gnu: Add r-jquerylib.

[jackhill/guix/guix.git] / gnu / packages / cran.scm

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a9a6261..0daf67e 100644 (file)
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1344,6 +1344,65 @@ are used.  Fastmap avoids this memory leak issue by implementing the map using
 data structures in C++.")
     (license license:expat)))
 
+;; This package includes minified JavaScript files.  When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-jquerylib
+  (package
+    (name "r-jquerylib")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jquerylib" version))
+       (sha256
+        (base32
+         "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
+       (snippet
+        '(for-each delete-file
+                   '("inst/lib/jquery-1.12.4.min.js"
+                     "inst/lib/jquery-2.2.4.min.js"
+                     "inst/lib/jquery-3.5.1.min.js")))))
+    (properties `((upstream-name . "jquerylib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (srfi srfi-1))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'process-javascript
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion "inst/lib/"
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `(("jquery-1.12.4.js"
+                         "jquery-1.12.4.min.js")
+                        ("jquery-2.2.4.js"
+                         "jquery-2.2.4.min.js")
+                        ("jquery-3.5.1.js"
+                         "jquery-3.5.1.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (invoke "esbuild" source "--minify"
+                                       (string-append "--outfile=" target)))
+                             sources targets)))))))))
+    (propagated-inputs
+     `(("r-htmltools" ,r-htmltools)))
+    (native-inputs
+     `(("esbuild" ,esbuild)))
+    (home-page "https://cran.r-project.org/package=jquerylib")
+    (synopsis "Obtain jQuery as an HTML dependency object")
+    (description
+     "Obtain any major version of jQuery and use it in any webpage generated
+by htmltools (e.g. shiny, htmlwidgets, and rmarkdown).  Most R users don't
+need to use this package directly, but other R packages (e.g. shiny,
+rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
+jQuery.")
+    (license license:expat)))
+
 (define-public r-shiny
   (package
     (name "r-shiny")
@@ -9873,14 +9932,14 @@ and permutation inference in the framework of Strasser and Weber (1999).")
 (define-public r-coin
   (package
     (name "r-coin")
-    (version "1.4-0")
+    (version "1.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "coin" version))
        (sha256
         (base32
-         "1n2ad4m3zw8px6yc0h750k59pci3fqpnr742hhvsqirrwcdzp6zv"))))
+         "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-libcoin" ,r-libcoin)
@@ -9936,14 +9995,14 @@ Bayesian modeling.")
 (define-public r-tmb
   (package
     (name "r-tmb")
-    (version "1.7.18")
+    (version "1.7.19")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "TMB" version))
        (sha256
         (base32
-         "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
+         "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
     (properties `((upstream-name . "TMB")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10039,14 +10098,14 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.8.0")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw"))))
+         "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10066,14 +10125,14 @@ ROPE percentage and pd).")
 (define-public r-performance
   (package
     (name "r-performance")
-    (version "0.6.1")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "performance" version))
        (sha256
         (base32
-         "0wz2zc98r99pg6r4l09qxxzv1fwxwp1md6wmhay401568kd8h5zn"))))
+         "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -10351,14 +10410,14 @@ user credentials.")
 (define-public r-gert
   (package
     (name "r-gert")
-    (version "1.0.2")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gert" version))
        (sha256
         (base32
-         "1lq4hgv2727lwcv8vha5af26nslj99rjxjrgflshmmcihawpls1n"))))
+         "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8"))))
     (properties `((upstream-name . "gert")))
     (build-system r-build-system)
     (inputs
@@ -10369,6 +10428,7 @@ user credentials.")
        ("r-credentials" ,r-credentials)
        ("r-openssl" ,r-openssl)
        ("r-rstudioapi" ,r-rstudioapi)
+       ("r-sys" ,r-sys)
        ("r-zip" ,r-zip)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -10386,14 +10446,14 @@ User credentials are shared with command line git through the
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "0m4qnnkdiizsdvq33x502zwkn98hw2qcfm45cjj031vaydcjpai2"))))
+         "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -10679,14 +10739,14 @@ algorithms, clusterings, and individual clusters.")
 (define-public r-tweedie
   (package
     (name "r-tweedie")
-    (version "2.3.2")
+    (version "2.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tweedie" version))
        (sha256
         (base32
-         "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
+         "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/tweedie/")
@@ -11070,13 +11130,13 @@ isosurfaces.")
