From d2dde99e99afb041132b903fbddb0c3a7387f193 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 30 May 2018 22:46:12 +0300
Subject: [PATCH 01/60] gnu: mariadb: Update to 10.1.33.

* gnu/packages/databases.scm (mariadb): Update to 10.1.33.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 51b0d7e253..83d5909538 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -627,7 +627,7 @@ (define-public mysql
 (define-public mariadb
   (package
     (name "mariadb")
-    (version "10.1.29")
+    (version "10.1.33")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://downloads.mariadb.org/f/"
@@ -635,7 +635,7 @@ (define-public mariadb
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1m3ya6c3snnsyscd0waklayqfv0vhws52iizv2j5masj5xhdbfvk"))))
+                "0bax748j4srsyhw5cs5jvwigndh0zwmf4r2cjvhja31ckx8jqccl"))))
     (build-system cmake-build-system)
     (arguments
      '(#:configure-flags

From 2aab213e36aa35637d5071f9f676301032f9d911 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 31 May 2018 04:14:57 -0400
Subject: [PATCH 02/60] gnu: linux-libre@4.4: Update to 4.4.135.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.135.
Remove patch.
---
 gnu/packages/linux.scm | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 98e92a62f8..4e2a6a1680 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -438,18 +438,9 @@ (define-public linux-libre-4.9
                     #: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

From 55b68174aa44e38eb396e83994edcfcfcdf3b234 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 31 May 2018 04:16:05 -0400
Subject: [PATCH 03/60] gnu: linux-libre@4.9: Update to 4.9.105.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.105.
Remove patch.
---
 gnu/packages/linux.scm | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 4e2a6a1680..b218ccbceb 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -423,18 +423,9 @@ (define-public linux-libre-4.14
                     #: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

From 966e9575a3a110d14f37acb43b5f605737a7a4a3 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 31 May 2018 04:17:22 -0400
Subject: [PATCH 04/60] gnu: linux-libre@4.14: Update to 4.14.47.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.47.
(%linux-libre-4.14-hash): Update hash.
(linux-libre-arm-generic-4.14, linux-libre-arm-omap2plus-4.14)
(linux-libre-4.14): Remove patch.
---
 gnu/packages/linux.scm | 31 ++-----------------------------
 1 file changed, 2 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b218ccbceb..da994d8ac9 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -404,22 +404,13 @@ (define-public linux-libre
                     %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
@@ -452,15 +443,6 @@ (define-public linux-libre-arm-generic-4.14
                     %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
@@ -475,15 +457,6 @@ (define-public linux-libre-arm-omap2plus-4.14
                     %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"))
 
 

From 3ca317359ce0c99dfaecbf051867fcef19da7953 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 09:19:08 +0200
Subject: [PATCH 05/60] gnu: r-vegan: Update to 2.5-2.

* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-2.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3168291f48..d1db06f398 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6119,20 +6119,20 @@ (define-public r-centipede
 (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)

From fe1495e35c0304f45f9114e388468dcf5f640c39 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:25:07 +0200
Subject: [PATCH 06/60] gnu: Add r-jomo.

* gnu/packages/cran.scm (r-jomo): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 96044e114a..39114c7a16 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1841,6 +1841,32 @@ (define-public r-stringdist
 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-mice
   (package
     (name "r-mice")

From 03e718fbb1edeb242fea07d8b7c8485c33a4afce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:25:22 +0200
Subject: [PATCH 07/60] gnu: Add r-pan.

* gnu/packages/cran.scm (r-pan): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 39114c7a16..55487af358 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1867,6 +1867,26 @@ (define-public r-jomo
 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-mice
   (package
     (name "r-mice")

From 84e7147ae36e582f1c7b0d229697cd2ae63184b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:25:34 +0200
Subject: [PATCH 08/60] gnu: Add r-mitml.

* gnu/packages/cran.scm (r-mitml): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 55487af358..2bab856bd2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1887,6 +1887,31 @@ (define-public r-pan
 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")

From d182828f53f15bfd13d38aaa5dc04486df8ad431 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:25:53 +0200
Subject: [PATCH 09/60] gnu: Add r-zip.

* gnu/packages/cran.scm (r-zip): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2bab856bd2..5263e89888 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3837,6 +3837,26 @@ (define-public r-abc
 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")

From 9f56ceecf35fc13baa08b5f95fc2a6ad9e0d3313 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:26:09 +0200
Subject: [PATCH 10/60] gnu: Add r-reticulate.

* gnu/packages/cran.scm (r-reticulate): New variable.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5263e89888..39b9a64660 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -36,6 +36,7 @@ (define-module (gnu packages cran)
   #: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 web))
 
@@ -4151,3 +4152,29 @@ (define-public r-analytics
 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)))

From 11de8673d18418c580d9264f9efb2cab98115dc9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:26:25 +0200
Subject: [PATCH 11/60] gnu: Add r-bibtex.

