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-rw-r--r--gnu/packages/cran.scm1086
1 files changed, 878 insertions, 208 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d928f971d0..8754f83f72 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
@@ -15,6 +15,7 @@
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
+;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -53,7 +54,7 @@
#:use-module (gnu packages gnome)
#:use-module (gnu packages graph)
#:use-module (gnu packages gtk)
- #:use-module (gnu packages haskell)
+ #:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
@@ -97,14 +98,14 @@ the system clipboards.")
(define-public r-ellipsis
(package
(name "r-ellipsis")
- (version "0.2.0.1")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ellipsis" version))
(sha256
(base32
- "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f"))))
+ "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)))
@@ -166,14 +167,14 @@ objects.")
(define-public r-sys
(package
(name "r-sys")
- (version "3.2")
+ (version "3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "sys" version))
(sha256
(base32
- "1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698"))))
+ "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
(build-system r-build-system)
(home-page "https://github.com/jeroen/sys")
(synopsis "Powerful and reliable tools for running system commands in R")
@@ -212,14 +213,14 @@ read a protected key.")
(define-public r-vegan
(package
(name "r-vegan")
- (version "2.5-5")
+ (version "2.5-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
- "0wb90ng02gi13854bjq0b8a2vrknyhb0s0l1v3z38c4zy9k54sw7"))))
+ "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -370,14 +371,14 @@ such as copy/paste from an R session.")
(define-public r-callr
(package
(name "r-callr")
- (version "3.3.1")
+ (version "3.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "callr" version))
(sha256
(base32
- "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z"))))
+ "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
@@ -447,13 +448,13 @@ into a pipeline of data manipulation and visualisation.")
(define-public r-httpuv
(package
(name "r-httpuv")
- (version "1.5.1")
+ (version "1.5.2")
(source (origin
(method url-fetch)
(uri (cran-uri "httpuv" version))
(sha256
(base32
- "042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm"))))
+ "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
@@ -524,31 +525,18 @@ directory.")
(define-public r-htmltools
(package
(name "r-htmltools")
- (version "0.3.6")
+ (version "0.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
- "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"))))
+ "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; See https://github.com/rstudio/htmltools/pull/68
- ;; The resource files are in the store and have mode 444. After
- ;; copying the files R fails to remove them again because it doesn't
- ;; have write access to them.
- (add-after 'unpack 'copy-files-without-mode
- (lambda _
- (substitute* "R/html_dependency.R"
- (("file.copy\\(from, to, " prefix)
- (string-append prefix
- "copy.mode = FALSE, ")))
- #t)))))
(propagated-inputs
`(("r-digest" ,r-digest)
- ("r-rcpp" ,r-rcpp)))
+ ("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)))
(home-page "https://cran.r-project.org/web/packages/htmltools")
(synopsis "R tools for HTML")
(description
@@ -558,13 +546,13 @@ directory.")
(define-public r-htmlwidgets
(package
(name "r-htmlwidgets")
- (version "1.3")
+ (version "1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "htmlwidgets" version))
(sha256
(base32
- "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i"))))
+ "1h2sj5h9vcssb73nz63gmw5bajs73m9q807fsypvr621gb1s124i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
@@ -581,14 +569,14 @@ applications.")
(define-public r-htmltable
(package
(name "r-htmltable")
- (version "1.13.1")
+ (version "1.13.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "htmlTable" version))
(sha256
(base32
- "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8"))))
+ "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh"))))
(properties `((upstream-name . "htmlTable")))
(build-system r-build-system)
(propagated-inputs
@@ -614,13 +602,13 @@ LaTeX.")
(define-public r-curl
(package
(name "r-curl")
- (version "4.0")
+ (version "4.2")
(source (origin
(method url-fetch)
(uri (cran-uri "curl" version))
(sha256
(base32
- "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89"))))
+ "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -796,6 +784,84 @@ extensive prebuilt widgets make it possible to build beautiful,
responsive, and powerful applications with minimal effort.")
(license license:artistic2.0)))
+;; This package includes minified JavaScript files. When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-shinytree
+ (package
+ (name "r-shinytree")
+ (version "0.2.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shinyTree" version))
+ (sha256
+ (base32
+ "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete minified JavaScript
+ (for-each delete-file
+ '("inst/www/jsTree-3.3.7/libs/require.js"
+ "inst/www/jsTree-3.3.7/libs/jquery.js"
+ "inst/www/jsTree-3.3.7/jstree.min.js"))
+ #t))))
+ (properties `((upstream-name . "shinyTree")))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1)
+ (ice-9 popen))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'replace-minified-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/www/jsTree-3.3.7/"
+ (symlink (string-append (assoc-ref inputs "js-requirejs")
+ "/share/javascript/require.min.js")
+ "libs/require.js")
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(assoc-ref inputs "js-jquery")
+ "libs/jquery.js")
+ ("jstree.js"
+ "jstree.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #t "Processing ~a --> ~a~%"
+ source target)
+ (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+ (call-with-output-file target
+ (lambda (port)
+ (dump-port minified port)))))
+ sources targets))))
+ #t)))))
+ (propagated-inputs
+ `(("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-promises" ,r-promises)
+ ("r-shiny" ,r-shiny)
+ ("r-stringr" ,r-stringr)))
+ (inputs
+ `(("js-requirejs" ,js-requirejs)))
+ (native-inputs
+ `(("uglify-js" ,uglify-js)
+ ("js-jquery"
+ ,(origin
+ (method url-fetch)
+ (uri "https://code.jquery.com/jquery-3.3.1.js")
+ (sha256
+ (base32
+ "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
+ (home-page "https://cran.r-project.org/web/packages/shinyTree/")
+ (synopsis "jsTree bindings for Shiny")
+ (description
+ "This package exposes R bindings to jsTree, a JavaScript library that
+supports interactive trees, to enable rich, editable trees in Shiny.")
+ (license license:expat)))
+
(define-public r-shinydashboard
(package
(name "r-shinydashboard")
@@ -867,19 +933,44 @@ this gives the user direct access to the file system without the need to
well as file saving is available.")
(license license:gpl2+)))
+(define-public r-shinythemes
+ (package
+ (name "r-shinythemes")
+ (version "1.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shinythemes" version))
+ (sha256
+ (base32
+ "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
+ (properties `((upstream-name . "shinythemes")))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-shiny" ,r-shiny)))
+ (home-page "http://rstudio.github.io/shinythemes/")
+ (synopsis "Themes for Shiny")
+ (description
+ "This package provides themes for use with Shiny. It includes several
+Bootstrap themes, which are packaged for use with Shiny applications.")
