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 1b36503..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")
@@ -21664,17 +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)
@@ -22163,30 +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)
@@ -22196,8 +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
@@ -23543,6 +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)
@@ -24340,14 +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)
@@ -24361,14 +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
@@ -24451,14 +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)))
@@ -25909,13 +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
@@ -25952,11 +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)
@@ -26303,13 +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)
@@ -26328,13 +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)
@@ -26388,14 +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
@@ -26405,6 +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
@@ -26416,13 +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)