Merge branch 'master' into staging

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 56875be..31dff49 100644 (file)
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -66,8 +66,10 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages tcl)
+  #:use-module (gnu packages tex)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
@@ -177,7 +179,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.5.3")
+    (version "3.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -185,7 +187,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1337irx9y0r3jm1rcq1dcwnxsgfhnvgjs5wadcyh17vhpnvkgyib"))))
+                "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -251,6 +253,10 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                (("(install_package_description\\(.*\"')\\)\"" line prefix)
                 (string-append prefix ", builtStamp='1970-01-01')\"")))
 
+             (substitute* "src/library/Recommended/Makefile.in"
+               (("INSTALL_OPTS =" m)
+                (string-append m " --built-timestamp=1970-01-01" m)))
+
              ;; R bundles an older version of help2man, which does not respect
              ;; SOURCE_DATE_EPOCH.  We cannot just use the latest help2man,
              ;; because that breaks a test.
@@ -312,6 +318,17 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
+       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+                                        texlive-fonts-ec
+                                        texlive-latex-amsfonts
+                                        texlive-latex-base
+                                        texlive-latex-fancyvrb
+                                        texlive-latex-graphics
+                                        texlive-latex-hyperref
+                                        texlive-latex-oberdiek
+                                        texlive-latex-tools
+                                        texlive-latex-upquote
+                                        texlive-latex-url)))
        ("tzdata" ,tzdata-for-tests)
        ("xz" ,xz)))
     (inputs
@@ -379,14 +396,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-20")
+    (version "1.3-22")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
+         "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
@@ -400,14 +417,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51.3")
+    (version "7.3-51.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "1dh8cvvdsf9dx29x6va47qdkswmr03k3yjycinq98fnl0ivhw3jv"))))
+         "0x1ckf51y851g0kvbhsgdxb26vfpmbw3xdbcnh3ck7fjm13da4cr"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -443,16 +460,16 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
 (define-public r-cluster
   (package
     (name "r-cluster")
-    (version "2.0.8")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cluster" version))
        (sha256
         (base32
-         "0jkmlhjknndh0lmyvqz7s7j1hhnarixm6zb39np4ssw47flk0nfc"))))
+         "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
     (build-system r-build-system)
-    (inputs
+    (native-inputs
      `(("gfortran" ,gfortran)))
     (home-page "https://cran.r-project.org/web/packages/cluster")
     (synopsis "Methods for cluster analysis")
@@ -570,14 +587,14 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-139")
+    (version "3.1-140")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
         (base32
-         "0fap121c18nbznyzvnqvsdiszg2nbmkas6zhgrz1f8jiv1lzqq04"))))
+         "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -636,14 +653,14 @@ single hidden layer, and for multinomial log-linear models.")
 (define-public r-rpart
   (package
     (name "r-rpart")
-    (version "4.1-13")
+    (version "4.1-15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rpart" version))
        (sha256
         (base32
-         "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
+         "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rpart")
     (synopsis "Recursive partitioning and regression trees")
@@ -786,13 +803,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.18")
+    (version "0.6.19")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj"))))
+        (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -1120,18 +1137,17 @@ legends.")
 (define-public r-ggplot2
   (package
     (name "r-ggplot2")
-    (version "3.1.1")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggplot2" version))
        (sha256
-        (base32 "0y8cks9r9hvjlx0isnvbgs3p0al167hlr3q7c3syfcj77dzjkpmz"))))
+        (base32 "1cvk9pw59kxx19kamqwa15h26rbznp0vvqpn7y8kgjssnrzqkdii"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
        ("r-gtable" ,r-gtable)
-       ("r-plyr" ,r-plyr)
        ("r-lazyeval" ,r-lazyeval)
        ("r-mass" ,r-mass)
        ("r-mgcv" ,r-mgcv)
@@ -1182,14 +1198,14 @@ agnes cluster diagrams.")
 (define-public r-gdtools
   (package
     (name "r-gdtools")
-    (version "0.1.8")
+    (version "0.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdtools" version))
        (sha256
         (base32
-         "1ayy0s699ghaz34lklvcskfwman3x2n2772s5sa5x9k9xgsnxwcl"))))
+         "0w4fihf52q5qxxk0lg36x6yvjjl8vw66y60ncdjs5fvnxqn5z2vb"))))
     (build-system r-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -1209,19 +1225,19 @@ and to generate base64 encoded string from raster matrix.")
