diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 267 |
1 files changed, 187 insertions, 80 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eed776e0c6..129c5c07c8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com> ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz> +;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -42,6 +43,7 @@ #:use-module (guix utils) #:use-module (guix build-system r) #:use-module (gnu packages algebra) + #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) @@ -759,7 +761,7 @@ data structures in C++.") (define-public r-shiny (package (name "r-shiny") - (version "1.4.0") + (version "1.4.0.2") (source (origin (method git-fetch) @@ -769,7 +771,7 @@ data structures in C++.") (file-name (git-file-name name version)) (sha256 (base32 - "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7")))) + "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs")))) (build-system r-build-system) (arguments `(#:modules ((guix build r-build-system) @@ -837,15 +839,19 @@ data structures in C++.") #t))))) (propagated-inputs `(("r-crayon" ,r-crayon) + ("r-digest" ,r-digest) ("r-fastmap" ,r-fastmap) + ("r-htmltools" ,r-htmltools) ("r-httpuv" ,r-httpuv) - ("r-mime" ,r-mime) ("r-jsonlite" ,r-jsonlite) - ("r-xtable" ,r-xtable) - ("r-digest" ,r-digest) - ("r-htmltools" ,r-htmltools) + ("r-later" ,r-later) + ("r-mime" ,r-mime) + ("r-promises" ,r-promises) ("r-r6" ,r-r6) - ("r-sourcetools" ,r-sourcetools))) + ("r-rlang" ,r-rlang) + ("r-sourcetools" ,r-sourcetools) + ("r-withr" ,r-withr) + ("r-xtable" ,r-xtable))) (inputs `(("js-datatables" ,js-datatables) ("js-html5shiv" ,js-html5shiv) @@ -856,7 +862,8 @@ data structures in C++.") ("js-highlight" ,js-highlight) ("js-es5-shim" ,js-es5-shim))) (native-inputs - `(("uglify-js" ,uglify-js))) + `(("uglify-js" ,uglify-js) + ("gfortran" ,gfortran))) (home-page "http://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description @@ -4931,6 +4938,28 @@ files.") environment within Shiny.") (license license:expat))) +(define-public r-randomizr + (package + (name "r-randomizr") + (version "0.20.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "randomizr" version)) + (sha256 + (base32 + "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h")))) + (properties `((upstream-name . "randomizr"))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://declaredesign.org/r/randomizr/") + (synopsis "Tools for common forms of random assignment and sampling") + (description + "This package provides tools for generating random assignments for common +experimental designs and random samples for common sampling designs.") + (license license:expat))) + (define-public r-base64url (package (name "r-base64url") @@ -4961,14 +4990,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.0.6") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg")) + "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs")) (modules '((guix build utils))) (snippet '(begin @@ -4986,15 +5015,17 @@ systems.") ("r-dt" ,r-dt) ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) ("r-import" ,r-import) ("r-jsonlite" ,r-jsonlite) ("r-knitr" ,r-knitr) ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-markdown" ,r-markdown) + ("r-mass" ,r-mass) + ("r-patchwork" ,r-patchwork) ("r-plotly" ,r-plotly) ("r-psych" ,r-psych) + ("r-randomizr" ,r-randomizr) ("r-readr" ,r-readr) ("r-readxl" ,r-readxl) ("r-rlang" ,r-rlang) @@ -6864,14 +6895,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "0qkp1byl2xspxaaf0by6mvvrhg7wlz6fxmynz2hkh0ds24w7ig9m")))) + "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -11583,14 +11614,14 @@ lasso, adaptive lasso and Ridge regression based on cross-validation.") (define-public r-mcmc (package (name "r-mcmc") - (version "0.9-6.1") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "mcmc" version)) (sha256 (base32 - "1i1nhdapyijvm58zx38q28zk01ndmi6smjivxk5xs2cx9b6v2av9")))) + "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p")))) (build-system r-build-system) (home-page "https://www.stat.umn.edu/geyer/mcmc/") (synopsis "Markov chain Monte Carlo") @@ -15040,14 +15071,14 @@ extends the lme4 package.") (define-public r-batchtools (package (name "r-batchtools") - (version "0.9.12") + (version "0.9.13") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 - "16x524hvy9d8p7r4fi1c8mixcvzgsjbf3y0vxaa56ssbbab4p7f9")))) + "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) @@ -15062,6 +15093,8 @@ extends the lme4 package.") ("r-rappdirs" ,r-rappdirs) ("r-stringi" ,r-stringi) ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description @@ -15322,20 +15355,22 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "0.90.0.2") + (version "1.0.0.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194")))) + "0fx5qjpjjirzhplddqmxlysyqszp79w74x00b5shp6p2lzy6yd9a")))) (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description @@ -15561,35 +15596,31 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (license license:gpl3))) (define-public r-patchwork - ;; There has been no public release yet. - (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242") - (revision "1")) - (package - (name "r-patchwork") - (version (git-version "0.0.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/thomasp85/patchwork.