Merge branch 'master' into core-updates

7 files changed, 281 insertions, 175 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index abea913723..b4988aeb7b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6134,20 +6134,20 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.5-1")
+    (version "2.5-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r"))))
+         "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
-       ("r-knitr" ,r-knitr)
+       ("r-knitr" ,r-knitr) ; needed for vignettes
        ("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
        ("r-mgcv" ,r-mgcv)
@@ -9702,13 +9702,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.3.0")
+    (version "2.3.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0"))
+                "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9752,7 +9752,6 @@ Main-Class: ModularityOptimizer\n")))
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
-       ("r-gridextra" ,r-gridextra)
        ("r-hmisc" ,r-hmisc)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
@@ -9773,6 +9772,7 @@ Main-Class: ModularityOptimizer\n")))
        ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reshape2" ,r-reshape2)
+       ("r-reticulate" ,r-reticulate)
        ("r-rocr" ,r-rocr)
        ("r-rtsne" ,r-rtsne)
        ("r-sdmtools" ,r-sdmtools)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 96044e114a..fa71035796 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -36,7 +36,9 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages web))
 
 (define-public r-tidyverse
@@ -167,21 +169,18 @@ such as copy/paste from an R session.")
 (define-public r-callr
   (package
     (name "r-callr")
-    (version "2.0.3")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "callr" version))
        (sha256
         (base32
-         "1k3mflgn10hcvy74y4pbigpv74zb66fz1phfd3c8isqmn88xbxzi"))))
+         "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-assertthat" ,r-assertthat)
-       ("r-crayon" ,r-crayon)
-       ("r-debugme" ,r-debugme)
-       ("r-r6" ,r-r6)
-       ("r-testthat" ,r-testthat)))
+     `(("r-r6" ,r-r6)
+       ("r-processx" ,r-processx)))
     (home-page "https://github.com/r-lib/callr#readme")
     (synopsis "Call R from R")
     (description
@@ -316,14 +315,14 @@ and several other tools.")
 (define-public r-abbyyr
   (package
     (name "r-abbyyr")
-    (version "0.5.1")
+    (version "0.5.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abbyyR" version))
        (sha256
         (base32
-         "1s8zf18sh0s89vk3dl09fzrq50csmmfvmsanf5vfkv9n5lx6pklg"))))
+         "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx"))))
     (properties `((upstream-name . "abbyyR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -427,13 +426,13 @@ error stream.")
 (define-public r-rcpp
   (package
     (name "r-rcpp")
-    (version "0.12.16")
+    (version "0.12.17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Rcpp" version))
        (sha256
-        (base32 "1rm8hcy72p1jvxikvmkwg20pjqmvmfvqb45lfghmddp2adp67qfl"))))
+        (base32 "08xg8h3w25sdb3xr18g9pa0x8cirkdgljqapxmw56ss1j9fc89s2"))))
     (build-system r-build-system)
     (home-page "http://www.rcpp.org")
     (synopsis "Seamless R and C++ integration")
@@ -729,14 +728,14 @@ any subsequent lookup as it keeps the hash table in memory.")
 (define-public r-ff
   (package
     (name "r-ff")
-    (version "2.2-13")
+    (version "2.2-14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ff" version))
        (sha256
         (base32
-         "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
+         "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-bit" ,r-bit)))
     (home-page "http://ff.r-forge.r-project.org/")
@@ -843,23 +842,26 @@ package also provides a C++ API, that works with or without Rcpp.")
 (define-public r-ggally
   (package
     (name "r-ggally")
-    (version "1.3.2")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "GGally" version))
        (sha256
         (base32
-         "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l"))))
+         "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
     (properties `((upstream-name . "GGally")))
     (build-system r-build-system)
+    (inputs
+     `(("libressl" ,libressl)))
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
        ("r-gtable" ,r-gtable)
        ("r-plyr" ,r-plyr)
        ("r-progress" ,r-progress)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-reshape" ,r-reshape)))
+       ("r-reshape" ,r-reshape)
+       ("r-rlang" ,r-rlang)))
     (home-page "https://ggobi.github.io/ggally")
     (synopsis "Extension to ggplot2")
     (description
@@ -1077,13 +1079,13 @@ by Li, Brown, Huang, and Bickel")
 (define-public r-inline
   (package
     (name "r-inline")
-    (version "0.3.14")
+    (version "0.3.15")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "inline" version))
               (sha256
                (base32
-                "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
+                "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/inline")
     (synopsis "Functions to inline C, C++, Fortran function calls from R")
@@ -1122,14 +1124,14 @@ classes in the @code{stats4} package.")