 (define-public r-ks
   (package
     (name "r-ks")
-    (version "1.11.7")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ks" version))
        (sha256
-        (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
+        (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fnn" ,r-fnn)
@@ -11086,7 +11146,8 @@ isosurfaces.")
        ("r-mclust" ,r-mclust)
        ("r-mgcv" ,r-mgcv)
        ("r-multicool" ,r-multicool)
-       ("r-mvtnorm" ,r-mvtnorm)))
+       ("r-mvtnorm" ,r-mvtnorm)
+       ("r-plot3d" ,r-plot3d)))
     (home-page "http://www.mvstat.net/tduong/")
     (synopsis "Kernel smoothing")
     (description
@@ -11100,17 +11161,18 @@ hypothesis testing.")
 (define-public r-feature
   (package
     (name "r-feature")
-    (version "1.2.14")
+    (version "1.2.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "feature" version))
        (sha256
         (base32
-         "1c12rny9nx8dynzxbcf49h76a7wlmsk1m131wh0jiyqx3c3y41y1"))))
+         "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-ks" ,r-ks)))
+     `(("r-ks" ,r-ks)
+       ("r-plot3d" ,r-plot3d)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "http://www.mvstat.net/tduong/")
@@ -12242,14 +12304,14 @@ Emphasis is always given to methods for visualizing the data.")
 (define-public r-pixmap
   (package
     (name "r-pixmap")
-    (version "0.4-11")
+    (version "0.4-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pixmap" version))
        (sha256
         (base32
-         "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
+         "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/pixmap")
     (synopsis "Tools for bitmap images")
@@ -12280,16 +12342,18 @@ library.")
 (define-public r-ontologyindex
   (package
     (name "r-ontologyindex")
-    (version "2.5")
+    (version "2.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ontologyIndex" version))
        (sha256
         (base32
-         "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
+         "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
     (properties `((upstream-name . "ontologyIndex")))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
     (synopsis "Functions for processing ontologies in R")
     (description
@@ -12418,14 +12482,14 @@ Precision Floating-Point Reliable} (MPFR) library.")
 (define-public r-assertive-base
   (package
     (name "r-assertive-base")
-    (version "0.0-7")
+    (version "0.0-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "assertive.base" version))
        (sha256
         (base32
-         "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
+         "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
     (properties
      `((upstream-name . "assertive.base")))
     (build-system r-build-system)
@@ -13180,14 +13244,14 @@ model with finite state space using the Aalen-Johansen estimator.")
 (define-public r-epi
   (package
     (name "r-epi")
-    (version "2.42")
+    (version "2.43")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Epi" version))
        (sha256
         (base32
-         "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl"))))
+         "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089"))))
     (properties `((upstream-name . "Epi")))
     (build-system r-build-system)
     (propagated-inputs
@@ -13200,6 +13264,7 @@ model with finite state space using the Aalen-Johansen estimator.")
        ("r-mgcv" ,r-mgcv)
        ("r-numderiv" ,r-numderiv)
        ("r-plyr" ,r-plyr)
+       ("r-purrr" ,r-purrr)
        ("r-survival" ,r-survival)
        ("r-zoo" ,r-zoo)))
     (home-page "https://BendixCarstensen.com/Epi/")
@@ -14262,14 +14327,14 @@ graphs.")
 (define-public r-pbdzmq
   (package
     (name "r-pbdzmq")
-    (version "0.3-4")
+    (version "0.3-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbdZMQ" version))
        (sha256
         (base32
-         "0adiac53yq305ymhrds1gas4jm0rn1ddv7c7df5ky2cfhpb4ny87"))))
+         "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
     (properties `((upstream-name . "pbdZMQ")))
     (build-system r-build-system)
     (inputs
@@ -14290,14 +14355,14 @@ compatible with @code{rzmq} are also provided.")
 (define-public r-repr
   (package
     (name "r-repr")
-    (version "1.1.0")
+    (version "1.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "repr" version))
        (sha256
         (base32
-         "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
+         "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)
@@ -14314,14 +14379,14 @@ several formats and MIME types.")
