Merge branch 'master' into core-updates

1 files changed, 35 insertions, 30 deletions

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d4d9c0e786..7c6ca70314 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -703,13 +703,13 @@ effects of different types of color-blindness.")
 (define-public r-digest
   (package
     (name "r-digest")
-    (version "0.6.12")
+    (version "0.6.13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "digest" version))
        (sha256
-        (base32 "1awy9phxdvqnadby7rvwy2hkbrj210bqf4xvi27asdq028zlcyd4"))))
+        (base32 "1bsgl07bvf4nk6bn7n3l2ilvk4qvn3nk7yxp22miil7x405xdks6"))))
     (build-system r-build-system)
     ;; Vignettes require r-knitr, which requires r-digest, so we have to
     ;; disable them and the tests.
@@ -988,13 +988,13 @@ the input of another.")
 (define-public r-reshape2
   (package
     (name "r-reshape2")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "reshape2" version))
        (sha256
-        (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd"))))
+        (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-plyr" ,r-plyr)
@@ -1328,13 +1328,13 @@ syntax that can be converted to XHTML or other formats.")
 (define-public r-yaml
   (package
     (name "r-yaml")
-    (version "2.1.14")
+    (version "2.1.16")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "yaml" version))
               (sha256
                (base32
-                "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1"))))
+                "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/yaml/")
     (synopsis "Methods to convert R data to YAML and back")
@@ -1502,20 +1502,23 @@ R packages that praise their users.")
 (define-public r-testthat
   (package
     (name "r-testthat")
-    (version "1.0.2")
+    (version "2.0.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "testthat" version))
               (sha256
                (base32
-                "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
+                "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-digest" ,r-digest)
+     `(("r-cli" ,r-cli)
        ("r-crayon" ,r-crayon)
+       ("r-digest" ,r-digest)
        ("r-magrittr" ,r-magrittr)
        ("r-praise" ,r-praise)
-       ("r-r6" ,r-r6)))
+       ("r-r6" ,r-r6)
+       ("r-rlang" ,r-rlang)
+       ("r-withr" ,r-withr)))
     (home-page "https://github.com/hadley/testthat")
     (synopsis "Unit testing for R")
     (description
@@ -1898,15 +1901,17 @@ chain.")
 (define-public r-ade4
   (package
     (name "r-ade4")
-    (version "1.7-8")
+    (version "1.7-10")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "ade4" version))
         (sha256
           (base32
-            "1a5p3wf8l9cp1bjp57b1pc5bqs39kw1v21i4waj9j18wawzlmpb6"))))
+            "0zk81x0yn30gbyc0jpzyw1nxd08ccihl6vyk0ijvj3aw3nr5flc6"))))
     (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
     (home-page "http://pbil.univ-lyon1.fr/ADE-4")
     (synopsis "Multivariate data analysis and graphical display")
     (description
@@ -2007,14 +2012,14 @@ limited to R.")
 (define-public r-backports
   (package
     (name "r-backports")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "backports" version))
        (sha256
         (base32
-         "15w8psmv203wzijrk4hvwaw3i4byh2m5s09yrkqwhfckhaj82kj9"))))
+         "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
@@ -2278,13 +2283,13 @@ functions make it easy to control additional request components.")
 (define-public r-git2r
   (package
     (name "r-git2r")
-    (version "0.19.0")
+    (version "0.20.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "git2r" version))
               (sha256
                (base32
-                "0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q"))))
+                "1pqggijvsalb5cc2pr5gwfj3s713s63f4xii1xrd0qagfgbgz846"))))
     (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
@@ -2415,13 +2420,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.6-6")
+    (version "3.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "07hywp3ym0gbpqdj3f4vhr0bhmynhby8vh6p1b9cm2hv26pzs9q4"))))
+                "0rw81n9p3d2i03b4pgcfj5blryc94f29bm9a4j9bnp5h8qjj6pry"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -2474,13 +2479,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.8.100.1.0")
+    (version "0.8.300.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "19sghlkslz6llcrjk5pd8c6dsb338jsi4dnwrbbrjkfq6jdr5jlp"))))
+                "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (native-inputs
@@ -2545,14 +2550,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
 (define-public r-rprojroot
   (package
     (name "r-rprojroot")
-    (version "1.2")
+    (version "1.3-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rprojroot" version))
        (sha256
         (base32
-         "1fgyxv1zv04sllcclzz089xl6hpdzac7xk61l0l4acb7rqsx5d18"))))
+         "1jigr2jh3hzy35h94im52yq81lyikw7nfvmbxij84a1b9c32r332"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
@@ -2859,14 +2864,14 @@ statements.")
 (define-public r-segmented
   (package
     (name "r-segmented")
-    (version "0.5-2.2")
+    (version "0.5-3.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "segmented" version))
        (sha256
         (base32
-         "1wdjxkgqjqw5q2nywmgkf6y21lb0alhvaqg0m0dr2xyxf1ii79rs"))))
+         "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/segmented")
     (synopsis "Regression models with breakpoints estimation")
@@ -2923,14 +2928,14 @@ standard R subsetting and Kronecker products.")
 (define-public r-iterators
   (package
     (name "r-iterators")
-    (version "1.0.8")
+    (version "1.0.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "iterators" version))
        (sha256
         (base32
-         "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
+         "16sycjq912ix52fjxjhcwiaqr0yj1v5iqmrvjljd3z857031w06y"))))
     (build-system r-build-system)
     (home-page "http://cran.r-project.org/web/packages/iterators")
     (synopsis "Iterator construct for R")
@@ -3144,14 +3149,14 @@ options and registries, vignette, unit test and bibtex related utilities.")
  (define-public r-registry
    (package
      (name "r-registry")
-     (version "0.3")
+     (version "0.5")
      (source
       (origin
         (method url-fetch)
         (uri (cran-uri "registry" version))
         (sha256
          (base32
-          "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
+          "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
      (build-system r-build-system)
      (home-page "http://cran.r-project.org/web/packages/registry")
      (synopsis "Infrastructure for R package registries")
@@ -4394,14 +4399,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
 (define-public r-cowplot
   (package
     (name "r-cowplot")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cowplot" version))
        (sha256
         (base32
-         "0iq0wsi7467cj8hqml06whk3xsiv89x8dvm9ynwp411pzzbdjgwm"))))
+         "13yjw7yv7imyqiawqqp304hkp6x36iv6rf6gn03dwzwkj9zwx4lb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)