diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 756 |
1 files changed, 606 insertions, 150 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f3c90b073e..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. ;;; @@ -107,14 +108,14 @@ degree elevation and curve fitting.") (define-public r-v8 (package (name "r-v8") - (version "3.1.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "0xdljralgwyivdhx2a7kqf3yv4ijl4rdrz2p7p59lj2x5d2qyanf")))) + "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments @@ -193,6 +194,26 @@ programming packages such as @code{knitr} and @code{rmarkdown}.") the system clipboards.") (license license:gpl3))) +(define-public r-zoo + (package + (name "r-zoo") + (version "1.8-8") + (source (origin + (method url-fetch) + (uri (cran-uri "zoo" version)) + (sha256 + (base32 + "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://zoo.R-Forge.R-project.org/") + (synopsis "S3 infrastructure for regular and irregular time series") + (description "This package contains an S3 class with methods for totally +ordered indexed observations. It is particularly aimed at irregular time +series of numeric vectors/matrices and factors.") + (license license:gpl2+))) + (define-public r-ggpmisc (package (name "r-ggpmisc") @@ -802,14 +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 @@ -850,17 +873,17 @@ directory.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v")))) + "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-rcpp" ,r-rcpp) + `(("r-base64enc" ,r-base64enc) + ("r-digest" ,r-digest) ("r-rlang" ,r-rlang))) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") @@ -894,14 +917,13 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "1.13.3") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 - "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl")))) + (base32 "0ma52kajzxfg9w811d6ldhghzn9xhyr8bh7k5v265k82bzx7rac6")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs @@ -912,6 +934,8 @@ applications.") ("r-magrittr" ,r-magrittr) ("r-rstudioapi" ,r-rstudioapi) ("r-stringr" ,r-stringr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description @@ -1040,7 +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 @@ -1414,7 +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 @@ -1981,13 +2005,13 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.4.6") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5")))) + (base32 "012wbj446k1wz6bp6bpf6h77ypvcsw69xvnax6qf6vyc7dj2qimq")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -2071,13 +2095,13 @@ is provided.") (define-public r-calibrate (package (name "r-calibrate") - (version "1.7.6") + (version "1.7.7") (source (origin (method url-fetch) (uri (cran-uri "calibrate" version)) (sha256 - (base32 "0h91mxf4fy3xk4mavf6cdllglyq5fra8zpz7yvc63n5jigpy2lhd")))) + (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -2237,14 +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 @@ -2323,7 +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 @@ -3263,14 +3287,14 @@ multivariate and 5 functional classification problems are included.") (define-public r-gower (package (name "r-gower") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "gower" version)) (sha256 (base32 - "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg")))) + "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/gower") (synopsis "Gower's distance") @@ -3387,22 +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))) @@ -3424,14 +3449,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.12") + (version "0.1.13") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "0hbnrqgzazg401nk5fhljif7wnspicki179qf215r34y9wm8g3xj")))) + "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -3439,6 +3464,7 @@ provides a one-row summary of model-level statistics.") ("r-glue" ,r-glue) ("r-gower" ,r-gower) ("r-ipred" ,r-ipred) + ("r-lifecycle" ,r-lifecycle) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) @@ -3504,7 +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 @@ -3684,18 +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))) @@ -4185,14 +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) @@ -4333,13 +4359,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.14") + (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "183f6d7lr116f90j37a8hfr6ni1x9xkqj79s8lnky1jwr6zj3ha9")))) + (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -4435,19 +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))) @@ -4481,14 +4509,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.23") + (version "0.24") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "084jd1m2i3zyxxlls7skq3jxv3b5cgps3yk60q1yzyy9sxslab7m")))) + "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4924,17 +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 @@ -5315,14 +5345,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.3.4") + (version "1.3.9") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs")) + "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0")) (modules '((guix build utils))) (snippet '(begin @@ -6012,14 +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 @@ -6229,14 +6259,14 @@ and adds the annotation to the plot.") (define-public r-rstatix (package (name "r-rstatix") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 - "0ikbjmr58ah39rlwyiix50kl3yk9j7jngsvl6hh973392qdvmch6")))) + "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs @@ -6244,6 +6274,7 @@ and adds the annotation to the plot.") ("r-car" ,r-car) ("r-corrplot" ,r-corrplot) ("r-dplyr" ,r-dplyr) + ("r-generics" ,r-generics) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) ("r-rlang" ,r-rlang) @@ -6265,14 +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) @@ -6579,14 +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 @@ -6606,14 +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) @@ -6718,14 +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))) @@ -6901,14 +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))) @@ -7251,19 +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) @@ -7732,14 +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) @@ -8302,14 +8335,14 @@ multiple-imputation datasets.") (define-public r-magick (package (name "r-magick") - (version "2.3") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8")))) + "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -8319,7 +8352,8 @@ multiple-imputation datasets.") ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description @@ -8743,14 +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) @@ -8948,14 +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 @@ -8980,14 +9014,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1")))) + "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -9034,14 +9068,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.14.3") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd")))) + "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r")))) (build-system r-build-system) (propagated-inputs `(("r-insight" ,r-insight) @@ -9180,14 +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) @@ -9531,20 +9565,18 @@ and related methods.") (define-public r-rcppgsl (package (name "r-rcppgsl") - (version "0.3.7") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 - (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5")))) + (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("gsl" ,gsl))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://cran.r-project.org/web/packages/RcppGSL/") (synopsis "Rcpp integration for GSL vectors and matrices") (description @@ -9749,14 +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/") @@ -10382,14 +10414,14 @@ R packages (on CRAN, Bioconductor or Github).") (define-public r-docopt (package (name "r-docopt") - (version "0.6.1") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "docopt" version)) (sha256 (base32 - "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068")))) + "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz")))) (build-system r-build-system) (home-page "https://github.com/docopt/docopt.R") (synopsis "Command-line interface specification language") @@ -12161,14 +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) @@ -12193,14 +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 @@ -12328,14 +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))) @@ -12577,13 +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))) @@ -12854,14 +12886,14 @@ latent growth curve models.") (define-public r-nonnest2 (package (name "r-nonnest2") - (version "0.5-3") + (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "nonnest2" version)) (sha256 (base32 - "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c")))) + "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2")))) (build-system r-build-system) (propagated-inputs `(("r-compquadform" ,r-compquadform) @@ -13173,7 +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 @@ -13586,14 +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 @@ -13699,14 +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) @@ -13721,6 +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 @@ -14047,14 +14081,14 @@ inbred lines, F2 intercrosses, and association mapping populations.") (define-public r-ldheatmap (package (name "r-ldheatmap") - (version "0.99-7") + (version "0.99-8") (source (origin (method url-fetch) (uri (cran-uri "LDheatmap" version)) (sha256 (base32 - "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc")))) + "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z")))) (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs @@ -14138,13 +14172,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.19") + (version "0.20") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "137l0cyzw9ij2l3zyk3mm1k2db9vhbax6c9y4rydvh4i9gka5vlq")))) + "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -14340,14 +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 @@ -14741,14 +14775,14 @@ sets of URLs.") (define-public r-ggforce (package (name "r-ggforce") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "ggforce" version)) (sha256 (base32 - "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0")))) + "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -15134,17 +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) @@ -15187,7 +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) @@ -15687,14 +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 @@ -15753,14 +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 @@ -15956,14 +16000,14 @@ easily.") (define-public r-umap (package (name "r-umap") - (version "0.2.5.0") + (version "0.2.6.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 - "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d")))) + "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f")))) (build-system r-build-system) (propagated-inputs `(("r-openssl" ,r-openssl) @@ -16167,14 +16211,14 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (define-public r-patchwork (package (name "r-patchwork") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 - "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb")))) + "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -16199,7 +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 @@ -16519,13 +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 @@ -17492,14 +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))) @@ -17808,14 +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 @@ -20135,18 +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) @@ -20892,14 +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 @@ -20909,10 +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 @@ -21101,20 +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 @@ -21128,14 +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 @@ -21144,6 +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 @@ -21161,14 +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 @@ -21184,7 +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) @@ -21194,7 +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 @@ -21298,26 +21350,61 @@ Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in climate data.") (license license:lgpl2.1))) +(define-public r-rlinsolve + (package + (name "r-rlinsolve") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rlinsolve" version)) + (sha256 + (base32 + "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc")))) + (properties `((upstream-name . "Rlinsolve"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rdpack" ,r-rdpack))) + (home-page "https://cran.r-project.org/web/packages/Rlinsolve/") + (synopsis "Iterative solvers for (sparse) linear system of equations") + (description + "Solving a system of linear equations is one of the most fundamental +computational problems for many fields of mathematical studies, such as +regression problems from statistics or numerical partial differential +equations. This package provides basic stationary iterative solvers such as +Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods. +Nonstationary, also known as Krylov subspace methods are also provided. +Sparse matrix computation is also supported in that solving large and sparse +linear systems can be manageable using the @code{Matrix} package along with +@code{RcppArmadillo}.") + (license license:gpl3+))) + (define-public r-zvcv (package (name "r-zvcv") - (version "1.