X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/ddb4062784c66ecc0c42910b209dc80356a197ea..862959813f40b1b9d25ffc6cca4f24c66e991f69:/gnu/packages/statistics.scm

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 06f0aa1e75..259c29b989 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -57,6 +57,7 @@
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages libffi)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
@@ -74,6 +75,7 @@
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -396,14 +398,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-22")
+    (version "1.3-23")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
+         "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
@@ -460,14 +462,14 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
 (define-public r-cluster
   (package
     (name "r-cluster")
-    (version "2.0.9")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cluster" version))
        (sha256
         (base32
-         "1bg5dvs4bzj0rp75jpxaklz12rvyh5w99h7zkvfgpgn86ljg1rlf"))))
+         "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -501,14 +503,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-71")
+    (version "0.8-72")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
+         "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -587,14 +589,14 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-140")
+    (version "3.1-141")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
         (base32
-         "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
+         "0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -803,13 +805,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.19")
+    (version "0.6.20")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
+        (base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -1137,18 +1139,17 @@ 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)
@@ -1199,14 +1200,14 @@ 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)))
@@ -1327,13 +1328,13 @@ 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")
@@ -1347,13 +1348,13 @@ 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")
@@ -1386,13 +1387,13 @@ 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")
@@ -1404,13 +1405,13 @@ 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
@@ -1603,18 +1604,19 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "2.1.1")
+    (version "2.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
+                "0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
        ("r-crayon" ,r-crayon)
        ("r-digest" ,r-digest)
+       ("r-evaluate" ,r-evaluate)
        ("r-magrittr" ,r-magrittr)
        ("r-praise" ,r-praise)
        ("r-r6" ,r-r6)
@@ -1652,13 +1654,13 @@ 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")
@@ -1670,14 +1672,14 @@ 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)
@@ -1696,13 +1698,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "0.8.1")
+    (version "0.8.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
+                "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1731,14 +1733,14 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "0f4gfkzl07gfwihyc747kdnzxahaw2g28wli4jmikrvczldvjqjx"))))
+         "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -1979,13 +1981,13 @@ inference for statistical models.")
 (define-public r-coda
   (package
     (name "r-coda")
-    (version "0.19-2")
+    (version "0.19-3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "coda" version))
               (sha256
                (base32
-                "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
+                "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -2021,14 +2023,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
+         "0186d7r36xw1z9f8ajz35a0dz4ch6hmrjl9536yc7vq78v4vn5an"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)
@@ -2136,14 +2138,14 @@ R version.")
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "1.9.3")
+    (version "1.9.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
+         "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -2333,14 +2335,14 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.3")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "1gx4mk7js1irzkql5rgk48ja9c6mm28ccxz483ngbhdd57az90qw"))))
+         "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
@@ -2366,13 +2368,13 @@ integers.")
 (define-public r-httr
   (package
     (name "r-httr")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httr" version))
               (sha256
                (base32
-                "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
+                "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -2392,20 +2394,16 @@ functions make it easy to control additional request components.")
 (define-public r-git2r
   (package
     (name "r-git2r")
-    (version "0.25.2")
+    (version "0.26.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "git2r" version))
               (sha256
                (base32
-                "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
+                "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
     (build-system r-build-system)
-    ;; This R package contains modified sources of libgit2.  This modified
-    ;; version of libgit2 is built as the package is built.  Hence libgit2 is
-    ;; not among the inputs of this package.
     (inputs
-     `(("libssh2" ,libssh2) ; for SSH transport
-       ("openssl" ,openssl)
+     `(("libgit2" ,libgit2)
        ("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -2438,13 +2436,13 @@ informative error messages when it's not available.")
 (define-public r-devtools
   (package
     (name "r-devtools")
-    (version "2.0.2")
+    (version "2.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "devtools" version))
               (sha256
                (base32
-                "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
+                "0393v7nr22gr5g9afgrhq4ab3lwbqy6fd3shnmlhdpqam5357xy1"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -2457,9 +2455,11 @@ informative error messages when it's not available.")
        ("r-pkgbuild" ,r-pkgbuild)
        ("r-pkgload" ,r-pkgload)
        ("r-rcmdcheck" ,r-rcmdcheck)
+       ("r-roxygen2" ,r-roxygen2)
        ("r-remotes" ,r-remotes)
        ("r-rstudioapi" ,r-rstudioapi)
        ("r-sessioninfo" ,r-sessioninfo)
+       ("r-testthat" ,r-testthat)
        ("r-usethis" ,r-usethis)
        ("r-withr" ,r-withr)))
     (home-page "https://github.com/hadley/devtools")
@@ -2490,18 +2490,19 @@ were originally a part of the r-devtools package.")