 (define-public r-emdbook
   (package
     (name "r-emdbook")
-    (version "1.3.9")
+    (version "1.3.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emdbook" version))
        (sha256
         (base32
-         "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
+         "0880cx6rqm9vgd2zxnd2k0igfl80gy7ak15w36clwlzavab59hmv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bbmle" ,r-bbmle)
@@ -1234,14 +1236,14 @@ data).  Weighted versions of MLE, MME and QME are available.")
 (define-public r-energy
   (package
     (name "r-energy")
-    (version "1.7-2")
+    (version "1.7-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "energy" version))
        (sha256
         (base32
-         "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p"))))
+         "12skvlridfq4jd5mh0yxl79ps0zi2xnlh4hsdgxad0gm7qky8awd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-boot" ,r-boot)
@@ -1315,14 +1317,14 @@ samples.")
 (define-public r-cvst
   (package
     (name "r-cvst")
-    (version "0.2-1")
+    (version "0.2-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CVST" version))
        (sha256
         (base32
-         "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2"))))
+         "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
     (properties `((upstream-name . "CVST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1774,14 +1776,14 @@ for certain use cases.")
 (define-public r-ggrepel
   (package
     (name "r-ggrepel")
-    (version "0.7.0")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggrepel" version))
        (sha256
         (base32
-         "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618"))))
+         "1m3p84d6nh9mzzvxb82vgig3ngcvkz86rjwzl9a66ckdf5p611k3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -1841,23 +1843,98 @@ can be computed between character vectors while taking proper care of encoding
 or between integer vectors representing generic sequences.")
     (license license:gpl3+)))
 
+(define-public r-jomo
+  (package
+    (name "r-jomo")
+    (version "2.6-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jomo" version))
+       (sha256
+        (base32
+         "0zyqwa2y08asj9xqwnngh6da1b9cqcx8pzc9cxwrmgnxd5nnsjb7"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lme4" ,r-lme4)
+       ("r-survival" ,r-survival)))
+    (home-page "https://cran.r-project.org/web/packages/jomo/")
+    (synopsis "Multilevel Joint Modelling Multiple Imputation")
+    (description
+     "Similarly to Schafer's package pan, jomo is a package for multilevel
+joint modelling multiple imputation @url{Carpenter and Kenward (2013),
+http://doi.org/10.1002/9781119942283}.  Novel aspects of jomo are the
+possibility of handling binary and categorical data through latent normal
+variables, the option to use cluster-specific covariance matrices and to
+impute compatibly with the substantive model.")
+    (license license:gpl2)))
+
+(define-public r-pan
+  (package
+    (name "r-pan")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pan" version))
+       (sha256
+        (base32
+         "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/pan/")
+    (synopsis "Multiple imputation for multivariate panel or clustered data")
+    (description
+     "This package implements multiple imputation for multivariate panel or
+clustered data.")
+    (license license:gpl3)))
+
+(define-public r-mitml
+  (package
+    (name "r-mitml")
+    (version "0.3-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mitml" version))
+       (sha256
+        (base32
+         "1s888r9y2ri39b48h1iypps6lddqkqv3g31l2sjmi2pvyccfpkwb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-haven" ,r-haven)
+       ("r-jomo" ,r-jomo)
+       ("r-pan" ,r-pan)))
+    (home-page "https://cran.r-project.org/web/packages/mitml/")
+    (synopsis "Tools for multiple imputation in multilevel modeling")
+    (description
+     "This package provides tools for multiple imputation of missing data in
+multilevel modeling.  It includes a user-friendly interface to the packages
+pan and jomo, and several functions for visualization, data management and the
+analysis of multiply imputed data sets.")