+ ;; The package is released under version 3 of the GPL, but it includes
+ ;; source files that are covered by the Expat license. It also includes
+ ;; fonts under SIL or the ASL.
+ (license (list license:gpl3 license:expat
+ license:silofl1.1 license:asl2.0))))
+
;; The package sources include minified variants of d3.js and non-minified
;; source code of d3-jetpack.
(define-public r-d3r
(package
(name "r-d3r")
- (version "0.8.6")
+ (version "0.8.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "d3r" version))
(sha256
(base32
- "0vcmiyhd000xyl28k6rm7ba50x5sz5b2cpllxnq36q13qhdnqw6k"))))
+ "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
(build-system r-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -1059,14 +1150,14 @@ work well on small screens.")
(define-public r-feather
(package
(name "r-feather")
- (version "0.3.3")
+ (version "0.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "feather" version))
(sha256
(base32
- "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa"))))
+ "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-hms" ,r-hms)
@@ -1122,14 +1213,14 @@ coordinates.")
(define-public r-rgooglemaps
(package
(name "r-rgooglemaps")
- (version "1.4.3")
+ (version "1.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "RgoogleMaps" version))
(sha256
(base32
- "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
+ "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
(properties `((upstream-name . "RgoogleMaps")))
(build-system r-build-system)
(propagated-inputs `(("r-png" ,r-png)))
@@ -1388,14 +1479,13 @@ error stream.")
(define-public r-pls
(package
(name "r-pls")
- (version "2.7-1")
+ (version "2.7-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pls" version))
(sha256
- (base32
- "0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq"))))
+ (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
(build-system r-build-system)
(home-page "http://mevik.net/work/software/pls.html")
(synopsis "Partial Least Squares and Principal Component Regression")
@@ -1441,14 +1531,14 @@ processes. Most of its code is based on the @code{psutil} Python package.")
(define-public r-pkgbuild
(package
(name "r-pkgbuild")
- (version "1.0.4")
+ (version "1.0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "pkgbuild" version))
(sha256
(base32
- "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
+ "0y4i85axwajrk67h3w6fiqfm6wxmhn3dr240w5l2nvqg3ahpxc8q"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@@ -1589,14 +1679,13 @@ is provided.")
(define-public r-calibrate
(package
(name "r-calibrate")
- (version "1.7.2")
+ (version "1.7.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "calibrate" version))
(sha256
- (base32
- "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
+ (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)))
@@ -1629,14 +1718,13 @@ ellipses, circles, cylinders, arrows, ...")
(define-public r-globaloptions
(package
(name "r-globaloptions")
- (version "0.1.0")
+ (version "0.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "GlobalOptions" version))
(sha256
- (base32
- "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
+ (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
(properties `((upstream-name . "GlobalOptions")))
(build-system r-build-system)
(home-page "https://github.com/jokergoo/GlobalOptions")
@@ -1649,14 +1737,14 @@ validation and filtering on the values, making options invisible or private.")
(define-public r-circlize
(package
(name "r-circlize")
- (version "0.4.6")
+ (version "0.4.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "circlize" version))
(sha256
(base32
- "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f"))))
+ "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-colorspace" ,r-colorspace)
@@ -2230,14 +2318,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).")
(define-public r-lpsolve
(package
(name "r-lpsolve")
- (version "5.6.13.2")
+ (version "5.6.13.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "lpSolve" version))
(sha256
(base32
- "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m"))))
+ "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
(properties `((upstream-name . "lpSolve")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/lpSolve")
@@ -2663,14 +2751,14 @@ Optimization problems by using the simplex algorithm.")
(define-public r-geometry
(package
(name "r-geometry")
- (version "0.4.2")
+ (version "0.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "geometry" version))
(sha256
(base32
- "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
+ "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-magic" ,r-magic)
@@ -2892,14 +2980,14 @@ provides a one-row summary of model-level statistics.")
(define-public r-recipes
(package
(name "r-recipes")
- (version "0.1.6")
+ (version "0.1.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "recipes" version))
(sha256
(base32
- "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i"))))
+ "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -3476,14 +3564,14 @@ of Eigenmatrices} (JADE).")
(define-public r-dtw
(package
(name "r-dtw")
- (version "1.20-1")
+ (version "1.21-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "dtw" version))
(sha256
(base32
- "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
+ "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
(build-system r-build-system)
(propagated-inputs `(("r-proxy" ,r-proxy)))
(home-page "http://dtw.r-forge.r-project.org/")
@@ -3765,14 +3853,14 @@ Markdown documents.")
(define-public r-seriation
(package
(name "r-seriation")
- (version "1.2-7")
+ (version "1.2-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "seriation" version))
(sha256
(base32
- "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
+ "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
@@ -3799,14 +3887,13 @@ iVAT).")
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.8")
+ (version "0.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32
- "05jlbi5byqpw0fkhmmxqglnaxh9gwbcigx77kcpw1pkxnpwfry62"))))
+ (base32 "065ygh046ah43p5aqyrkv2vkxcnvnb4j7blfdygysg6hmqzp4pbv"))))
(build-system r-build-system)
(home-page "https://github.com/yihui/xfun")
(synopsis "Miscellaneous functions")
@@ -3944,14 +4031,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.15")
+ (version "0.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "145dmgq7h55mmqqlnnj153j484x2a9s1fbvjbjkdyqzpnz9qh2ax"))))
+ "1dadq9l0527v038b1k1dyfs0dklsgxnmplls3qhqprfgskif8mga"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -4062,21 +4149,20 @@ generation, and 2D/3D network visualization.")
(define-public r-ttr
(package
(name "r-ttr")
- (version "0.23-4")
+ (version "0.23-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "TTR" version))
(sha256
(base32
- "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb"))))
+ "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
(properties `((upstream-name . "TTR")))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
("r-xts" ,r-xts)
("r-zoo" ,r-zoo)))
- (native-inputs `(("gfortran" ,gfortran)))
(home-page "https://github.com/joshuaulrich/TTR")
(synopsis "Technical trading rules")
(description
@@ -4649,14 +4735,14 @@ files.")