 (define-public r-svglite
   (package
     (name "r-svglite")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "svglite" version))
        (sha256
         (base32
-         "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
+         "1gwv51wqp6pgm2f9gavsiq65njs77fr49n8y6y9ax60k3a4vvg14"))))
     (build-system r-build-system)
-    (native-inputs  `(("r-rcpp" ,r-rcpp)))
     (propagated-inputs
      `(("r-bh" ,r-bh)
-       ("r-gdtools" ,r-gdtools)))
+       ("r-gdtools" ,r-gdtools)
+       ("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/hadley/svglite")
     (synopsis "SVG graphics device")
     (description
@@ -1310,13 +1326,13 @@ for template use among CRAN packages.")
 (define-public r-evaluate
   (package
     (name "r-evaluate")
-    (version "0.13")
+    (version "0.14")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "evaluate" version))
               (sha256
                (base32
-                "0igvc27rsqxcswjb9slnpi5d509rffxn1y5d82hgqvv970nl3p2q"))))
+                "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
     (build-system r-build-system)
     (home-page "https://github.com/hadley/evaluate")
     (synopsis "Parsing and evaluation tools for R")
@@ -1330,13 +1346,13 @@ adapted for other output formats, such as HTML or LaTeX.")
 (define-public r-formatr
   (package
     (name "r-formatr")
-    (version "1.6")
+    (version "1.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "formatR" version))
               (sha256
                (base32
-                "0a9229rg3s9qga5v2fwfdqr0z3bk2yycv8kijrcm3jh66l68zjgm"))))
+                "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
     (build-system r-build-system)
     (home-page "http://yihui.name/formatR")
     (synopsis "Format R code automatically")
@@ -1369,13 +1385,13 @@ supported via Andre Simon's highlight package.")
 (define-public r-mime
   (package
     (name "r-mime")
-    (version "0.6")
+    (version "0.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mime" version))
               (sha256
                (base32
-                "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7"))))
+                "12vpip67ajb90b8p96w43ir7mavrw2i61bwvpfnrlmlj9kj3w20i"))))
     (build-system r-build-system)
     (home-page "https://github.com/yihui/mime")
     (synopsis "R package to map filenames to MIME types")
@@ -1387,13 +1403,13 @@ data derived from /etc/mime.types in UNIX-type systems.")
 (define-public r-markdown
   (package
     (name "r-markdown")
-    (version "0.9")
+    (version "1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "markdown" version))
               (sha256
                (base32
-                "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h"))))
+                "19nrz0ba1yd5kicd65crkkz2r3kialm2hm6zdkp495l2s5r80b8p"))))
     (build-system r-build-system)
     ;; Skip check phase because the tests require the r-knitr package to be
     ;; installed. This prevents installation failures. Knitr normally
@@ -1431,13 +1447,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.22")
+    (version "1.23")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "1iks80g1cj25rvgyf0y2jc2pmfvsq4sbgdp788w9016bk71wzdcs"))))
+                "16ba4258c915xydhniw4cw7fvv1vp4cnwd1w49ykx7zw00rznfq6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-evaluate" ,r-evaluate)
@@ -1586,13 +1602,13 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "2.0.1")
+    (version "2.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "1cafy5xsjx6m08s45456mjsal7mfxzwpbrds0p4z3gwam948gpzy"))))
+                "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -1635,13 +1651,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.3.4")
+    (version "0.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "1pks7d2xavzgaxqrnk3f79qsmv4wqv93f8991jv93pnb1mxpyijf"))))
+                "038mmbmklw17ncgz53vrdx2506c1jj6di3y165bbx2sl2yia8j4p"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1653,14 +1669,14 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "2.1.1")
+    (version "2.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "111jl0hdjhh7hkydxvsr5l19gb0ylxq7xrkc28awnc9pzglpgis5"))))
+         "06jfayiip8j8ibdhw3fvxn4n8aqbqhwanrszpzlsf92xdfgfm34s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -1679,13 +1695,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.8.0.1")
+    (version "0.8.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "0p6dbjrgqyklc67g53v1a5xdp9x2jpcsdcs6v3djf9d366fqh244"))))
+                "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1714,14 +1730,14 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.3.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "07p23vyvi7s4abldhkyir05kcf7xnfc18igfryq12j67xd0jql0m"))))
+         "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1847,14 +1863,14 @@ and fast file reading.")