 (define-public r-irdisplay
   (package
     (name "r-irdisplay")
-    (version "0.7.0")
+    (version "1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "IRdisplay" version))
        (sha256
         (base32
-         "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
+         "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
     (properties `((upstream-name . "IRdisplay")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15206,13 +15271,13 @@ lspec, polyclass, and polymars.")
 (define-public r-rms
   (package
     (name "r-rms")
-    (version "6.1-0")
+    (version "6.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rms" version))
        (sha256
-        (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq"))))
+        (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
@@ -15252,14 +15317,14 @@ generalized linear models, and quantile regression.")
 (define-public r-arsenal
   (package
     (name "r-arsenal")
-    (version "3.5.0")
+    (version "3.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arsenal" version))
        (sha256
         (base32
-         "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
+         "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy"))))
     (properties `((upstream-name . "arsenal")))
     (build-system r-build-system)
     (propagated-inputs `(("r-knitr" ,r-knitr)))
@@ -16335,14 +16400,14 @@ using the three.js visualization library.")
 (define-public r-mlbench
   (package
     (name "r-mlbench")
-    (version "2.1-1")
+    (version "2.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mlbench" version))
        (sha256
         (base32
-         "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
+         "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/mlbench/")
     (synopsis "Machine learning benchmark problems")
@@ -16988,14 +17053,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
 (define-public r-ingredients
   (package
     (name "r-ingredients")
-    (version "2.0")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ingredients" version))
        (sha256
         (base32
-         "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
+         "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
     (properties `((upstream-name . "ingredients")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17122,19 +17187,22 @@ and model output.")
 (define-public r-enrichr
   (package
     (name "r-enrichr")
-    (version "2.1")
+    (version "3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "enrichR" version))
        (sha256
         (base32
-         "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
+         "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
     (properties `((upstream-name . "enrichR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-httr" ,r-httr)
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-httr" ,r-httr)
        ("r-rjson" ,r-rjson)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/enrichR/")
     (synopsis "R Interface to Enrichr database for analyzing gene sets")
     (description
@@ -17482,14 +17550,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
 (define-public r-leiden
   (package
     (name "r-leiden")
-    (version "0.3.6")
+    (version "0.3.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "leiden" version))
        (sha256
         (base32
-         "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7"))))
+         "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
     (properties `((upstream-name . "leiden")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17808,14 +17876,14 @@ cell RNA-seq experiments.")
 (define-public r-assertr
   (package
     (name "r-assertr")
-    (version "2.7")
+    (version "2.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "assertr" version))
        (sha256
         (base32
-         "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
+         "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -17864,13 +17932,13 @@ effect size.")
 (define-public r-rgdal
   (package
     (name "r-rgdal")
-    (version "1.5-19")
+    (version "1.5-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rgdal" version))
        (sha256
-        (base32 "1cii2azm3zv5l6fn33xzwahp8349z3pb2769vpdxkf7734dxggvg"))))
+        (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
     (properties `((upstream-name . "rgdal")))
     (build-system r-build-system)
     (inputs
@@ -17893,14 +17961,14 @@ PROJ.4 library.")
 (define-public r-insol
   (package
     (name "r-insol")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insol" version))
        (sha256
         (base32
-         "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
+         "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
     (properties `((upstream-name . "insol")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17950,17 +18018,19 @@ signalled with increasing levels of non-invasive verbosity.")
 (define-public r-assertable
   (package
     (name "r-assertable")
-    (version "0.2.7")
+    (version "0.2.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "assertable" version))
        (sha256
         (base32
-         "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
+         "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (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
@@ -18026,12 +18096,12 @@ to ODEs by numerical differencing.")
 (define-public r-pracma
   (package
     (name "r-pracma")
-    (version "2.2.9")
+    (version "2.3.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "pracma" version))
               (sha256
-               (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
+               (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/pracma/")
     (synopsis "Practical numerical math functions")
@@ -20364,14 +20434,14 @@ API; see the package vignette for details.")
 (define-public r-actuar
   (package
     (name "r-actuar")
-    (version "3.1-0")
+    (version "3.1-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "actuar" version))
        (sha256
         (base32
-         "15a8axb2ym46j8vlm7icwnsc950p8m66hp0armha7drk0725y77k"))))
+         "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
     (properties `((upstream-name . "actuar")))
     (build-system r-build-system)
     (propagated-inputs `(("r-expint" ,r-expint)))
@@ -21257,14 +21327,14 @@ both exclusive and shared locking.")