* gnu/packages/cran.scm (r-bibtex): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 39b9a64660..0567195ba5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4178,3 +4178,22 @@ (define-public r-reticulate
 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+)))

From 5479e3e63976b0b4a46a9cdff7e1d16c1d4acc0f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:26:55 +0200
Subject: [PATCH 12/60] gnu: r-abbyyr: Update to 0.5.4.

* gnu/packages/cran.scm (r-abbyyr): Update to 0.5.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0567195ba5..58c42c29d3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -317,14 +317,14 @@ (define-public r-ape
 (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

From c81497b1416fbca75f19bf7df7ac8f36af62e1d2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:27:09 +0200
Subject: [PATCH 13/60] gnu: r-rcpp: Update to 0.12.17.

* gnu/packages/cran.scm (r-rcpp): Update to 0.12.17.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 58c42c29d3..b97408f8a4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -428,13 +428,13 @@ (define-public r-plogr
 (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")

From 207c497e1491d9e8b3e59866f274fb6409b966c3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:27:21 +0200
Subject: [PATCH 14/60] gnu: r-ff: Update to 2.2-14.

* gnu/packages/cran.scm (r-ff): Update to 2.2-14.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b97408f8a4..9c17c8d635 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -730,14 +730,14 @@ (define-public r-fastmatch
 (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/")

From 0acbf8bbb7f698141d5dd970b1b144fdc691b712 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:27:38 +0200
Subject: [PATCH 15/60] gnu: r-inline: Update to 0.3.15.

* gnu/packages/cran.scm (r-inline): Update to 0.3.15.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9c17c8d635..850039984e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1078,13 +1078,13 @@ (define-public r-idr
 (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")

From 90f1ecb9394120de6e1e2c61c2685e68206de342 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:27:50 +0200
Subject: [PATCH 16/60] gnu: r-emdbook: Update to 1.3.10.

* gnu/packages/cran.scm (r-emdbook): Update to 1.3.10.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 850039984e..24099e1dc8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1123,14 +1123,14 @@ (define-public r-bbmle
 (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)

From 975ea10d6f15f438e5fb55cf08d185ed45bc8700 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:28:07 +0200
Subject: [PATCH 17/60] gnu: r-energy: Update to 1.7-4.

* gnu/packages/cran.scm (r-energy): Update to 1.7-4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 24099e1dc8..030fcea303 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1235,14 +1235,14 @@ (define-public r-fitdistrplus
 (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)

From b13b56743b7419e2b5358b85e16f2379bc20aef8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:28:19 +0200
Subject: [PATCH 18/60] gnu: r-cvst: Update to 0.2-2.

* gnu/packages/cran.scm (r-cvst): Update to 0.2-2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 030fcea303..40f4fa58c9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1316,14 +1316,14 @@ (define-public r-ksamples
 (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

From 0759d87dfc5fd707af437df7f63b21d2b66c6e92 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:28:32 +0200
Subject: [PATCH 19/60] gnu: r-ggrepel: Update to 0.8.0.

* gnu/packages/cran.scm (r-ggrepel): Update to 0.8.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 40f4fa58c9..0f2cb31e32 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1775,14 +1775,14 @@ (define-public r-pdist
 (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)

From da5cca36b7ff72dc3c2b5e7c79d388c7c0ac3381 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:28:46 +0200
Subject: [PATCH 20/60] gnu: r-hardyweinberg: Update to 1.6.1.

* gnu/packages/cran.scm (r-hardyweinberg): Update to 1.6.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0f2cb31e32..9207a3ae62 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1995,14 +1995,14 @@ (define-public r-rsolnp
 (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

From 1e31e8bc7449b27876be4c0e6aecec96cd35ab30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:28:57 +0200
Subject: [PATCH 21/60] gnu: r-sm: Update to 2.2-5.5.

* gnu/packages/cran.scm (r-sm): Update to 2.2-5.5.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9207a3ae62..a6b6af1679 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2027,14 +2027,14 @@ (define-public r-hardyweinberg
 (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/")

From fabf09934b9d6de9bfe8e97547491b4a7e57cbdb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:29:09 +0200
Subject: [PATCH 22/60] gnu: r-ica: Update to 1.0-2.

* gnu/packages/cran.scm (r-ica): Update to 1.0-2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a6b6af1679..67bec4323e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2218,14 +2218,14 @@ (define-public r-vcd
 (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")

From cda93e8399969237e7071a8d47c27e1e3befca36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:29:22 +0200
Subject: [PATCH 23/60] gnu: r-dtw: Update to 1.20-1.

* gnu/packages/cran.scm (r-dtw): Update to 1.20-1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 67bec4323e..dcaeed92ae 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2238,14 +2238,14 @@ (define-public r-ica
 (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/")

From c36745cf95213f59e4277a4791af83f40e067e30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:29:34 +0200
Subject: [PATCH 24/60] gnu: r-ggjoy: Update to 0.4.1.

