;;; 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.
;;;
#: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)
(define-public r-shiny
(package
(name "r-shiny")
- (version "1.4.0")
+ (version "1.4.0.2")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "17ac48g414h9dhi0k4wrah4gyik0q5r0xw3kc01c02qfjwimqsx7"))))
+ "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
(build-system r-build-system)
(arguments
`(#:modules ((guix build r-build-system)
#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)
("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
(define-public r-ggally
(package
(name "r-ggally")
- (version "1.4.0")
+ (version "1.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "GGally" version))
(sha256
(base32
- "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
+ "082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
(properties `((upstream-name . "GGally")))
(build-system r-build-system)
(inputs
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")
(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
("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)
(define-public r-hdf5r
(package
(name "r-hdf5r")
- (version "1.3.1")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "hdf5r" version))
(sha256
(base32
- "0hvi2cvyv6zlxgpawnmsihxclp2ln88slbrnmaxagmjswskxsrpx"))))
+ "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
(build-system r-build-system)
(inputs
`(("hdf5" ,hdf5)
(propagated-inputs
`(("r-bit64" ,r-bit64)
("r-r6" ,r-r6)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://hhoeflin.github.io/hdf5r")
(synopsis "Interface to the HDF5 binary data format")
(description
(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
(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")
(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)
("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
(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
(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
(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
(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)
("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
@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)))
HCoop / jackhill / guix / guix.git / blobdiff