 (define-public r-xtable
   (package
     (name "r-xtable")
-    (version "1.8-3")
+    (version "1.8-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xtable" version))
        (sha256
         (base32
-         "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk"))))
+         "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
@@ -2056,13 +2072,13 @@ jackknifed confidence intervals are available for most estimates.")
 (define-public r-rversions
   (package
     (name "r-rversions")
-    (version "1.0.3")
+    (version "2.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rversions" version))
               (sha256
                (base32
-                "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
+                "0mkg9zrjxlbwqzijiysivrs523x48syqj30xdfp88clpkqfk435m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -2096,14 +2112,14 @@ limited to R.")
 (define-public r-backports
   (package
     (name "r-backports")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "backports" version))
        (sha256
         (base32
-         "1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4"))))
+         "00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
@@ -2119,14 +2135,14 @@ R version.")
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "1.9.1")
+    (version "1.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "1y4ylzn55kpyfpzcx9rxb9413d3ck6hair36ldl0ak61ia5kc75p"))))
+         "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -2185,14 +2201,14 @@ or source files in a key-value fashion.")
 (define-public r-batchjobs
   (package
     (name "r-batchjobs")
-    (version "1.7")
+    (version "1.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "BatchJobs" version))
        (sha256
         (base32
-         "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
+         "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
     (properties `((upstream-name . "BatchJobs")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2316,14 +2332,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.3")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "1gx4mk7js1irzkql5rgk48ja9c6mm28ccxz483ngbhdd57az90qw"))))
+         "0mh4xwb9wnn5j2n1zzmjldqjqv2nn4wdidiixxciaqrqsi0l9834"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
@@ -2421,13 +2437,13 @@ informative error messages when it's not available.")
 (define-public r-devtools
   (package
     (name "r-devtools")
-    (version "2.0.1")
+    (version "2.0.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "devtools" version))
               (sha256
                (base32
-                "1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f"))))
+                "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -2521,13 +2537,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-4")
+    (version "3.7-6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj"))))
+                "0ijfjlr7ls5hvfyzdmwab6bx0w3nvp0c8fgynj4355cj8mbzgmc3"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -2580,13 +2596,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.300.2.0")
+    (version "0.9.500.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "02zha49v6s8g39dcmk5dz0pygx0jibgmcwsyzybp9wmlqxnmdvip"))))
+                "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     ;; All needed for vignettes
@@ -2678,14 +2694,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.12")
+    (version "1.13")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "0milpdaf4nd36kq6sci9wc5dhwswl4w9c9fychfbppgjsgfp6kfv"))))
+            "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2697,6 +2713,7 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-mime" ,r-mime)
        ("r-stringr" ,r-stringr)
        ("r-tinytex" ,r-tinytex)
+       ("r-xfun" ,r-xfun)
        ("r-yaml" ,r-yaml)
        ("ghc-pandoc" ,ghc-pandoc)))
     (home-page "http://rmarkdown.rstudio.com")
@@ -2864,13 +2881,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.98-1.19")
+    (version "3.98-1.20")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "1axyfa56q45x7z4zd56aasdn9hz9niv2vv5qm1zp9i94vyic9cc1"))))
+                "0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)
@@ -2987,14 +3004,14 @@ statements.")
 (define-public r-segmented
   (package
     (name "r-segmented")
-    (version "0.5-3.0")
+    (version "1.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "segmented" version))
        (sha256
         (base32
-         "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
+         "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/segmented")
     (synopsis "Regression models with breakpoints estimation")
@@ -3145,13 +3162,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.5")
+    (version "0.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf"))))
+                "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3221,14 +3238,14 @@ analysis of large sparse or dense matrices.")
 (define-public r-glmnet
   (package
    (name "r-glmnet")
-   (version "2.0-16")
+   (version "2.0-18")
    (source
     (origin
      (method url-fetch)
      (uri (cran-uri "glmnet" version))
      (sha256
       (base32
-       "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55"))))
+       "0sr5akaiaab1sdh9c8gfmc4kp9b4vqhd90d9ig0rqpqhp3bykp78"))))
    (build-system r-build-system)
    (inputs
     `(("gfortran" ,gfortran)))
@@ -3297,14 +3314,14 @@ package registries.")