(define-public r-shinyace
(package
(name "r-shinyace")
- (version "0.4.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinyAce" version))
(sha256
(base32
- "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1"))))
+ "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
(properties `((upstream-name . "shinyAce")))
(build-system r-build-system)
(propagated-inputs
@@ -4699,14 +4785,14 @@ systems.")
(define-public r-radiant-data
(package
(name "r-radiant-data")
- (version "1.0.0")
+ (version "1.0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "radiant.data" version))
(sha256
(base32
- "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
+ "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5064,14 +5150,14 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).")
(define-public r-arules
(package
(name "r-arules")
- (version "1.6-3")
+ (version "1.6-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "arules" version))
(sha256
(base32
- "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y"))))
+ "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
@@ -5161,14 +5247,14 @@ misclassification probabilities of different models.")
(define-public r-zip
(package
(name "r-zip")
- (version "2.0.3")
+ (version "2.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "zip" version))
(sha256
(base32
- "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
+ "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
(build-system r-build-system)
(home-page "https://github.com/gaborcsardi/zip")
(synopsis "Cross-platform Zip compression")
@@ -5240,14 +5326,14 @@ simple method for converting between file types.")
(define-public r-maptools
(package
(name "r-maptools")
- (version "0.9-5")
+ (version "0.9-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "maptools" version))
(sha256
(base32
- "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
+ "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
@@ -5268,14 +5354,14 @@ exchanging spatial objects with other R packages.")
(define-public r-later
(package
(name "r-later")
- (version "0.8.0")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "later" version))
(sha256
(base32
- "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
+ "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
@@ -5291,14 +5377,14 @@ time after the current time, after the R execution stack has emptied.")
(define-public r-promises
(package
(name "r-promises")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "promises" version))
(sha256
(base32
- "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
+ "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-later" ,r-later)
@@ -5569,14 +5655,14 @@ and adds the annotation to the plot.")
(define-public r-ggpubr
(package
(name "r-ggpubr")
- (version "0.2.2")
+ (version "0.2.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpubr" version))
(sha256
(base32
- "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw"))))
+ "0i81mmz4qn9yzcgfa6dhkcrx4ddlflkm2c3b40isc8all43rm8rn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cowplot" ,r-cowplot)
@@ -5761,14 +5847,14 @@ results to the user.")
(define-public r-hdf5r
(package
(name "r-hdf5r")
- (version "1.2.0")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hdf5r" version))
(sha256
(base32
- "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
+ "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
(build-system r-build-system)
(inputs
`(("hdf5" ,hdf5)
@@ -5851,14 +5937,14 @@ functions.")
(define-public r-rjags
(package
(name "r-rjags")
- (version "4-8")
+ (version "4-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "rjags" version))
(sha256
(base32
- "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m"))))
+ "1vrmxxfnia2mkmfkp5yaq5qrlh4xg3ggab6fnj14mrp1231wb91a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-coda" ,r-coda)))
@@ -6091,14 +6177,14 @@ other add-on packages.")
(define-public r-insight
(package
(name "r-insight")
- (version "0.4.1")
+ (version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "insight" version))
(sha256
(base32
- "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
+ "0lrh2l9n2zd9n3zzknsxz6nlasnrayx3bplxlz7m616g56gr5nfp"))))
(build-system r-build-system)
(home-page "https://easystats.github.io/insight/")
(synopsis "Easy access to model information for various model objects")
@@ -6117,14 +6203,14 @@ information are missing.")
(define-public r-sjlabelled
(package
(name "r-sjlabelled")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjlabelled" version))
(sha256
(base32
- "0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
+ "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-haven" ,r-haven)
@@ -6146,14 +6232,14 @@ vice versa), or to deal with multiple declared missing values.")
(define-public r-sjmisc
(package
(name "r-sjmisc")
- (version "2.8.1")
+ (version "2.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjmisc" version))
(sha256
(base32
- "1a30n3cyd9h9ilaiai9ywy53f03nikafc47rvpws2c2vghc8mbn7"))))
+ "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -6161,7 +6247,8 @@ vice versa), or to deal with multiple declared missing values.")
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
- ("r-sjlabelled" ,r-sjlabelled)))
+ ("r-sjlabelled" ,r-sjlabelled)
+ ("r-tidyselect" ,r-tidyselect)))
(home-page "https://github.com/strengejacke/sjmisc")
(synopsis "Data and variable transformation functions")
(description
@@ -6823,13 +6910,13 @@ and coverage methods to tune the choice of threshold.")
(define-public r-ggstance
(package
(name "r-ggstance")
- (version "0.3.2")
+ (version "0.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggstance" version))
(sha256
- (base32 "078ih9s5b0xzf582qg0vjnxvg5qad5ms1v2vdd062ckahi8zz1r8"))))
+ (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -6873,13 +6960,13 @@ and coverage methods to tune the choice of threshold.")
(define-public r-ggformula
(package
(name "r-ggformula")
- (version "0.9.1")
+ (version "0.9.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggformula" version))
(sha256
- (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx"))))
+ (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -6921,14 +7008,14 @@ used to teach mathematics, statistics, computation and modeling.")
(define-public r-raster
(package
(name "r-raster")
- (version "2.9-23")
+ (version "3.0-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "raster" version))
(sha256
(base32
- "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
+ "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rcpp" ,r-rcpp)
@@ -7489,14 +7576,14 @@ multiple-imputation datasets.")
(define-public r-magick
(package
(name "r-magick")
- (version "2.1")
+ (version "2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "magick" version))
(sha256
(base32
- "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
+ "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
(build-system r-build-system)
(inputs
`(("imagemagick" ,imagemagick)
@@ -7878,14 +7965,14 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.4")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
+ "1fpawaxnmj67md169a9mzrnnh2d0c973xydfg6hw865933jil9lq"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
@@ -7927,14 +8014,14 @@ Cohen (1988).")
(define-public r-libcoin
(package
(name "r-libcoin")
- (version "1.0-4")
+ (version "1.0-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "libcoin" version))
(sha256
(base32
- "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i"))))
+ "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
(build-system r-build-system)
(propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
(home-page "https://cran.r-project.org/web/packages/libcoin")
@@ -7947,14 +8034,14 @@ and permutation inference in the framework of Strasser and Weber (1999).")