+    (license license:gpl2+)))
+
 (define-public r-mice
   (package
     (name "r-mice")
-    (version "2.46.0")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "mice" version))
        (sha256
         (base32
-         "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax"))))
+         "1p8a5ham90iaak4w17114pdnw535r2l9sxr402yrkc4gbwfbpdlq"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lattice" ,r-lattice)
+     `(("r-broom" ,r-broom)
+       ("r-dplyr" ,r-dplyr)
+       ("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
+       ("r-mitml" ,r-mitml)
        ("r-nnet" ,r-nnet)
        ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
        ("r-rpart" ,r-rpart)
        ("r-survival" ,r-survival)))
     (home-page "https://cran.r-project.org/web/packages/mice/")
@@ -1923,14 +2000,14 @@ programming} (SQP) based solver).")
 (define-public r-hardyweinberg
   (package
     (name "r-hardyweinberg")
-    (version "1.5.9")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "HardyWeinberg" version))
        (sha256
         (base32
-         "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz"))))
+         "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz"))))
     (properties `((upstream-name . "HardyWeinberg")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1955,14 +2032,14 @@ acceptance regions, log-ratio plots and Q-Q plots.")
 (define-public r-sm
   (package
     (name "r-sm")
-    (version "2.2-5.4")
+    (version "2.2-5.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sm" version))
        (sha256
         (base32
-         "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9"))))
+         "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3"))))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
     (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
@@ -2146,14 +2223,14 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).")
 (define-public r-ica
   (package
     (name "r-ica")
-    (version "1.0-1")
+    (version "1.0-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ica" version))
        (sha256
         (base32
-         "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq"))))
+         "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/ica/")
     (synopsis "Independent component analysis")
@@ -2166,14 +2243,14 @@ of Eigenmatrices} (JADE).")
 (define-public r-dtw
   (package
     (name "r-dtw")
-    (version "1.18-1")
+    (version "1.20-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dtw" version))
        (sha256
         (base32
-         "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr"))))
+         "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-proxy" ,r-proxy)))
     (home-page "http://dtw.r-forge.r-project.org/")
@@ -2256,14 +2333,14 @@ plots in @code{ggplot2}.")
 (define-public r-ggjoy
   (package
     (name "r-ggjoy")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggjoy" version))
        (sha256
         (base32
-         "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb"))))
+         "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
@@ -2341,20 +2418,20 @@ constants, and control debugging of packages via environment variables.")
 (define-public r-processx
   (package
     (name "r-processx")
-    (version "2.0.0.1")
+    (version "3.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "processx" version))
        (sha256
         (base32
-         "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg"))))
+         "0wjr3cqwvnjxbvln25szffmkns5w0xysivdjr6chxap4nh515b0i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-crayon" ,r-crayon)
-       ("r-debugme" ,r-debugme)
-       ("r-r6" ,r-r6)))
+       ("r-r6" ,r-r6)
+       ("r-testthat" ,r-testthat)))
     (home-page "https://github.com/r-lib/processx3")
     (synopsis "Execute and control system processes")
     (description
@@ -2551,14 +2628,14 @@ packages maintained by Yihui Xie.")
 (define-public r-utf8
   (package
     (name "r-utf8")
-    (version "1.1.3")
+    (version "1.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "utf8" version))
        (sha256
         (base32
-         "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3"))))
+         "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
     (build-system r-build-system)
     (home-page "https://github.com/patperry/r-utf8")
     (synopsis "Unicode text processing")
@@ -2571,14 +2648,14 @@ display.")
 (define-public r-pillar
   (package
     (name "r-pillar")
-    (version "1.2.2")
+    (version "1.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pillar" version))
        (sha256
         (base32
-         "1kmqvny3rw4p5kgxz6mhqfpp7j3nnpp22dfai4kjrr2cfmj6wvb7"))))
+         "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -3263,18 +3340,19 @@ files.")
 (define-public r-shinyace
   (package
     (name "r-shinyace")
-    (version "0.2.1")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "shinyAce" version))
        (sha256
         (base32
-         "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9"))))
+         "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb"))))
     (properties `((upstream-name . "shinyAce")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-shiny" ,r-shiny)))
+     `(("r-shiny" ,r-shiny)
+       ("r-jsonlite" ,r-jsonlite)))
     (home-page "http://cran.r-project.org/web/packages/shinyAce")
     (synopsis "Ace editor bindings for Shiny")
     (description
@@ -3384,14 +3462,14 @@ It also includes interpolation functions.")