 (define-public r-hms
   (package
     (name "r-hms")
-    (version "0.4.2")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hms" version))
        (sha256
         (base32
-         "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
+         "06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
-       ("r-pkgconfig" ,r-pkgconfig)))
+       ("r-pkgconfig" ,r-pkgconfig)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/rstats-db/hms")
     (synopsis "Pretty time of day")
     (description
@@ -2538,13 +2539,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-5")
+    (version "3.7-6")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "0k6ivryac1k81z2dijjds376a9jxwk8rf5g48snj67cnjffkybxj"))))
+                "0ijfjlr7ls5hvfyzdmwab6bx0w3nvp0c8fgynj4355cj8mbzgmc3"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -2597,13 +2598,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.400.3.0")
+    (version "0.9.600.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1c0kmp54xgg67hxpqm8bibcxmmwljbdvm9p1d9wzirp83x86v4sn"))))
+                "07jg2667xyhmp1fbcdi5nnhmkk81da76s9rlswfq4k2sjsmbfmr0"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     ;; All needed for vignettes
@@ -2695,14 +2696,14 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.12")
+    (version "1.14")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
           (base32
-            "0milpdaf4nd36kq6sci9wc5dhwswl4w9c9fychfbppgjsgfp6kfv"))))
+            "0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2714,6 +2715,7 @@ 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")
@@ -2787,17 +2789,18 @@ that package, other packages are unaffected.")
 (define-public r-blob
   (package
     (name "r-blob")
-    (version "1.1.1")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "blob" version))
               (sha256
                (base32
-                "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
+                "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-prettyunits" ,r-prettyunits)
-       ("r-tibble" ,r-tibble)))
+       ("r-rlang" ,r-rlang)
+       ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/hadley/blob")
     (synopsis "Simple S3 Class for representing vectors of binary data")
     (description "Raw vectors in R are useful for storing a single binary
@@ -2809,13 +2812,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.1.1")
+    (version "2.1.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
+                "1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2881,13 +2884,13 @@ 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)
@@ -3004,14 +3007,14 @@ statements.")
 (define-public r-segmented
   (package
     (name "r-segmented")
-    (version "0.5-4.0")
+    (version "1.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "segmented" version))
        (sha256
         (base32
-         "0wa0xjda2j33284jkp5hj1wdjysc5f4paj1s1lcixgawj4ckmxkz"))))
+         "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/segmented")
     (synopsis "Regression models with breakpoints estimation")
@@ -3068,14 +3071,14 @@ standard R subsetting and Kronecker products.")
 (define-public r-iterators
   (package
     (name "r-iterators")
-    (version "1.0.10")
+    (version "1.0.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iterators" version))
        (sha256
         (base32
-         "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
+         "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/iterators")
     (synopsis "Iterator construct for R")
@@ -3088,14 +3091,14 @@ data.")
 (define-public r-foreach
   (package
     (name "r-foreach")
-    (version "1.4.4")
+    (version "1.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreach" version))
        (sha256
         (base32
-         "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
+         "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-codetools" ,r-codetools)
@@ -3116,14 +3119,14 @@ parallel.")
 (define-public r-doparallel
   (package
     (name "r-doparallel")
-    (version "1.0.14")
+    (version "1.0.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "doParallel" version))
        (sha256
         (base32
-         "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
+         "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
     (properties `((upstream-name . "doParallel")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3162,13 +3165,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.6")
+    (version "0.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "05kr88yshq6siarp5q7aapvsr63vx3p0aqablwgifn8m2sfqxmif"))))
+                "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3364,14 +3367,14 @@ 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)))
@@ -3542,13 +3545,13 @@ 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
@@ -3622,13 +3625,13 @@ 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)))
@@ -4314,13 +4317,13 @@ 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)))
@@ -4470,13 +4473,13 @@ 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
@@ -4748,14 +4751,14 @@ 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)))
@@ -4771,14 +4774,14 @@ 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)
@@ -4967,14 +4970,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.1-11.2")
+    (version "2.2-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "0wjjp9xn283acfg6cm1wa6fsi7pf0z97227hrnlpmprks3mbj8kr"))))
+         "1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -4984,10 +4987,8 @@ 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
@@ -5139,14 +5140,14 @@ 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)))
@@ -5270,14 +5271,14 @@ 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)
@@ -5377,14 +5378,14 @@ 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")
@@ -5767,62 +5768,76 @@ as a boxplot function.")