(define-public r-coin
(package
(name "r-coin")
- (version "1.3-0")
+ (version "1.3-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "coin" version))
(sha256
(base32
- "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd"))))
+ "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)
@@ -8036,14 +8123,14 @@ detection, parallelism through BLAS and parallel user templates.")
(define-public r-sjstats
(package
(name "r-sjstats")
- (version "0.17.5")
+ (version "0.17.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjstats" version))
(sha256
(base32
- "1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
+ "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -8055,6 +8142,7 @@ detection, parallelism through BLAS and parallel user templates.")
("r-magrittr" ,r-magrittr)
("r-mass" ,r-mass)
("r-modelr" ,r-modelr)
+ ("r-parameters" ,r-parameters)
("r-performance" ,r-performance)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
@@ -8110,14 +8198,14 @@ differentiation.")
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.2.5")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "08d3bsb6li59n17bx1zrqnlnvniyb3vls9kl856km4chx3b2ff82"))))
+ "0r453zb106hj9w53jjgckxqajjf7shlrgv10gjxsv8if6qybdz5b"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@@ -8162,14 +8250,14 @@ effects models and Bayesian models.")
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "0.11.0")
+ (version "0.12.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
+ "0idfycjk05gyykfp9ibmhxfcjvd01ikh1dl0fb4nqw6znw3ar0xp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -8196,14 +8284,13 @@ results using @code{ggplot2}.")
(define-public r-sjplot
(package
(name "r-sjplot")
- (version "2.7.0")
+ (version "2.7.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
- (base32
- "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
+ (base32 "1kx1qqgp4fhwwwpqn9mv8m1pnpjxfs7ww36ns7j1ja4a7ydwn2hp"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
@@ -8518,14 +8605,14 @@ ways.")
(define-public r-summarytools
(package
(name "r-summarytools")
- (version "0.9.3")
+ (version "0.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "summarytools" version))
(sha256
(base32
- "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f"))))
+ "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
(build-system r-build-system)
(propagated-inputs
`(("r-checkmate" ,r-checkmate)
@@ -8696,14 +8783,14 @@ analysing multivariate abundance data in community ecology.")
(define-public r-afex
(package
(name "r-afex")
- (version "0.24-1")
+ (version "0.25-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "afex" version))
(sha256
(base32
- "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
+ "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-car" ,r-car)
@@ -8811,14 +8898,14 @@ address a bug.")
(define-public r-rcppannoy
(package
(name "r-rcppannoy")
- (version "0.0.12")
+ (version "0.0.13")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppAnnoy" version))
(sha256
(base32
- "1b0fmip9c4i0my1yjrvqy8jxfiiqcggq2kms135q0b53njxnqwwg"))))
+ "1jibp9b07c5ka1kif0nl7f168hxfvysj32wnmnxg85l663hmvm8j"))))
(properties `((upstream-name . "RcppAnnoy")))
(build-system r-build-system)
(propagated-inputs
@@ -8838,14 +8925,14 @@ This package provides an R interface.")
(define-public r-rcpphnsw
(package
(name "r-rcpphnsw")
- (version "0.1.0")
+ (version "0.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppHNSW" version))
(sha256
(base32
- "158a069n42pbnjrlmvqsr6bm2cfp9hxpnk3nhp3dwi9qjlq4r9bm"))))
+ "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
(properties `((upstream-name . "RcppHNSW")))
(build-system r-build-system)
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
@@ -8860,14 +8947,14 @@ package provides a minimal R interface by relying on the Rcpp package.")
(define-public r-rcppparallel
(package
(name "r-rcppparallel")
- (version "4.4.3")
+ (version "4.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppParallel" version))
(sha256
(base32
- "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s"))))
+ "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
(properties `((upstream-name . "RcppParallel")))
(build-system r-build-system)
(home-page "http://rcppcore.github.io/RcppParallel")
@@ -8930,14 +9017,14 @@ Bioconductor packages.")
(define-public r-rgl
(package
(name "r-rgl")
- (version "0.100.26")
+ (version "0.100.30")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgl" version))
(sha256
(base32
- "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
+ "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
(build-system r-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))
@@ -9122,17 +9209,18 @@ Scientific.")
(define-public r-activity
(package
(name "r-activity")
- (version "1.2")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "activity" version))
(sha256
(base32
- "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs"))))
+ "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
(build-system r-build-system)
(propagated-inputs
`(("r-circular" ,r-circular)
+ ("r-insol" ,r-insol)
("r-pbapply" ,r-pbapply)))
(home-page "https://cran.r-project.org/web/packages/activity/")
(synopsis "Animal activity statistics")
@@ -9325,6 +9413,51 @@ in-memory raw vectors.")
;; Either of these two license versions.
(license (list license:gpl2 license:gpl3))))
+(define-public r-nlp
+ (package
+ (name "r-nlp")
+ (version "0.2-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NLP" version))
+ (sha256
+ (base32
+ "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
+ (properties `((upstream-name . "NLP")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/NLP/")
+ (synopsis "Natural language processing infrastructure")
+ (description
+ "This package provides basic classes and methods for Natural Language
+Processing.")
+ (license license:gpl3)))
+
+(define-public r-tm
+ (package
+ (name "r-tm")
+ (version "0.7-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tm" version))
+ (sha256
+ (base32
+ "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
+ (properties `((upstream-name . "tm")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-nlp" ,r-nlp)
+ ("r-rcpp" ,r-rcpp)
+ ("r-slam" ,r-slam)
+ ("r-xml2" ,r-xml2)))
+ (home-page "http://tm.r-forge.r-project.org/")
+ (synopsis "Text mining package")
+ (description
+ "This package provides a framework for text mining applications within R.")
+ (license license:gpl3)))
+
(define-public r-waveslim
(package
(name "r-waveslim")
@@ -9364,7 +9497,10 @@ pairs (Selesnick 2001, 2002).")
(build-system r-build-system)
(propagated-inputs
`(("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)))
+ ("r-rcpp" ,r-rcpp)
+ ;; The "tm" package is only "suggested" according to CRAN, but the
+ ;; wordcloud package cannot be loaded without it.
+ ("r-tm" ,r-tm)))
(home-page "https://cran.r-project.org/web/packages/wordcloud")
(synopsis "Word clouds")
(description
@@ -9396,14 +9532,14 @@ maps.")