 (define-public r-psych
   (package
     (name "r-psych")
-    (version "1.8.3.3")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "psych" version))
        (sha256
         (base32
-         "1zhp8j81nkzd65168zdw9ylypb9n07ajan21x0wqcn8jdbg970sg"))))
+         "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
@@ -3766,19 +3844,41 @@ measuring the accuracy of ABC estimates, and to calculate the
 misclassification probabilities of different models.")
     (license license:gpl3+)))
 
+(define-public r-zip
+  (package
+    (name "r-zip")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "zip" version))
+       (sha256
+        (base32
+         "0rgr9pcdhdq3k8n29h2ircp3ri1ibhrx81gja1y7331v15xyrabg"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/gaborcsardi/zip")
+    (synopsis "Cross-platform Zip compression")
+    (description
+     "This package provides a cross-platform Zip compression library for R.
+It is a replacement for the @code{zip} function, that does not require any
+additional external tools on any platform.")
+    (license license:cc0)))
+
 (define-public r-openxlsx
   (package
     (name "r-openxlsx")
-    (version "4.0.17")
+    (version "4.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openxlsx" version))
        (sha256
         (base32
-         "1mq4lasp12kc30sxcsmz9gskd114l8s7z7wd6svv2nm8qllrhsqi"))))
+         "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb"))))
     (build-system r-build-system)
-    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-zip" ,r-zip)))
     (home-page "https://github.com/awalker89/openxlsx")
     (synopsis "Read, write and edit XLSX files")
     (description
@@ -4060,3 +4160,48 @@ bootstrap using a truncated geometric distribution, a comprehensive test for
 weak stationarity, column means by group, weighted biplots, and a heuristic to
 obtain a better initial configuration in non-metric MDS.")
     (license license:gpl2)))
+
+(define-public r-reticulate
+  (package
+    (name "r-reticulate")
+    (version "1.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "reticulate" version))
+       (sha256
+        (base32
+         "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy"))))
+    (build-system r-build-system)
+    (inputs `(("python" ,python)))
+    (propagated-inputs
+     `(("r-jsonlite" ,r-jsonlite)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/rstudio/reticulate")
+    (synopsis "R interface to Python")
+    (description
+     "This package provides an interface from R to Python modules, classes,
+and functions.  When calling into Python, R data types are automatically
+converted to their equivalent Python types.  When values are returned from
+Python to R they are converted back to R types.")
+    (license license:asl2.0)))
+
+(define-public r-bibtex
+  (package
+    (name "r-bibtex")
+    (version "0.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bibtex" version))
+       (sha256
+        (base32
+         "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-stringr" ,r-stringr)))
+    (home-page "https://github.com/romainfrancois/bibtex")
+    (synopsis "Bibtex parser")
+    (description "This package provides a utility for R to parse a bibtex
+file.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 6205df361f..fcf6030752 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -28,7 +28,7 @@
 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Pierre Langlois <pierre.langlois@gmx.com>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Kristofer Buffington <kristoferbuffington@gmail.com>
 ;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
@@ -2061,14 +2061,14 @@ and web services platform functionality.")
 (define-public r-rmysql
   (package
     (name "r-rmysql")
-    (version "0.10.14")
+    (version "0.10.15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RMySQL" version))
        (sha256
         (base32
-         "01891kn263b02y6addgpy3gn5axg7m10bqbqv7dg9yx9k85am590"))))
+         "0bmc7w5fnkjaf333sgc0hskiy332m9gmfaxg0yzkjxscpizdw43n"))))
     (properties `((upstream-name . "RMySQL")))
     (build-system r-build-system)
     (native-inputs
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 4100db5d8a..8c12141260 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -404,52 +404,25 @@ It has been modified to remove all non-free binary blobs.")
