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class))) @@ -17831,14 +17852,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.1-6") + (version "5.1-7") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr")))) + "0ywqwsp4k6jgnicp1gdsglji61l5cnackl52700v8kmkk83bq4c8")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -20158,18 +20179,19 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "2.0.1") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz")))) + "0qxvm75g6r0d1clj8b19gjqwkfrqypapf4zysb8nyfbmn33h8xc7")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) ("r-extrafont" ,r-extrafont) ("r-fastmatch" ,r-fastmatch) ("r-ggplot2" ,r-ggplot2) @@ -20915,14 +20937,14 @@ Haberman's interaction model when all items are dichotomously scored.") (define-public r-iheatmapr (package (name "r-iheatmapr") - (version "0.4.12") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "iheatmapr" version)) (sha256 (base32 - "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw")))) + "0s2lc088rq2siy2wzmg1y6nss68rs33mf7w2izqqmg6kbx6d7y9h")))) (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) (propagated-inputs @@ -20932,10 +20954,10 @@ Haberman's interaction model when all items are dichotomously scored.") ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description @@ -21124,20 +21146,23 @@ using the @code{rstan} and @code{rstanarm} packages).") (define-public r-rstantools (package (name "r-rstantools") - (version "2.0.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "rstantools" version)) (sha256 (base32 - "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa")))) + "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) (inputs `(("pandoc" ,ghc-pandoc))) (propagated-inputs `(("r-desc" ,r-desc) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://mc-stan.org/rstantools/") (synopsis "Tools for developing R packages interfacing with Stan") (description @@ -21151,14 +21176,13 @@ recommendations for developers.") (define-public r-loo (package (name "r-loo") - (version "2.2.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "loo" version)) (sha256 - (base32 - "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6")))) + (base32 "12z0k8lhz0rxygs5lc7076nw6qhk0pda8nxf65hkinfrf4dy53fr")))) (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs @@ -21167,6 +21191,8 @@ recommendations for developers.") (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-matrixstats" ,r-matrixstats))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://mc-stan.org/loo/") (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") (description @@ -21184,14 +21210,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.19.3") + (version "2.21.1") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np")))) + "0fxxh2jmrgfp98195qkqli1r9ni457vnjdvqm5l91j6aagkbk8zz")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -21207,7 +21233,8 @@ techniques to average Bayesian predictive distributions.") #t))))) (native-inputs `(("tzdata" ,tzdata-for-tests) - ("pandoc" ,ghc-pandoc))) + ("pandoc" ,ghc-pandoc) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-bh" ,r-bh) ("r-ggplot2" ,r-ggplot2) @@ -21217,7 +21244,9 @@ techniques to average Bayesian predictive distributions.") ("r-pkgbuild" ,r-pkgbuild) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) - ("r-stanheaders" ,r-stanheaders))) + ("r-rcppparallel" ,r-rcppparallel) + ("r-stanheaders" ,r-stanheaders) + ("r-v8" ,r-v8))) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description @@ -22063,14 +22092,14 @@ included in this package as well.") (define-public r-brms (package (name "r-brms") - (version "2.13.0") + (version "2.13.3") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0vdncdawxawi16f326qrgy9jjjipmqdjxh741y9p7xdzd4fwaxx3")))) + "13gnc517yssvi2mnih5bln06hcbn4y80gd9h3szacs6n3mwpig5f")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -22192,17 +22221,19 @@ permuted copies (shadows).") (define-public r-directlabels (package (name "r-directlabels") - (version "2020.1.31") + (version "2020.6.17") (source (origin (method url-fetch) (uri (cran-uri "directlabels" version)) (sha256 (base32 - "08s1gnwp4bn8xahwjaq0f1qzhwh2dvybzhq3z7xyzn8cnyzmis6c")))) + "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://directlabels.r-forge.r-project.org/") (synopsis "Direct labels for multicolor plots") (description @@ -22325,3 +22356,211 @@ across a wide array of bioinformatic R packages.") and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning.") (license license:gpl3))) + +(define-public r-shapforxgboost + (package + (name "r-shapforxgboost") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "SHAPforxgboost" version)) + (sha256 + (base32 + "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq")))) + (properties + `((upstream-name . "SHAPforxgboost"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bbmisc" ,r-bbmisc) + ("r-data-table" ,r-data-table) + ("r-ggextra" ,r-ggextra) + ("r-ggforce" ,r-ggforce) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-xgboost" ,r-xgboost))) + (home-page "https://github.com/liuyanguu/SHAPforxgboost") + (synopsis "SHAP Plots for XGBoost") + (description + "The aim of @code{SHAPforxgboost} is to aid in visual data investigations +using @dfn{SHAP} (Shapley additive explanation) visualization plots for +@code{XGBoost}. It provides summary plot, dependence plot, interaction plot, +and force plot. It relies on