(define-public r-tidytree
(package
(name "r-tidytree")
- (version "0.2.5")
+ (version "0.2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidytree" version))
(sha256
(base32
- "0vfjv33352dmk9cr2qn0knzg761068rdk6jg32csd9vpmcma8awp"))))
+ "1hkddl8kj1g01dy7xiracx81f6b405b3ga2qp4wlrl552b9xxpby"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
@@ -9424,17 +9560,17 @@ manipulate tree data.")
(define-public r-rvcheck
(package
(name "r-rvcheck")
- (version "0.1.3")
+ (version "0.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "rvcheck" version))
(sha256
- (base32
- "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b"))))
+ (base32 "15222q3sglq0mad5q806p99fhrb96qizmpqw35fa1rb148f95paf"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-rlang" ,r-rlang)))
+ `(("r-biocmanager" ,r-biocmanager)
+ ("r-rlang" ,r-rlang)))
(home-page "https://cran.r-project.org/web/packages/rvcheck")
(synopsis "R package version check")
(description
@@ -10168,14 +10304,14 @@ and manipulating sets of ontological terms.")
(define-public r-gargle
(package
(name "r-gargle")
- (version "0.3.1")
+ (version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gargle" version))
(sha256
(base32
- "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
+ "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fs" ,r-fs)
@@ -10719,14 +10855,14 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.")
(define-public r-spam
(package
(name "r-spam")
- (version "2.2-2")
+ (version "2.3-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spam" version))
(sha256
(base32
- "024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi"))))
+ "194n5mgvyms9ckjqixl3h33apii8h9kqspqg2si9k741k578qb3w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dotcall64" ,r-dotcall64)))
@@ -10749,14 +10885,14 @@ Differences with other sparse matrix packages are:
(define-public r-fields
(package
(name "r-fields")
- (version "9.8-3")
+ (version "9.8-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "fields" version))
(sha256
(base32
- "1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1"))))
+ "07x95vk1idjfzi5ikn0ijal754mssdmgr1p4nswmx9w3i5ndcqaz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-maps" ,r-maps)
@@ -11104,14 +11240,14 @@ regression coefficients can be conducted via jackknifing.")
(define-public r-huge
(package
(name "r-huge")
- (version "1.3.2")
+ (version "1.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "huge" version))
(sha256
(base32
- "1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd"))))
+ "18f8w4hdp9fdi2k5ip6fnrn5z47w4ybgxs2m6a7jdvd2v4wfdr69"))))
(build-system r-build-system)
(propagated-inputs
`(("r-igraph" ,r-igraph)
@@ -11650,14 +11786,13 @@ such software by imputing dropout events.")
(define-public r-gamlss-dist
(package
(name "r-gamlss-dist")
- (version "5.1-4")
+ (version "5.1-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "gamlss.dist" version))
(sha256
- (base32
- "0zi87lgigr83l35zqq1y1g4cdq6ssjamripzz7yis74aznh6qg1l"))))
+ (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
(properties `((upstream-name . "gamlss.dist")))
(build-system r-build-system)
(propagated-inputs `(("r-mass" ,r-mass)))
@@ -11786,14 +11921,14 @@ select colors to use in your R code.")
(define-public r-ggextra
(package
(name "r-ggextra")
- (version "0.8")
+ (version "0.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggExtra" version))
(sha256
(base32
- "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
+ "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
(properties `((upstream-name . "ggExtra")))
(build-system r-build-system)
(propagated-inputs
@@ -11801,6 +11936,7 @@ select colors to use in your R code.")
("r-ggplot2" ,r-ggplot2)
("r-gtable" ,r-gtable)
("r-miniui" ,r-miniui)
+ ("r-r6" ,r-r6)
("r-scales" ,r-scales)
("r-shiny" ,r-shiny)
("r-shinyjs" ,r-shinyjs)))
@@ -11900,14 +12036,14 @@ probabilities from a standard bivariate normal CDF.")
(define-public r-lavaan
(package
(name "r-lavaan")
- (version "0.6-4")
+ (version "0.6-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "lavaan" version))
(sha256
(base32
- "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
+ "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -12189,14 +12325,14 @@ network.")
(define-public r-apcluster
(package
(name "r-apcluster")
- (version "1.4.7")
+ (version "1.4.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "apcluster" version))
(sha256
(base32
- "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
+ "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)
@@ -12347,17 +12483,16 @@ extensions.")
(define-public r-wgaim
(package
(name "r-wgaim")
- (version "1.4-11")
+ (version "2.0-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "wgaim" version))
(sha256
- (base32
- "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg"))))
+ (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-lattice" ,r-lattice)
+ `(("r-ggplot2" ,r-ggplot2)
("r-qtl" ,r-qtl)))
(home-page "https://cran.r-project.org/web/packages/wgaim")
(synopsis "Whole genome average interval mapping for QTL detection")
@@ -12541,14 +12676,14 @@ barplots or heatmaps.")
(define-public r-seqinr
(package
(name "r-seqinr")
- (version "3.4-5")
+ (version "3.6-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqinr" version))
(sha256
(base32
- "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
+ "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
@@ -12566,14 +12701,14 @@ utilities for sequence data management under the ACNUC system.")
(define-public r-units
(package
(name "r-units")
- (version "0.6-3")
+ (version "0.6-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "units" version))
(sha256
(base32
- "0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3"))))
+ "1jz0mzd78sdfxkhqw041ji50hmhjk2ha55i31yjvz35nsw30lwi5"))))
(build-system r-build-system)
(inputs
`(("udunits" ,udunits)))
@@ -12617,14 +12752,14 @@ univariate class intervals for mapping or other graphics purposes.")
(define-public r-spdata
(package
(name "r-spdata")
- (version "0.3.0")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "spData" version))
(sha256
(base32
- "162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y"))))
+ "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
(properties `((upstream-name . "spData")))
(build-system r-build-system)
(home-page "https://github.com/Nowosad/spData")
@@ -12691,14 +12826,14 @@ tessellation.")
(define-public r-sf
(package
(name "r-sf")
- (version "0.7-7")
+ (version "0.8-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i"))))
+ "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
(build-system r-build-system)
(inputs
`(("gdal" ,gdal)
@@ -12725,14 +12860,14 @@ datum transformations.")