                     %linux-compatible-systems
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.46")
-(define %linux-libre-4.14-hash "17imkhqk3m3djdj0m5h4lqs9cfdh9zq1cz83q8ldyald56rbn622")
+(define %linux-libre-4.14-version "4.14.47")
+(define %linux-libre-4.14-hash "1hm1vk6cdrwr971g5rcbq425fadn49580xa27zp1h6jz40n119wd")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version
                     %linux-libre-4.14-hash
                     '("x86_64-linux" "i686-linux" "armhf-linux")
-                    #:patches
-                    (list %boot-logo-patch
-                          (origin
-                            ;; The sole fix in the 4.14.47 release.
-                            (method url-fetch)
-                            (uri "https://git.kernel.org/pub/scm/linux/kernel/\
-git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719")
-                            (sha256
-                             (base32 "1hk1qd6v97zf8an3zww60zhsah1wwax22b3bpdzmfjhhbndyram9"))))
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.104"
-                    "0b6y24vfsjhiv7qq7xqx7h9krc81c49dqh0189nm1lhfwciyir57"
+  (make-linux-libre "4.9.105"
+                    "0kzznalr69c3z63y4gs38zs6cb0jmn41ggvz4i1gp2sqpmjm6ybb"
                     %intel-compatible-systems
-                    #:patches
-                    (list %boot-logo-patch
-                          (origin
-                            ;; The sole fix in the 4.9.105 release.
-                            (method url-fetch)
-                            (uri "https://git.kernel.org/pub/scm/linux/kernel/\
-git/stable/linux-stable.git/patch/?id=98d69fb3b175855cdd4c37d41a4b477a0860b1a0")
-                            (sha256
-                             (base32 "1r52fr0w94fgw7nfxrysjk0mljlnqwqsnl0cp84c1sly466i79dv"))))
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.134"
-                    "137mklzyv56yhc48l5h5i0h01gm1q40x2a8nk51lwhbjv592xr8x"
+  (make-linux-libre "4.4.135"
+                    "0jdf5yx8b6q4zw7q9k8vv0ky8wlvclr9qz70wgrrvmm5dh1662j9"
                     %intel-compatible-systems
-                    #:patches
-                    (list %boot-logo-patch
-                          (origin
-                            ;; The sole fix in the 4.4.135 release.
-                            (method url-fetch)
-                            (uri "https://git.kernel.org/pub/scm/linux/kernel/\
-git/stable/linux-stable.git/patch/?id=393e9b3c30d571c2f655aa24b0dee5be9ce249b5")
-                            (sha256
-                             (base32 "02wk036v525qwqs42ndqqj4mv8xfkpavibfg5ns6hkg2wc5a1jid"))))
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.1
@@ -470,15 +443,6 @@ git/stable/linux-stable.git/patch/?id=393e9b3c30d571c2f655aa24b0dee5be9ce249b5")
                     %linux-libre-4.14-hash
                     '("armhf-linux")
                     #:defconfig "multi_v7_defconfig"
-                    #:patches
-                    (list %boot-logo-patch
-                          (origin
-                            ;; The sole fix in the 4.14.47 release.
-                            (method url-fetch)
-                            (uri "https://git.kernel.org/pub/scm/linux/kernel/\
-git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719")
-                            (sha256
-                             (base32 "1hk1qd6v97zf8an3zww60zhsah1wwax22b3bpdzmfjhhbndyram9"))))
                     #:extra-version "arm-generic"))
 
 (define-public linux-libre-arm-omap2plus
@@ -493,15 +457,6 @@ git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719")
                     %linux-libre-4.14-hash
                     '("armhf-linux")
                     #:defconfig "omap2plus_defconfig"
-                    #:patches
-                    (list %boot-logo-patch
-                          (origin
-                            ;; The sole fix in the 4.14.47 release.
-                            (method url-fetch)
-                            (uri "https://git.kernel.org/pub/scm/linux/kernel/\
-git/stable/linux-stable.git/patch/?id=3e496be2038a100fc53627238fe120dc4c948719")
-                            (sha256
-                             (base32 "1hk1qd6v97zf8an3zww60zhsah1wwax22b3bpdzmfjhhbndyram9"))))
                     #:extra-version "arm-omap2plus"))
 
 
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e6f7a18346..15e4d45749 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -592,14 +592,14 @@ geometric models.")