 (define-public r-rngtools
   (package
     (name "r-rngtools")
-    (version "1.3.1")
+    (version "1.3.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngtools" version))
        (sha256
         (base32
-         "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn"))))
+         "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -3347,14 +3364,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
 (define-public r-e1071
   (package
     (name "r-e1071")
-    (version "1.7-1")
+    (version "1.7-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "e1071" version))
        (sha256
         (base32
-         "1zlxz3da216q6v6r4ff60il121xwz7g7m639vzdwglhw3jjh8psw"))))
+         "0lipj692rjjw8rrhqh2k9i5dh8y2sjrw9q53rwm32irhx2f2j73j"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)))
@@ -3525,13 +3542,13 @@ maintenance for package developers.")
 (define-public r-r-utils
   (package
     (name "r-r-utils")
-    (version "2.8.0")
+    (version "2.9.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.utils" version))
               (sha256
                (base32
-                "1jaarld1jgpzh18kh9g3rlzcrk51vdgn2n1d1y28szzxlz94vifg"))))
+                "1w4zn2db15bggfnh64fbyi2z2sj47rcd4xn53b28dsnkamdcramj"))))
     (properties `((upstream-name . "R.utils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3605,13 +3622,13 @@ vignettes.")
 (define-public r-mvtnorm
   (package
     (name "r-mvtnorm")
-    (version "1.0-10")
+    (version "1.0-11")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mvtnorm" version))
               (sha256
                (base32
-                "04md0wmqgif24g0a4hx19ifn4kk8nx10986vf2d9vascig6ikpri"))))
+                "0lkjph661blc1nwfzg9w48a60wvj6ffh4zjwlisvracsx4nn2883"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
@@ -3760,14 +3777,14 @@ and tidyr provides no margins or aggregation.")
 (define-public r-hexbin
   (package
     (name "r-hexbin")
-    (version "1.27.2")
+    (version "1.27.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hexbin" version))
        (sha256
         (base32
-         "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
+         "14f181lw6sj5xhfxbrpyyinsjfl0nzqilq6z80lgrhj2cnkj593y"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -3805,13 +3822,13 @@ features present in other programming languages.")
 (define-public r-plotly
   (package
     (name "r-plotly")
-    (version "4.8.0")
+    (version "4.9.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotly" version))
               (sha256
                (base32
-                "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq"))))
+                "1kz2hm7vnkn4clxr6yyxxnmdmkz9zwjq6bzysw7j27r3721i8qgp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-base64enc" ,r-base64enc)
@@ -4092,14 +4109,14 @@ hierarchical clustering dendrograms.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.44.0")
+    (version "1.46.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"))))
+         "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -4138,14 +4155,14 @@ existing packages provide.")
 (define-public r-sfsmisc
   (package
     (name "r-sfsmisc")
-    (version "1.1-3")
+    (version "1.1-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sfsmisc" version))
        (sha256
         (base32
-         "1y25nnw09qfm66523w1z4q766lv15a6ykvsq30r154n7m7aggvsq"))))
+         "0zaw617zarmwir8l60riky0z6r1j3mwfnm1f32vqcbljb74akdj4"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/sfsmisc")
     (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
@@ -4297,13 +4314,13 @@ mechanism.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-5")
+    (version "1.8-6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "09p8gmd5ifz80ahnhiianarsr5xx3nz76jzp90d7v3fjffcrcww7"))))
+                "1k1pmzr9nfwbxq1xf0jzn3nawv4sgnkxkgzxnm1i887jcbrs85r2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -4427,13 +4444,13 @@ data at that region, and avoids over-plotting.")
 (define-public r-ggthemes
   (package
     (name "r-ggthemes")
-    (version "4.1.0")
+    (version "4.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggthemes" version))
               (sha256
                (base32
-                "1a6r384v72hb91qkg9rz2m7s3qskbl9haxynf2vzz6v1ak9xd4c5"))))
+                "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -4453,13 +4470,13 @@ Wall Street Journal, among others.  This package also provides
 (define-public r-statmod
   (package
     (name "r-statmod")
-    (version "1.4.30")
+    (version "1.4.32")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "statmod" version))
               (sha256
                (base32
-                "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
+                "083yyp84xj85zg4bhz7i90bqzl3p6155ch4abwsfc9k1lv7s2rrg"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/statmod")
     (native-inputs
@@ -4731,14 +4748,14 @@ models, generalized linear models and model-based clustering.")