(define-public r-spdep
(package
(name "r-spdep")
- (version "1.1-2")
+ (version "1.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "spdep" version))
(sha256
(base32
- "06mk81kc1ml2wjc8wwwgr0wasjcr4mwrxpfa8vfc373bmnha635s"))))
+ "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-boot" ,r-boot)
@@ -12799,14 +12934,13 @@ also provided to illustrate various methods.")
(define-public r-pegas
(package
(name "r-pegas")
- (version "0.11")
+ (version "0.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "pegas" version))
(sha256
- (base32
- "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx"))))
+ (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
(build-system r-build-system)
(propagated-inputs
`(("r-adegenet" ,r-adegenet)
@@ -12907,14 +13041,13 @@ either PDF/EPS files.")
(define-public r-polspline
(package
(name "r-polspline")
- (version "1.1.15")
+ (version "1.1.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "polspline" version))
(sha256
- (base32
- "19zs4kpagsrzhng1byjbz1c4jxnfk58h4rgr096ml1bjwrgamnwc"))))
+ (base32 "0d49h7if8h6d784nsnqqxakg19kvl8cmz8k53901m2h0c0amlfxa"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/polspline/")
@@ -13121,14 +13254,14 @@ exact test for Hardy-Weinberg equilibrium.")
(define-public r-tdthap
(package
(name "r-tdthap")
- (version "1.1-9")
+ (version "1.1-11")
(source
(origin
(method url-fetch)
(uri (cran-uri "tdthap" version))
(sha256
(base32
- "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r"))))
+ "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/tdthap/")
(synopsis "TDT tests for extended haplotypes")
@@ -13164,13 +13297,13 @@ SELECT or UPDATE queries to an end-point.")
(define-public r-bookdown
(package
(name "r-bookdown")
- (version "0.12")
+ (version "0.14")
(source (origin
(method url-fetch)
(uri (cran-uri "bookdown" version))
(sha256
(base32
- "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
+ "1jiq2d292y0l3f4npyfzfpnmb0sqxsl212kkjfbjg5301h0na762"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
@@ -13188,14 +13321,14 @@ authoring books and technical documents with R Markdown.")
(define-public r-optparse
(package
(name "r-optparse")
- (version "1.6.2")
+ (version "1.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
- "0zrp6jakjhawrwfri270ym83vj5a7nvjk0w6b41z41ahw2da99dm"))))
+ "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
@@ -13558,14 +13691,14 @@ the XKCD web comic.")
(define-public r-msigdbr
(package
(name "r-msigdbr")
- (version "6.2.1")
+ (version "7.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "msigdbr" version))
(sha256
(base32
- "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg"))))
+ "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -13764,14 +13897,14 @@ sets of URLs.")
(define-public r-ggforce
(package
(name "r-ggforce")
- (version "0.2.2")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggforce" version))
(sha256
(base32
- "0snxx9zhcccxa7pz9pf3bjqmcmv9mz4m47v81hklnhm25jj40xg2"))))
+ "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
@@ -13782,7 +13915,9 @@ sets of URLs.")
("r-rcppeigen" ,r-rcppeigen)
("r-rlang" ,r-rlang)
("r-scales" ,r-scales)
- ("r-tweenr" ,r-tweenr)))
+ ("r-tidyselect" ,r-tidyselect)
+ ("r-tweenr" ,r-tweenr)
+ ("r-withr" ,r-withr)))
(home-page "https://ggforce.data-imaginist.com")
(synopsis "Accelerating ggplot2")
(description
@@ -13830,14 +13965,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.")
(define-public r-ggraph
(package
(name "r-ggraph")
- (version "1.0.2")
+ (version "2.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggraph" version))
(sha256
(base32
- "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c"))))
+ "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@@ -13845,12 +13980,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.")
("r-ggforce" ,r-ggforce)
("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
+ ("r-graphlayouts" ,r-graphlayouts)
("r-gtable" ,r-gtable)
("r-igraph" ,r-igraph)
("r-mass" ,r-mass)
- ("r-plyr" ,r-plyr)
("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
("r-scales" ,r-scales)
+ ("r-tidygraph" ,r-tidygraph)
("r-viridis" ,r-viridis)))
(home-page "https://cran.r-project.org/web/packages/ggraph/")
(synopsis "Implementation of grammar of graphics for graphs and networks")
@@ -14614,14 +14751,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
(define-public r-dalex
(package
(name "r-dalex")
- (version "0.4.4")
+ (version "0.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "DALEX" version))
(sha256
(base32
- "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
+ "0iiwkf0pfdb90lf1xhv43qd32z3cjmkmf0ly9841n5lldkjazy3h"))))
(properties `((upstream-name . "DALEX")))
(build-system r-build-system)
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
@@ -14640,14 +14777,14 @@ and model output.")
(define-public r-enrichr
(package
(name "r-enrichr")
- (version "2.0")
+ (version "2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "enrichR" version))
(sha256
(base32
- "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
+ "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
(properties `((upstream-name . "enrichR")))
(build-system r-build-system)
(propagated-inputs
@@ -14750,14 +14887,14 @@ into R and converted to @code{BibEntry} objects.")
(define-public r-citr
(package
(name "r-citr")
- (version "0.3.1")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "citr" version))
(sha256
(base32
- "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc"))))
+ "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -14810,17 +14947,18 @@ easily.")
(define-public r-umap
(package
(name "r-umap")
- (version "0.2.2.0")
+ (version "0.2.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "umap" version))
(sha256
(base32
- "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31"))))
+ "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcpp" ,r-rcpp)
+ `(("r-openssl" ,r-openssl)
+ ("r-rcpp" ,r-rcpp)
("r-reticulate" ,r-reticulate)
("r-rspectra" ,r-rspectra)))
(home-page "https://github.com/tkonopka/umap")
@@ -14834,14 +14972,14 @@ in R, including a translation of the original algorithm into R.")
(define-public r-uwot
(package
(name "r-uwot")
- (version "0.1.3")
+ (version "0.1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "uwot" version))
(sha256
(base32
- "1mq6qi8q9xslh1b99srj480s2a08pfv4bs9m2ykyijj44j9fcdj9"))))
+ "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dqrng" ,r-dqrng)
@@ -14905,14 +15043,13 @@ customize styles using a readable syntax.")