 (define-public r-kernlab
   (package
     (name "r-kernlab")
-    (version "0.9-25")
+    (version "0.9-26")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kernlab" version))
        (sha256
         (base32
-         "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr"))))
+         "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/kernlab")
     (synopsis "Kernel-based machine learning tools")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index eb21fcd303..434f26dbe3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -649,14 +649,14 @@ curves, Cox models, and parametric accelerated failure time models.")
 (define-public r-bit
   (package
     (name "r-bit")
-    (version "1.1-13")
+    (version "1.1-14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bit" version))
        (sha256
         (base32
-         "1yhpwvfkxpb773h8khjzyamqxl2jn7pjjmxjfawq626hhds8fsh6"))))
+         "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
     (build-system r-build-system)
     (home-page "http://ff.r-forge.r-project.org")
     (synopsis "Class for vectors of 1-bit booleans")
@@ -762,14 +762,14 @@ non-estimable cases correctly.")
 (define-public r-pheatmap
   (package
     (name "r-pheatmap")
-    (version "1.0.8")
+    (version "1.0.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pheatmap" version))
        (sha256
         (base32
-         "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
+         "1jzxs5hwbz3r0z2pp09i7fd14sndxnrbm3zibaac3kny4nzydzf7"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-gtable" ,r-gtable)
@@ -1386,19 +1386,20 @@ generation in R using Literate Programming techniques.")
 (define-public r-knitrbootstrap
   (package
     (name "r-knitrbootstrap")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "knitrBootstrap" version))
        (sha256
         (base32
-         "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p"))))
+         "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
     (properties `((upstream-name . "knitrBootstrap")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-knitr" ,r-knitr)
-       ("r-rmarkdown" ,r-rmarkdown)))
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-markdown" ,r-markdown)))
     (home-page "https://github.com/jimhester/knitrBootstrap")
     (synopsis "Knitr bootstrap framework")
     (description
@@ -1561,13 +1562,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.2.0")
+    (version "0.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "0f87fhw5pj6s2zjdxnpnd7pwn78czdz71b0xhm5adqg1p38sfwj8"))))
+                "0ghg66vyri8nck4p6kl1nh47qdppbmxvjiyms69nhvipphk4ifpj"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1753,13 +1754,13 @@ times.")
 (define-public r-data-table
   (package
     (name "r-data-table")
-    (version "1.11.0")
+    (version "1.11.4")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "data.table" version))
               (sha256
                (base32
-                "0n1p35c9sni2272ykxsfbsy7xma62br7v668a5bvc37g75xf10df"))))
+                "1mc1drqj5i5ar2za3nkh5j70y37s7z7xwqri2r2b72zkqggg3k7x"))))
     (build-system r-build-system)
     (home-page "https://github.com/Rdatatable/data.table/wiki")
     (synopsis "Enhanced version of data.frame R object")
@@ -2438,13 +2439,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-1")
+    (version "3.7-2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "16p6d2dna6dah7rg2xknhyy65jkfn0zzivx1nnfxhd4f5q0v87w2"))))
+                "0hx3xv94gzlyy7ny5k4mzs7w1798h1zka175m5bkzc524493cm88"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -2835,13 +2836,13 @@ plotted and compared with the asymptotic curve.")
 (define-public r-lambda-r
   (package
     (name "r-lambda-r")
-    (version "1.2.2")
+    (version "1.2.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "lambda.r" version))
               (sha256
                (base32
-                "05cfaq9dbgdnmmj3d6ggmsw300qgiw8k7f6h6k0ylv63cf3v6pkq"))))
+                "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
     (properties `((upstream-name . "lambda.r")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3164,20 +3165,24 @@ path-wise fashion.")
 (define-public r-pkgmaker
   (package
     (name "r-pkgmaker")
-    (version "0.22")
+    (version "0.27")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgmaker" version))
        (sha256
         (base32
-         "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
+         "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-codetools" ,r-codetools)
+     `(("r-bibtex" ,r-bibtex)
+       ("r-codetools" ,r-codetools)
        ("r-digest" ,r-digest)
+       ("r-magrittr" ,r-magrittr)
        ("r-registry" ,r-registry)
+       ("r-stringi" ,r-stringi)
        ("r-stringr" ,r-stringr)
+       ("r-withr" ,r-withr)
        ("r-xtable" ,r-xtable)))
     (home-page "https://renozao.github.io/pkgmaker")
     (synopsis "Package development utilities")
@@ -3209,14 +3214,14 @@ package registries.")