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4")))) - (build-system r-build-system) - (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable))) - (home-page "https://github.com/thomasp85/patchwork") - (synopsis "Compose ggplot2 plots") - (description - "The @code{ggplot2} package provides a strong API for sequentially + (package + (name "r-patchwork") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "patchwork" version)) + (sha256 + (base32 + "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-gtable" ,r-gtable))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/thomasp85/patchwork") + (synopsis "Compose ggplot2 plots") + (description + "The @code{ggplot2} package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API to allow for arbitrarily complex composition of plots by providing mathmatical operators for combining multiple plots.") - (license license:expat)))) + (license license:expat))) (define-public r-liger (package @@ -15666,43 +15697,47 @@ dataset-specific factors.") (license license:gpl3))) (define-public r-harmony - ;; There are no tagged commits - (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a") - (revision "1")) - (package - (name "r-harmony") - (version (git-version "1.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/immunogenomics/harmony") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85")))) - (build-system r-build-system) - (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppprogress" ,r-rcppprogress) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) - (home-page "https://github.com/immunogenomics/harmony") - (synopsis "Integration of single cell sequencing data") - (description - "This package provides an implementation of the Harmony algorithm for + (package + (name "r-harmony") + (version "0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/immunogenomics/harmony") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file '("config.status" "configure")) + #t)))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rcppprogress" ,r-rcppprogress) + ("r-rlang" ,r-rlang) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr))) + (native-inputs + `(("autoconf" ,autoconf))) + (home-page "https://github.com/immunogenomics/harmony") + (synopsis "Integration of single cell sequencing data") + (description + "This package provides an implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al @url{doi.org/10.1101/461954}. The package includes a standalone Harmony function and interfaces to external frameworks.") - (license license:gpl3)))) + (license license:gpl3))) (define-public r-covr (package @@ -18389,14 +18424,14 @@ it may be seen by an animal with less acute vision.") (define-public r-caret (package (name "r-caret") - (version "6.0-85") + (version "6.0-86") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "0jxbf2zcvbb5s2pnjzg182awjvylc57q7z5plx6gs6gm62zxjafs")))) + "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns")))) (build-system r-build-system) (propagated-inputs `(("r-foreach" ,r-foreach) @@ -18409,6 +18444,8 @@ it may be seen by an animal with less acute vision.") ("r-recipes" ,r-recipes) ("r-reshape2" ,r-reshape2) ("r-withr" ,r-withr))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description @@ -20910,3 +20947,73 @@ service. Functions are provided to work with the OAI-PMH verbs: @code{GetRecord}, @code{Identify}, @code{ListIdentifiers}, @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.") (license license:expat))) + +(define-public r-argon2 + (package + (name "r-argon2") + (version "0.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "argon2" version)) + (sha256 + (base32 + "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh")))) + (properties `((upstream-name . "argon2"))) + (build-system r-build-system) + (home-page "https://github.com/wrathematics/argon2") + (synopsis "Secure password hashing based on the argon2 algorithm") + (description + "This package provides utilities for secure password hashing via the +argon2 algorithm.") + (license license:bsd-2))) + +(define-public r-getpass + (package + (name "r-getpass") + (version "0.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "getPass" version)) + (sha256 + (base32 + "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc")))) + (properties `((upstream-name . "getPass"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rstudioapi" ,r-rstudioapi))) + (home-page "https://github.com/wrathematics/getPass") + (synopsis "Masked user input") + (description + "This package provides a micro-package for reading \"passwords\", i.e. +reading user input with masking, so that the input is not displayed as it is +typed. Currently, RStudio, the command line (every OS), and any platform +where tcltk is present are supported.") + (license license:bsd-2))) + +(define-public r-remoter + (package + (name "r-remoter") + (version "0.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "remoter" version)) + (sha256 + (base32 + "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl")))) + (properties `((upstream-name . "remoter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-argon2" ,r-argon2) + ("r-getpass" ,r-getpass) + ("r-pbdzmq" ,r-pbdzmq) + ("r-png" ,r-png))) + (home-page "https://github.com/RBigData/remoter") + (synopsis "Control a remote R session from a local one") + (description + "This package provides a set of utilities for client/server computing +with R, controlling a remote R session (the server) from a local one (the +client).") + (license license:bsd-2))) |