(define-public r-glasso
(package
(name "r-glasso")
- (version "1.10")
+ (version "1.11")
(source
(origin
(method url-fetch)
(uri (cran-uri "glasso" version))
(sha256
- (base32
- "0nshpx14v2yny7lr8ll6nnz71n0f02sddh2c2dglfprbk89p9yp6"))))
+ (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "http://www-stat.stanford.edu/~tibs/glasso")
@@ -14943,3 +15080,536 @@ path of values for the regularization parameter.")
library uses. It is also possible to control the number of threads in
OpenMP.")
(license license:agpl3+)))
+
+(define-public r-lda
+ (package
+ (name "r-lda")
+ (version "1.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lda" version))
+ (sha256
+ (base32
+ "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/lda/")
+ (synopsis "Collapsed Gibbs sampling methods for topic models")
+ (description
+ "This package implements @dfn{latent Dirichlet allocation} (LDA) and
+related models. This includes (but is not limited to) sLDA, corrLDA, and the
+mixed-membership stochastic blockmodel. Inference for all of these models is
+implemented via a fast collapsed Gibbs sampler written in C. Utility
+functions for reading/writing data typically used in topic models, as well as
+tools for examining posterior distributions are also included.")
+ ;; Any version of the LGPL
+ (license license:lgpl3+)))
+
+(define-public r-rann-l1
+ (package
+ (name "r-rann-l1")
+ (version "2.5.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RANN.L1" version))
+ (sha256
+ (base32
+ "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
+ (properties `((upstream-name . "RANN.L1")))
+ (build-system r-build-system)
+ (home-page "https://github.com/jefferis/RANN/tree/master-L1")
+ (synopsis "Fast nearest neighbour search using L1 metric")
+ (description
+ "This package provides tools to find the k nearest neighbours for every
+point in a given dataset in O(N log N) time using Arya and Mount's ANN
+library. There is support for approximate as well as exact searches, fixed
+radius searches and @code{bd} as well as @code{kd} trees. The distance is
+computed using the L1 (Manhattan, taxicab) metric.")
+ (license license:gpl3+)))
+
+(define-public r-leiden
+ (package
+ (name "r-leiden")
+ (version "0.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "leiden" version))
+ (sha256
+ (base32
+ "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
+ (properties `((upstream-name . "leiden")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-reticulate" ,r-reticulate)))
+ (home-page "https://github.com/TomKellyGenetics/leiden")
+ (synopsis "R implementation of Leiden clustering algorithm")
+ (description
+ "This package implements the Python @code{leidenalg} module to be called
+in R. It enables clustering using the Leiden algorithm for partitioning a
+graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
+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
+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))))
+
+(define-public r-liger
+ (package
+ (name "r-liger")
+ (version "0.4.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/MacoskoLab/liger.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file "inst/java/ModularityOptimizer.jar")
+ #t))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'build-java-part
+ (lambda* (#:key inputs #:allow-other-keys)
+ (invoke "unzip" (assoc-ref inputs "optimizer-src"))
+ (for-each (lambda (file) (invoke "javac" file))
+ (find-files "." "\\.java$"))
+ (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
+ (find-files "." "\\.class$"))
+ #t)))))
+ (propagated-inputs
+ `(("r-cowplot" ,r-cowplot)
+ ("r-dosnow" ,r-dosnow)
+ ("r-dplyr" ,r-dplyr)
+ ("r-fnn" ,r-fnn)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-hmisc" ,r-hmisc)
+ ("r-ica" ,r-ica)
+ ("r-irlba" ,r-irlba)
+ ("r-matrix" ,r-matrix)
+ ("r-mclust" ,r-mclust)
+ ("r-patchwork" ,r-patchwork)
+ ("r-plyr" ,r-plyr)
+ ("r-rann-l1" ,r-rann-l1)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-riverplot" ,r-riverplot)
+ ("r-rtsne" ,r-rtsne)
+ ("r-snow" ,r-snow)))
+ (native-inputs
+ `(("jdk" ,icedtea "jdk")
+ ;; See https://github.com/MacoskoLab/liger/issues/96
+ ;; The optimizer is released under the Expat license.
+ ("optimizer-src"
+ ,(origin
+ (method url-fetch)
+ (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
+ (sha256
+ (base32
+ "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
+ ("unzip" ,unzip)
+ ("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://github.com/MacoskoLab/liger")
+ (synopsis "Integrate and analyze multiple single-cell datasets")
+ (description
+ "LIGER is a package for integrating and analyzing multiple single-cell
+datasets, developed and maintained by the Macosko lab. It relies on
+integrative non-negative matrix factorization to identify shared and
+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
+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))))
+
+(define-public r-covr
+ (package
+ (name "r-covr")
+ (version "3.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "covr" version))
+ (sha256
+ (base32
+ "0fvd7v53w11x6kaw61hbml8n1j2ck9l2fv2wvqdsg689xic9rqcs"))))
+ (properties `((upstream-name . "covr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-crayon" ,r-crayon)
+ ("r-digest" ,r-digest)
+ ("r-httr" ,r-httr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rex" ,r-rex)
+ ("r-withr" ,r-withr)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://github.com/r-lib/covr")
+ (synopsis "Test coverage for R packages")
+ (description
+ "Thisp package enables you to track and report code coverage for your
+package and (optionally) upload the results to a coverage service. Code
+coverage is a measure of the amount of code being exercised by a set of tests.
+It is an indirect measure of test quality and completeness. This package is
+compatible with any testing methodology or framework and tracks coverage of
+both R code and compiled C/C++/FORTRAN code.")
+ (license license:gpl3)))
+
+(define-public r-systemfonts
+ (package
+ (name "r-systemfonts")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "systemfonts" version))
+ (sha256
+ (base32
+ "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
+ (properties `((upstream-name . "systemfonts")))
+ (build-system r-build-system)
+ (inputs
+ `(("fontconfig" ,fontconfig)
+ ("freetype" ,freetype)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://github.com/r-lib/systemfonts")
+ (synopsis "System native font finding")
+ (description
+ "This package provides system native access to the font catalogue. As
+font handling varies between systems it is difficult to correctly locate
+installed fonts across different operating systems. The 'systemfonts' package
+provides bindings to the native libraries for finding font files that can then
+be used further by e.g. graphic devices.")