 (define-public r-rngtools
   (package
     (name "r-rngtools")
-    (version "1.2.4")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngtools" version))
        (sha256
         (base32
-         "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
+         "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -3301,14 +3306,14 @@ bigmemory and synchronicity packages.")
 (define-public r-synchronicity
   (package
     (name "r-synchronicity")
-    (version "1.3.2")
+    (version "1.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "synchronicity" version))
        (sha256
         (base32
-         "1idrjzl7nkamf1ip55s6qcf64s63xs9j8z9jv3r89p6r5lw7k5mv"))))
+         "1km5hx82gy71m5nc6pkcksv0dn32fylhg2axpdsnarrxva14mgdg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -3638,14 +3643,14 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "0.8.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "1qjpbj1a2vw6nw4hdb6fgassnrxrdpqwf9a8i6wqnv3wxvjb6zqb"))))
+         "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -3694,14 +3699,14 @@ It uses and relies on grid graphics and formal (S4) classes and methods.")
 (define-public r-purrr
   (package
     (name "r-purrr")
-    (version "0.2.4")
+    (version "0.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "purrr" version))
        (sha256
         (base32
-         "0wgbnbrqncjpggg8f9bdpcd1gy351s5f0az5k8lc55cvs9lhz3gd"))))
+         "0dc53zzan3km2l9lzxjixcv6yn7dhw2ppmz8qf2awhak7x2qm9m4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-tibble" ,r-tibble)
@@ -3960,14 +3965,14 @@ conversion of R objects to LaTeX code, and recoding variables.")
 (define-public r-runit
   (package
     (name "r-runit")
-    (version "0.4.31")
+    (version "0.4.32")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RUnit" version))
        (sha256
         (base32
-         "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
+         "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
     (properties `((upstream-name . "RUnit")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/RUnit")
@@ -4328,13 +4333,13 @@ data at that region, and avoids over-plotting.")
 (define-public r-ggthemes
   (package
     (name "r-ggthemes")
-    (version "3.4.2")
+    (version "3.5.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggthemes" version))
               (sha256
                (base32
-                "0i7ygpizs00acizixc29bhbrci523ys7vzxbii9b3bcmfa3pj7i3"))))
+                "0drbzzb4i5jq1579fx1wmgh87ybnswjn7srak2l8g771ip49xwb8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
@@ -4746,14 +4751,14 @@ analysis} (PCA) by projection pursuit.")
 (define-public r-rrcov
   (package
     (name "r-rrcov")
-    (version "1.4-3")
+    (version "1.4-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rrcov" version))
        (sha256
         (base32
-         "0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq"))))
+         "0wn5h8vi0zyk5ah898m37ysz4kiih6y792nb9zdvhvd8r07f0sc5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
@@ -5021,14 +5026,14 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.35")
+    (version "5.36")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
         (base32
-         "18f3qxv1j1bqmq55hzssz8mnp5ww4flhy80rm2v1rk0mmg9paz7m"))))
+         "023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -5181,14 +5186,14 @@ to Applied regression, Second Edition, Sage, 2011.")
 (define-public r-caret
   (package
     (name "r-caret")
-    (version "6.0-79")
+    (version "6.0-80")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "caret" version))
        (sha256
         (base32
-         "1i6sjw279g6mj83vz5gv99x0nljcbpy7v0nbl72lmd80sf7rjshl"))))
+         "0xhdhazzfh0hiqv2hgxglj9ffd2p4ls8acqn2sjn0ndx6158f187"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreach" ,r-foreach)
@@ -5302,15 +5307,16 @@ multivariate case.")
 (define-public r-tclust
   (package
     (name "r-tclust")
-    (version "1.3-1")
+    (version "1.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tclust" version))
        (sha256
         (base32
-         "1li62wynv81kb17fx7nk63a26qlb78l8fdf63in8yzcl7fkpji7y"))))
+         "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
     (build-system r-build-system)
+    ;; These are all suggested packages, not build dependencies.