 (define-public r-archivist
   (package
     (name "r-archivist")
-    (version "2.3.4")
+    (version "2.3.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "archivist" version))
        (sha256
         (base32
-         "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
+         "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
     (properties `((upstream-name . "archivist")))
     (build-system r-build-system)
     (propagated-inputs
@@ -21276,6 +21346,8 @@ both exclusive and shared locking.")
        ("r-magrittr" ,r-magrittr)
        ("r-rcurl" ,r-rcurl)
        ("r-rsqlite" ,r-rsqlite)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://pbiecek.github.io/archivist/")
     (synopsis "Tools for storing, restoring and searching for R objects")
     (description
@@ -21535,20 +21607,18 @@ character codes as well as the UN M.49 area codes.")
 (define-public r-stopwords
   (package
     (name "r-stopwords")
-    (version "2.1")
+    (version "2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stopwords" version))
        (sha256
         (base32
-         "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8"))))
+         "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
     (properties `((upstream-name . "stopwords")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-desc" ,r-desc)
-       ("r-isocodes" ,r-isocodes)
-       ("r-usethis" ,r-usethis)))
+     `(("r-isocodes" ,r-isocodes)))
     (home-page "https://github.com/quanteda/stopwords")
     (synopsis "Multilingual stopword lists")
     (description
@@ -21653,17 +21723,17 @@ machine learning, visually representing text and text analyses, and more.")
 (define-public r-topicmodels
   (package
     (name "r-topicmodels")
-    (version "0.2-11")
+    (version "0.2-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "topicmodels" version))
        (sha256
         (base32
-         "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
+         "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
     (properties `((upstream-name . "topicmodels")))
     (build-system r-build-system)
-    (native-inputs
+    (inputs
      `(("gsl" ,gsl)))
     (propagated-inputs
      `(("r-modeltools" ,r-modeltools)
@@ -22152,30 +22222,26 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
 (define-public r-qgraph
   (package
     (name "r-qgraph")
-    (version "1.6.5")
+    (version "1.6.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "qgraph" version))
        (sha256
         (base32
-         "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
+         "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
     (properties `((upstream-name . "qgraph")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
-       ("r-bdgraph" ,r-bdgraph)
        ("r-colorspace" ,r-colorspace)
        ("r-corpcor" ,r-corpcor)
-       ("r-d3network" ,r-d3network)
        ("r-dplyr" ,r-dplyr)
        ("r-fdrtool" ,r-fdrtool)
        ("r-ggplot2" ,r-ggplot2)
-       ("r-ggraph" ,r-ggraph)
        ("r-glasso" ,r-glasso)
        ("r-gtools" ,r-gtools)
        ("r-hmisc" ,r-hmisc)
-       ("r-huge" ,r-huge)
        ("r-igraph" ,r-igraph)
        ("r-jpeg" ,r-jpeg)
        ("r-lavaan" ,r-lavaan)
@@ -22185,8 +22251,7 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
        ("r-png" ,r-png)
        ("r-psych" ,r-psych)
        ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-tidygraph" ,r-tidygraph)))
+       ("r-reshape2" ,r-reshape2)))
     (home-page "http://sachaepskamp.com/qgraph/")
     (synopsis "Weighted network visualization and analysis")
     (description
@@ -23532,6 +23597,17 @@ download images.")
         (base32
          "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'install-server-binary
+           ;; Makevars tries to install to R's store directory.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (substitute* "src/Makevars.in"
+                 (("\\$\\(R_HOME\\)") out))
+               (mkdir-p bin)))))))
     (propagated-inputs
      `(("r-checkmate" ,r-checkmate)
        ("r-mime" ,r-mime)
@@ -24329,14 +24405,14 @@ diagonals.  This package allows you to compute the tensor product of arrays.")
 (define-public r-spatstat-utils
   (package
     (name "r-spatstat-utils")
-    (version "1.20-2")
+    (version "2.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.utils" version))
        (sha256
         (base32
-         "066f35017wpbz9plwc14gji3ddq4a1h2lx4mcgxajrcrk0zl3hk2"))))
+         "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
     (properties
      `((upstream-name . "spatstat.utils")))
     (build-system r-build-system)
@@ -24350,14 +24426,14 @@ which may also be useful for other purposes.")