+ (license license:expat)))
+
+(define-public r-graphlayouts
+ (package
+ (name "r-graphlayouts")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "graphlayouts" version))
+ (sha256
+ (base32
+ "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
+ (properties `((upstream-name . "graphlayouts")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-igraph" ,r-igraph)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (home-page "https://github.com/schochastics/graphlayouts")
+ (synopsis "Additional layout algorithms for network visualizations")
+ (description
+ "This package provides several layout algorithms to visualize networks
+which are not part of the igraph library. Most are based on the concept of
+stress majorization by Gansner et al. (2004)
+<doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
+emphasize hidden group structures in networks or focus on specific nodes.")
+ (license license:expat)))
+
+(define-public r-tidygraph
+ (package
+ (name "r-tidygraph")
+ (version "1.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tidygraph" version))
+ (sha256
+ (base32
+ "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
+ (properties `((upstream-name . "tidygraph")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-pillar" ,r-pillar)
+ ("r-r6" ,r-r6)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://github.com/thomasp85/tidygraph")
+ (synopsis "Tidy API for graph manipulation")
+ (description
+ "This package provides a graph implementation that can be thought of as
+two tidy data frames describing node and edge data respectively. It provides
+an approach to manipulate these two virtual data frames using the API defined
+in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
+common graph algorithms.")
+ (license license:expat)))
+
+(define-public r-soupx
+ (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
+ (revision "1"))
+ (package
+ (name "r-soupx")
+ (version (git-version "0.3.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/constantAmateur/SoupX")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
+ (properties `((upstream-name . "SoupX")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-matrix" ,r-matrix)
+ ("r-seurat" ,r-seurat)))
+ (home-page "https://github.com/constantAmateur/SoupX")
+ (synopsis "Single cell mRNA Soup eXterminator")
+ (description
+ "This package provides a package for quantifying, profiling and
+removing cell free mRNA contamination (the \"soup\") from droplet based single
+cell RNA-seq experiments.")
+ (license license:gpl2))))
+
+(define-public r-assertr
+ (package
+ (name "r-assertr")
+ (version "2.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "assertr" version))
+ (sha256
+ (base32
+ "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-mass" ,r-mass)
+ ("r-rlang" ,r-rlang)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; needed for vignette
+ (home-page "https://github.com/ropensci/assertr")
+ (synopsis "Assertive programming for R analysis pipelines")
+ (description
+ "This package provides functionality to assert conditions that have to be
+met so that errors in data used in analysis pipelines can fail quickly. It is
+similar to @code{stopifnot()} but more powerful, friendly, and easier for use
+in pipelines.")
+ (license license:expat)))
+
+(define-public r-parameters
+ (package
+ (name "r-parameters")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "parameters" version))
+ (sha256
+ (base32
+ "1mgggb3l67wgjiccq4y84wbs2dw9qk01akd553yiwbwky9rpawgh"))))
+ (properties `((upstream-name . "parameters")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bayestestr" ,r-bayestestr)
+ ("r-insight" ,r-insight)))
+ (home-page "https://cran.r-project.org/web/packages/parameters")
+ (synopsis "Processing of model parameters")
+ (description
+ "This package provides utilities for processing the parameters of various
+statistical models. Beyond computing p values, CIs, and other indices for a
+wide variety of models, this package implements features like standardization
+or bootstrapping of parameters and models, feature reduction (feature
+extraction and variable selection) as well as conversion between indices of
+effect size.")
+ (license license:gpl3)))
+
+(define-public r-rgdal
+ (package
+ (name "r-rgdal")
+ (version "1.4-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "rgdal" version))
+ (sha256
+ (base32 "0lj1dax56dxxsj1hindxcvgz169p9dxd0y4wjypbyr01nja8rz4d"))))
+ (properties `((upstream-name . "rgdal")))
+ (build-system r-build-system)
+ (inputs
+ `(("gdal" ,gdal)
+ ("proj.4" ,proj.4)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-sp" ,r-sp)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "http://rgdal.r-forge.r-project.org")
+ (synopsis "Bindings for the Geospatial Data Abstraction Library")
+ (description
+ "This package provides bindings to the Geospatial Data Abstraction
+Library (GDAL) and access to projection/transformation operations from the
+PROJ.4 library.")
+ (license license:gpl2+)))
+
+(define-public r-insol
+ (package
+ (name "r-insol")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "insol" version))
+ (sha256
+ (base32
+ "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
+ (properties `((upstream-name . "insol")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-raster" ,r-raster)
+ ("r-rgdal" ,r-rgdal)))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://meteoexploration.com/R/insol/index.html")
+ (synopsis "Tools for calculating solar radiation")
+ (description
+ "This package provides functions to compute insolation on tilted
+surfaces, computes atmospheric transmittance and related parameters such as:
+Earth radius vector, declination, sunset and sunrise, daylength, equation of
+time, vector in the direction of the sun, vector normal to surface, and some
+atmospheric physics.")
+ (license license:gpl2+)))
+
+(define-public r-lifecycle
+ (package
+ (name "r-lifecycle")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lifecycle" version))
+ (sha256
+ (base32
+ "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
+ (properties `((upstream-name . "lifecycle")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-glue" ,r-glue)
+ ("r-rlang" ,r-rlang)))
+ (home-page "https://github.com/r-lib/lifecycle")
+ (synopsis "Manage the life cycle of your package functions")
+ (description
+ "Manage the life cycle of your exported functions with shared
+conventions, documentation badges, and non-invasive deprecation warnings. The
+lifecycle package defines four development stages (experimental, maturing,
+stable, and questioning) and three deprecation stages (soft-deprecated,
+deprecated, and defunct). It makes it easy to insert badges corresponding to
+these stages in your documentation. Usage of deprecated functions are
+signalled with increasing levels of non-invasive verbosity.")
+ (license license:gpl3)))
+
+(define-public r-assertable
+ (package
+ (name "r-assertable")
+ (version "0.2.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "assertable" version))
+ (sha256
+ (base32
+ "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)))
+ (home-page "https://cran.r-project.org/web/packages/assertable/")
+ (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
+ (description "This package provides simple, flexible assertions on
+data.frame or data.table objects with verbose output for vetting. While other
+assertion packages apply towards more general use-cases, @code{assertable} is
+tailored towards tabular data. It includes functions to check variable names
+and values, whether the dataset contains all combinations of a given set of
+unique identifiers, and whether it is a certain length. In addition,
+@code{assertable} includes utility functions to check the existence of target
+files and to efficiently import multiple tabular data files into one
+data.table.")
+ (license license:gpl3)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-11-19 23:59:47 +0000