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
        ("r-mclust" ,r-mclust)
@@ -5327,14 +5333,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
 (define-public r-ranger
   (package
     (name "r-ranger")
-    (version "0.9.0")
+    (version "0.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ranger" version))
        (sha256
         (base32
-         "1pilj5pxl8jl0gsy9vsyqxqdqfcxzvphbgvrlp4hf7r9mrfw9v0p"))))
+         "1yl833cm2jpfy9j7zchkq4mm5x1av70w89zrhpwdn8nq2npxxzf0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -5546,14 +5552,14 @@ parameters.")
 (define-public r-directlabels
   (package
     (name "r-directlabels")
-    (version "2017.03.31")
+    (version "2018.05.22")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "directlabels" version))
        (sha256
         (base32
-         "01ahw0c56mnzwl611s8hnghicww4c4dgf5v2wv6bl1s1pramw9pr"))))
+         "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-quadprog" ,r-quadprog)))
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index c5547ec2df..d9ce68ba51 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3824,21 +3824,19 @@ in systems and applications.")
 (define-public r-servr
   (package
     (name "r-servr")
-    (version "0.9")
+    (version "0.10")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "servr" version))
               (sha256
                (base32
-                "0bs0i5mjfzxfshqz8i30nhn7kvgwly4fqn5bfq6dqfdrn7biai2x"))))
+                "0yz3igqsiyqnjj1ngh199zicg3spx4kbmvl0wc8i8xahk6l9g06v"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-httpuv" ,r-httpuv)
        ("r-jsonlite" ,r-jsonlite)
        ("r-mime" ,r-mime)
        ("r-xfun" ,r-xfun)))
-    (native-inputs
-     `(("r-rcpp" ,r-rcpp)))
     (home-page "https://github.com/yihui/servr")
     (synopsis "Simple HTTP server to serve static files or dynamic documents")
     (description
@@ -3907,14 +3905,14 @@ applications.")
 (define-public r-htmltable
   (package
     (name "r-htmltable")
-    (version "1.11.2")
+    (version "1.12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "htmlTable" version))
        (sha256
         (base32
-         "1lbpi0kkk8b41w10scmlf27dg5azcv51a4q3p5bpqyphrnqp78k4"))))
+         "1n5136vb7mi4rxl5jgwdmdhn4mwv2pcqyw2mrj406ih4hy6hpxa2"))))
     (properties `((upstream-name . "htmlTable")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3998,14 +3996,14 @@ objects in HTML format.")
 (define-public r-rjson
   (package
     (name "r-rjson")
-    (version "0.2.18")
+    (version "0.2.19")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rjson" version))
        (sha256
         (base32
-         "18myz05ana8zlyqxi6i4xjs5vmafxln8459ab3ws5kk59c1ardfn"))))
+         "1g29vp3gfbh73a5br68jydsrigia4vnr5avc84avgwl6353749jw"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/rjson")
     (synopsis "JSON library for R")
@@ -5322,16 +5320,17 @@ snippets on @url{https://commandlinefu.com}.")
 (define-public r-shiny
   (package
     (name "r-shiny")
-    (version "1.0.3")
+    (version "1.1.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/rstudio/shiny/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rstudio/shiny.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "0z2v2s4hd44mvzjn7r70549kdzkrrch9nxhp27r6x2cy6micizm3"))))
+         "041q2gzvzs13syfhbirmkik96asdji8dxnnbs63j7v1ks97hrvvz"))))
     (build-system r-build-system)
     (arguments
      `(#:modules ((guix build r-build-system)
@@ -5396,7 +5395,8 @@ snippets on @url{https://commandlinefu.com}.")
                               "jquery.min.js")))))
              #t)))))
     (propagated-inputs
-     `(("r-httpuv" ,r-httpuv)
+     `(("r-crayon" ,r-crayon)
+       ("r-httpuv" ,r-httpuv)
        ("r-mime" ,r-mime)
        ("r-jsonlite" ,r-jsonlite)
        ("r-xtable" ,r-xtable)