 (define-public r-mclust
   (package
     (name "r-mclust")
-    (version "5.4.3")
+    (version "5.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mclust" version))
        (sha256
         (base32
-         "18x5ych9zi3y87rxi4pf6f23sl2918dp9xxpw1pqa7p7drw817p6"))))
+         "039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -4754,14 +4771,14 @@ and resampling-based inference.")
 (define-public r-prabclus
   (package
     (name "r-prabclus")
-    (version "2.2-7")
+    (version "2.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "prabclus" version))
        (sha256
         (base32
-         "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb"))))
+         "1h5k13w8mmmdy74l145zh64f339wy78z1nlg8xr3zg23gmv98cpg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -4801,14 +4818,14 @@ can be efficiently implemented directly in the R language.")
 (define-public r-robustbase
   (package
     (name "r-robustbase")
-    (version "0.93-4")
+    (version "0.93-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "robustbase" version))
        (sha256
         (base32
-         "1q56y0iqp7qhavm4xnpzhs64q7l893y7yiq3b20fllpghka077pa"))))
+         "0mkzbsjl5nihyj7mzks14p6kr3spp44xvygjz4ran11gspdn9rdx"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -4817,7 +4834,7 @@ can be efficiently implemented directly in the R language.")
     (home-page "http://robustbase.r-forge.r-project.org/")
     (synopsis "Basic robust statistics")
     (description
-     "This packages allows to analyze data with robust methods such as
+     "This package allows to analyze data with robust methods such as
 regression methodology including model selections and multivariate statistics.")
     (license license:gpl2+)))
 
@@ -4950,14 +4967,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.1-11.1")
+    (version "2.2-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc"))))
+         "1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -4967,10 +4984,8 @@ of the points.")
        ("r-kernlab" ,r-kernlab)
        ("r-mass" ,r-mass)
        ("r-mclust" ,r-mclust)
-       ("r-mvtnorm" ,r-mvtnorm)
        ("r-prabclus" ,r-prabclus)
-       ("r-robustbase" ,r-robustbase)
-       ("r-trimcluster" ,r-trimcluster)))
+       ("r-robustbase" ,r-robustbase)))
     (home-page "https://cran.r-project.org/web/packages/fpc")
     (synopsis "Flexible procedures for clustering")
     (description
@@ -5122,14 +5137,14 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.38")
+    (version "5.41")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
         (base32
-         "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"))))
+         "110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -5253,14 +5268,14 @@ Companion to Applied Regression, Third Edition, Sage.")
 (define-public r-car
   (package
     (name "r-car")
-    (version "3.0-2")
+    (version "3.0-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "car" version))
        (sha256
         (base32
-         "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
+         "0vy3g3bjljd2al8xb9qr45f98is7yppc9jilqn7b6zvf5yqpr07s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
@@ -5284,14 +5299,14 @@ to Applied regression, Second Edition, Sage, 2011.")
 (define-public r-caret
   (package
     (name "r-caret")
-    (version "6.0-82")
+    (version "6.0-84")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "caret" version))
        (sha256
         (base32
-         "0zgkmiiarl7ll2ffyciikah61jyps41fin5pjb5l8ja2b26lgrdg"))))
+         "03898irgb70q0p01kq99yb6q6xji0jx4jmj0yxlv8wcwd841r0x1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreach" ,r-foreach)
@@ -5360,14 +5375,14 @@ are computed via non-Monte Carlo methods.")
 (define-public r-numderiv
   (package
     (name "r-numderiv")
-    (version "2016.8-1")
+    (version "2016.8-1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "numDeriv" version))
        (sha256
         (base32
-         "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
+         "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
     (properties `((upstream-name . "numDeriv")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/numDeriv")
@@ -5380,14 +5395,14 @@ first and second order derivatives.")
 (define-public r-sn
   (package
     (name "r-sn")
-    (version "1.5-3")
+    (version "1.5-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sn" version))
        (sha256
         (base32
-         "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc"))))
+         "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mnormt" ,r-mnormt)
@@ -5395,7 +5410,7 @@ first and second order derivatives.")
     (home-page "http://azzalini.stat.unipd.it/SN")
     (synopsis "The skew-normal and skew-t distributions")
     (description
-     "This packages provides functionalities to build and manipulate
+     "This package provides functionalities to build and manipulate
 probability distributions of the skew-normal family and some related
 ones, notably the skew-t family, and provides related statistical
 methods for data fitting and diagnostics, in the univariate and the