 (define-public r-spatstat-data
   (package
     (name "r-spatstat-data")
-    (version "1.7-0")
+    (version "2.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatstat.data" version))
        (sha256
         (base32
-         "0by10dx72jjn6rvgrdj4xwh4zg6vxi4cp536aq4b6drb7za95hdv"))))
+         "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
     (properties `((upstream-name . "spatstat.data")))
     (build-system r-build-system)
     (propagated-inputs
@@ -24440,14 +24516,14 @@ for linear mixed models (AIREML).")
 (define-public r-cpp11
   (package
     (name "r-cpp11")
-    (version "0.2.5")
+    (version "0.2.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cpp11" version))
        (sha256
         (base32
-         "081f3b98mcxyilqsxbzzdnj2x6v7xycprrw7r5934163q0397vvg"))))
+         "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
     (properties `((upstream-name . "cpp11")))
     (build-system r-build-system)
     (native-inputs `(("r-knitr" ,r-knitr)))
@@ -25898,13 +25974,13 @@ other R users.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.2.3")
+    (version "4.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "11rzc7h2ad8z8k5r1sbz4d7y4rl3080qp2hh7vibwmipbkvlial3"))))
+                "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -25941,11 +26017,11 @@ other R users.")
        ("r-reticulate" ,r-reticulate)
        ("r-rlang" ,r-rlang)
        ("r-rocr" ,r-rocr)
-       ("r-rsvd" ,r-rsvd)
        ("r-rtsne" ,r-rtsne)
        ("r-scales" ,r-scales)
        ("r-scattermore" ,r-scattermore)
        ("r-sctransform" ,r-sctransform)
+       ("r-seuratobject" ,r-seuratobject)
        ("r-shiny" ,r-shiny)
        ("r-spatstat" ,r-spatstat)
        ("r-tibble" ,r-tibble)
@@ -26292,13 +26368,13 @@ package also supersedes the package @code{BBmisc}.")
 (define-public r-paradox
   (package
     (name "r-paradox")
-    (version "0.6.0")
+    (version "0.7.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "paradox" version))
               (sha256
                (base32
-                "1zv0q411wcwigkf4yggs3w2gz48lvv3jhnrddrv40qih8b70ywi3"))))
+                "1fz6sdwvvifm4qbmwgm27dil278mswvcfw8bbsvli5v4l1ghw8kj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)
@@ -26317,13 +26393,13 @@ implemented as @code{R6} classes.")
 (define-public r-mlr3
   (package
     (name "r-mlr3")
-    (version "0.9.0")
+    (version "0.10.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3" version))
               (sha256
                (base32
-                "0gg7rrzxwrnpg6sgm0aa6bmfwmqv3d3za0ghnqrnibg33p9ynpgb"))))
+                "1arqijbbmhv57mj8kyq30zxykah83ab1d1c7gs0cxs0xhfwln66g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-r6" ,r-r6)
@@ -26377,14 +26453,14 @@ vector machines, and gradient boosting.")
 (define-public r-bbotk
   (package
     (name "r-bbotk")
-    (version "0.2.2")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bbotk" version))
        (sha256
         (base32
-         "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv"))))
+         "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0"))))
     (properties `((upstream-name . "bbotk")))
     (build-system r-build-system)
     (propagated-inputs
@@ -26394,6 +26470,8 @@ vector machines, and gradient boosting.")
        ("r-mlr3misc" ,r-mlr3misc)
        ("r-paradox" ,r-paradox)
        ("r-r6" ,r-r6)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://bbotk.mlr-org.com")
     (synopsis "Black-Box Optimization Toolkit")
     (description "This package provides a common framework for optimization of
@@ -26405,13 +26483,13 @@ annealing.")
 (define-public r-mlr3tuning
   (package
     (name "r-mlr3tuning")
-    (version "0.5.0")
+    (version "0.6.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mlr3tuning" version))
               (sha256
                (base32
-                "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m"))))
+                "0kxf9wl1jnwyrj2zfmiz12w2594407y44m0xxwp9b2lrwxk31wm7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bbotk" ,r-bbotk)