the @code{XGBoost} package to produce SHAP +values.") + (license license:expat))) + +(define-public r-rismed + (package + (name "r-rismed") + (version "2.1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "RISmed" version)) + (sha256 + (base32 + "08dmkkxsmwp9b4h2g1bbx03cijn793fsnzkmbima8x9d42vxnm1l")))) + (properties `((upstream-name . "RISmed"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/RISmed") + (synopsis "Download content from NCBI databases") + (description + "This package provides a set of tools to extract bibliographic +content from the National Center for Biotechnology Information (NCBI) +databases, including PubMed. The name RISmed is a portmanteau of +RIS (for Research Information Systems, a common tag format for +bibliographic data) and PubMed.") + (license license:gpl2+))) + +(define-public r-semver + (package + (name "r-semver") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "semver" version)) + (sha256 + (base32 + "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy")))) + (properties `((upstream-name . "semver"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-rcpp" ,r-rcpp))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/johndharrison/semver") + (synopsis "Parser for Semantic Versioning 2.0.0") + (description + "This package provides tools and functions for parsing, rendering and +operating on semantic version strings. Semantic versioning is a simple set of +rules and requirements that dictate how version numbers are assigned and +incremented as outlined at @url{http://semver.org}.") + (license license:expat))) + +(define-public r-binman + (package + (name "r-binman") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "binman" version)) + (sha256 + (base32 + "0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az")))) + (properties `((upstream-name . "binman"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-rappdirs" ,r-rappdirs) + ("r-semver" ,r-semver) + ("r-xml2" ,r-xml2) + ("r-yaml" ,r-yaml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/ropensci/binman") + (synopsis "Binary download manager") + (description + "This package provides tools and functions for managing the download of +binary files. Binary repositories are defined in the YAML format. Defining +new pre-download, download and post-download templates allow additional +repositories to be added.") + (license license:expat))) + +(define-public r-wdman + (package + (name "r-wdman") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "wdman" version)) + (sha256 + (base32 + "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02")))) + (properties `((upstream-name . "wdman"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-binman" ,r-binman) + ("r-processx" ,r-processx) + ("r-semver" ,r-semver) + ("r-yaml" ,r-yaml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/wdman/") + (synopsis "Webdriver/Selenium binary manager") + (description + "There are a number of binary files associated with the +Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/}, +@url{https://sites.google.com/a/chromium.org/chromedriver/}, +@url{https://github.com/mozilla/geckodriver}, +@url{http://phantomjs.org/download.html}, and +@url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for +more information). This package provides functions to download these binaries +and to manage processes involving them.") + (license license:expat))) + +(define-public r-rselenium + (package + (name "r-rselenium") + (version "1.7.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "RSelenium" version)) + (sha256 + (base32 + "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir")))) + (properties `((upstream-name . "RSelenium"))) + (build-system r-build-system) + (propagated-inputs + `(("r-binman" ,r-binman) + ("r-catools" ,r-catools) + ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) + ("r-wdman" ,r-wdman) + ("r-xml" ,r-xml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://docs.ropensci.org/RSelenium/") + (synopsis "R bindings for Selenium WebDriver") + (description + "This package provides a set of R bindings for the Selenium 2.0 +WebDriver (see @url{https://selenium.dev/documentation/en/} for more +information) using the @code{JsonWireProtocol} (see +@url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more +information). Selenium 2.0 WebDriver allows driving a web browser natively as +a user would either locally or on a remote machine using the Selenium server +it marks a leap forward in terms of web browser automation. Selenium +automates web browsers (commonly referred to as browsers). Using RSelenium +you can automate browsers locally or remotely.") + (license license:agpl3+))) + +(define-public r-conquer + (package + (name "r-conquer") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "conquer" version)) + (sha256 + (base32 + "1c7id7wgspma5bdcirrhw7f9fp709zxpj31klivasdbvd4jgi4vb")))) + (properties `((upstream-name . "conquer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://github.com/XiaoouPan/conquer") + (synopsis "Convolution-type smoothed quantile regression") + (description + "This package provides fast and accurate convolution-type smoothed +quantile regression, implemented using Barzilai-Borwein gradient descent with +a Huber regression warm start. Confidence intervals for regression +coefficients are constructed using multiplier bootstrap.") + (license license:gpl3))) |