diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1086 |
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))) |