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "ZVCV" version)) (sha256 (base32 - "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8")))) + "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r")))) (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) + ("r-bh" ,r-bh) + ("r-dplyr" ,r-dplyr) ("r-glmnet" ,r-glmnet) + ("r-magrittr" ,r-magrittr) ("r-mvtnorm" ,r-mvtnorm) - ("r-partitions" ,r-partitions) ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rlinsolve" ,r-rlinsolve))) (home-page "https://cran.r-project.org/web/packages/ZVCV/") (synopsis "Zero-Variance Control Variates") (description @@ -21388,19 +21475,18 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (define-public r-isoband (package (name "r-isoband") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "isoband" version)) (sha256 (base32 - "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q")))) + "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx")))) (properties `((upstream-name . "isoband"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-testthat" ,r-testthat))) + `(("r-testthat" ,r-testthat))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/wilkelab/isoband") @@ -22006,14 +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 @@ -22108,3 +22194,373 @@ multi-state models.") "This package creates scatterpie plots, especially useful for plotting pies on a map.") (license license:artistic2.0))) + +(define-public r-boruta + (package + (name "r-boruta") + (version "7.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "Boruta" version)) + (sha256 + (base32 + "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg")))) + (properties `((upstream-name . "Boruta"))) + (build-system r-build-system) + (propagated-inputs `(("r-ranger" ,r-ranger))) + (home-page "https://gitlab.com/mbq/Boruta/") + (synopsis "Wrapper algorithm for all relevant feature selection") + (description + "This package provides an all relevant feature selection wrapper +algorithm. It finds relevant features by comparing original attributes' +importance with importance achievable at random, estimated using their +permuted copies (shadows).") + (license license:gpl2+))) + +(define-public r-directlabels + (package + (name "r-directlabels") + (version "2020.6.17") + (source + (origin + (method url-fetch) + (uri (cran-uri "directlabels" version)) + (sha256 + (base32 + "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 + "This package provides an extensible framework for automatically placing +direct labels onto multicolor plots. Label positions are described using +positioning methods that can be re-used across several different plots. There +are heuristics for examining @code{trellis} and @code{ggplot} objects and +inferring an appropriate positioning method.") + (license license:gpl3))) + +(define-public r-lsd + (package + (name "r-lsd") + (version "4.1-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "LSD" version)) + (sha256 + (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm")))) + (properties `((upstream-name . "LSD"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/LSD/") + (synopsis "Lots of superior depictions tool creates colorful plots") + (description + "This package creates lots of colorful plots in a multitude of variations. +Try a demo of the LSD by running @code{demotour()}.") + ;; Either version + (license (list license:gpl2 license:gpl3)))) + +(define-public r-fourcseq + (package + (name "r-fourcseq") + (version "1.21.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FourCSeq" version)) + (sha256 + (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x")))) + (properties `((upstream-name . "FourCSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-fda" ,r-fda) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gtools" ,r-gtools) + ("r-lsd" ,r-lsd) + ("r-matrix" ,r-matrix) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") + (synopsis "Analysis of multiplexed 4C sequencing data") + (description + "This package is an R package dedicated to the analysis of (multiplexed) +4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific +interactions between DNA elements and identify differential interactions +between conditions. The statistical analysis in R starts with individual bam +files for each sample as inputs. To obtain these files, the package contains +a Python script to demultiplex libraries and trim off primer sequences. With +a standard alignment software the required bam files can be then be +generated.") + (license license:gpl3+))) + +(define-public r-phylogram + (package + (name "r-phylogram") + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "phylogram" version)) + (sha256 + (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v")))) + (properties `((upstream-name . "phylogram"))) + (build-system r-build-system) + (propagated-inputs `(("r-ape" ,r-ape))) + (home-page "https://github.com/ropensci/phylogram/") + (synopsis "Dendrograms for evolutionary analysis") + (description + "The @code{r-phylogram} package is a tool for for developing phylogenetic +trees as deeply-nested lists known as \"dendrogram\" objects. It provides +functions for conversion between \"dendrogram\" and \"phylo\" class objects, +as well as several tools for command-line tree manipulation and import/export +via Newick parenthetic text. This improves accessibility to the comprehensive +range of object-specific analytical and tree-visualization functions found +across a wide array of bioinformatic R packages.") + (license license:gpl3))) + +(define-public r-kmer + (package + (name "r-kmer") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "kmer" version)) + (sha256 + (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww")))) + (properties `((upstream-name . "kmer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-openssl" ,r-openssl) + ("r-phylogram" ,r-phylogram) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/shaunpwilkinson/kmer/") + (synopsis "Fast K-Mer counting and clustering for biological sequence analysis") + (description + "@code{r-kmer} is an R package for rapidly computing distance matrices +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))) |