     (license license:lgpl3+)))
 
 (define-public python-rpy2
-  (package
-    (name "python-rpy2")
-    (version "2.9.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "rpy2" version))
-       (sha256
-        (base32
-         "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:modules ((ice-9 ftw)
-                  (srfi srfi-1)
-                  (srfi srfi-26)
-                  (guix build utils)
-                  (guix build python-build-system))
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             (let ((cwd (getcwd)))
-               (setenv "PYTHONPATH"
-                       (string-append cwd "/build/"
-                                      (find (cut string-prefix? "lib" <>)
-                                            (scandir (string-append cwd "/build")))
-                                      ":"
-                                      (getenv "PYTHONPATH"))))
-             (invoke "python" "-m" "rpy2.tests" "-v"))))))
-    (propagated-inputs
-     `(("python-six" ,python-six)
-       ("python-jinja2" ,python-jinja2)
-       ("python-pytz" ,python-pytz)))
-    (inputs
-     `(("readline" ,readline)
-       ("icu4c" ,icu4c)
-       ("pcre" ,pcre)
-       ("r-minimal" ,r-minimal)
-       ("r-survival" ,r-survival)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-dplyr" ,r-dplyr)
-       ("r-dbplyr" ,r-dbplyr)
-       ("python-numpy" ,python-numpy)))
-    (native-inputs
-     `(("zlib" ,zlib)))
-    (home-page "https://rpy2.bitbucket.io/")
-    (synopsis "Python interface to the R language")
-    (description "rpy2 is a redesign and rewrite of rpy.  It is providing a
+  ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
+  ;; it fixes a regression when using ggplot 3.2.0.
+  (let ((changeset "19868a8")
+        (revision "1"))
+    (package
+      (name "python-rpy2")
+      (version (git-version "3.0.4" revision changeset))
+      (source
+       (origin
+         (method hg-fetch)
+         (uri (hg-reference
+               (url "https://bitbucket.org/rpy2/rpy2")
+               (changeset changeset)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
+      (build-system python-build-system)
+      (arguments
+       '(#:modules ((ice-9 ftw)
+                    (srfi srfi-1)
+                    (srfi srfi-26)
+                    (guix build utils)
+                    (guix build python-build-system))
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda* (#:key outputs inputs #:allow-other-keys)
+               (let ((cwd (getcwd)))
+                 (setenv "TZ" "UTC")
+                 (setenv "PYTHONPATH"
+                         (string-append cwd "/build/"
+                                        (find (cut string-prefix? "lib" <>)
+                                              (scandir (string-append cwd "/build")))
+                                        ":"
+                                        (getenv "PYTHONPATH"))))
+               (invoke "pytest" "-v" "rpy/tests/"))))))
+      (propagated-inputs
+       `(("python-cffi" ,python-cffi)
+         ("python-six" ,python-six)
+         ("python-jinja2" ,python-jinja2)
+         ("python-numpy" ,python-numpy)
+         ("python-pandas" ,python-pandas)
+         ("python-pytz" ,python-pytz)
+         ("python-ipython" ,python-ipython)
+         ("python-tzlocal" ,python-tzlocal)))
+      (inputs
+       `(("readline" ,readline)
+         ("icu4c" ,icu4c)
+         ("pcre" ,pcre)
+         ("r-minimal" ,r-minimal)
+         ("r-survival" ,r-survival)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-rsqlite" ,r-rsqlite)
+         ("r-dplyr" ,r-dplyr)
+         ("r-dbplyr" ,r-dbplyr)
+         ("python-numpy" ,python-numpy)))
+      (native-inputs
+       `(("zlib" ,zlib)
+         ("python-pytest" ,python-pytest)))
+      (home-page "https://rpy2.bitbucket.io/")
+      (synopsis "Python interface to the R language")
+      (description "rpy2 is a redesign and rewrite of rpy.  It is providing a
 low-level interface to R from Python, a proposed high-level interface,
 including wrappers to graphical libraries, as well as R-like structures and
 functions.")
-    ;; Any of these licenses can be picked for the R interface.  The whole
-    ;; project is released under GPLv2+ according to the license declaration
-    ;; in "setup.py".
-    (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
+      ;; Any of these licenses can be picked for the R interface.  The whole
+      ;; project is released under GPLv2+ according to the license declaration
+      ;; in "setup.py".
+      (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
 
 (define-public java-jdistlib
   (package