* gnu/packages/cran.scm (r-ggjoy): Update to 0.4.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index dcaeed92ae..164b7f722e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2328,14 +2328,14 @@ (define-public r-ggridges
 (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)

From 65ea783f6c11ce5e20ea6bfc46e0dac2500e3a31 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:29:48 +0200
Subject: [PATCH 25/60] gnu: r-utf8: Update to 1.1.4.

* gnu/packages/cran.scm (r-utf8): Update to 1.1.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 164b7f722e..9ff19fee67 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2623,14 +2623,14 @@ (define-public r-xfun
 (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")

From aadb9ee6df66c819b2adb41df8ff1112f5699ea0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:30:06 +0200
Subject: [PATCH 26/60] gnu: r-pillar: Update to 1.2.3.

* gnu/packages/cran.scm (r-pillar): Update to 1.2.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9ff19fee67..9403175775 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2643,14 +2643,14 @@ (define-public r-utf8
 (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)

From 13079c143bdd9c96e76352889ec76c3c158a0e05 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:30:17 +0200
Subject: [PATCH 27/60] gnu: r-psych: Update to 1.8.4.

* gnu/packages/cran.scm (r-psych): Update to 1.8.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 9403175775..f6012fd91f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3456,14 +3456,14 @@ (define-public r-signal
 (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)

From 9944399ae3f7730dc75bb28be24cb0ad0d984aa3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:30:44 +0200
Subject: [PATCH 28/60] gnu: r-ggally: Update to 1.4.0.

* gnu/packages/cran.scm (r-ggally): Update to 1.4.0.
[inputs]: Add libressl.
[propagated-inputs]: Add r-rlang.
---
 gnu/packages/cran.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f6012fd91f..7ca2f11d41 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -38,6 +38,7 @@ (define-module (gnu packages cran)
   #: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
@@ -844,23 +845,26 @@ (define-public r-progress
 (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

From a80606308a1b66de792da2d35e66cfb455c90206 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:31:13 +0200
Subject: [PATCH 29/60] gnu: r-processx: Update to 3.1.0.

* gnu/packages/cran.scm (r-processx): Update to 3.1.0.
[propagated-inputs]: Remove r-debugme; add r-testthat.
---
 gnu/packages/cran.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7ca2f11d41..e5e5af839e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2417,20 +2417,20 @@ (define-public r-debugme
 (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

From e86d3cc5018833352a2d7a1a820e8e356b4c53f7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:31:42 +0200
Subject: [PATCH 30/60] gnu: r-shinyace: Update to 0.3.1.

* gnu/packages/cran.scm (r-shinyace): Update to 0.3.1.
[propagated-inputs]: Add r-jsonlite.
---
 gnu/packages/cran.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index e5e5af839e..1be84a9bc1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3339,18 +3339,19 @@ (define-public r-import
 (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

From a8b4677b7c365ce3e7a3a3d37e957500da2a4950 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:32:03 +0200
Subject: [PATCH 31/60] gnu: r-openxlsx: Update to 4.1.0.

* gnu/packages/cran.scm (r-openxlsx): Update to 4.1.0.
[propagated-inputs]: Add r-zip.
---
 gnu/packages/cran.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1be84a9bc1..8758515e06 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -3866,16 +3866,18 @@ (define-public r-zip
 (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

From 6034a62a1b11f8dd63ade6e0dac2e32727150ab0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:32:25 +0200
Subject: [PATCH 32/60] gnu: r-callr: Update to 2.0.4.

* gnu/packages/cran.scm (r-callr): Update to 2.0.4.
[propagated-inputs]: Add r-processx; remove r-assertthat, r-crayon, r-debugme,
and r-testthat.
---
 gnu/packages/cran.scm | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8758515e06..47b1f0afd3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -169,21 +169,18 @@ (define-public r-reprex
 (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

From aea3be250c89c80704750498545c9dd7398da748 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:33:07 +0200
Subject: [PATCH 33/60] gnu: r-mice: Update to 3.0.0.

* gnu/packages/cran.scm (r-mice): Update to 3.0.0.
[propagated-inputs]: Add r-broom, r-dplyr, r-mitml, and r-rlang.
---
 gnu/packages/cran.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 47b1f0afd3..fa71035796 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1917,20 +1917,24 @@ (define-public r-mitml
 (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/")

From ad016826c989b751d25a6c7942e515e9e062058a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:33:46 +0200
Subject: [PATCH 34/60] gnu: r-rmysql: Update to 0.10.15.

* gnu/packages/databases.scm (r-rmysql): Update to 0.10.15.
---
 gnu/packages/databases.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 83d5909538..fd5c1d73bd 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>
@@ -2063,14 +2063,14 @@ (define-public virtuoso-ose
 (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

From 3c441be0f30246e37436ed194028d2c72adc5447 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:34:06 +0200
Subject: [PATCH 35/60] gnu: r-kernlab: Update to 0.9-26.

* gnu/packages/machine-learning.scm (r-kernlab): Update to 0.9-26.
---
 gnu/packages/machine-learning.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e135ee0ee0..86853f039d 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>
@@ -591,14 +591,14 @@ (define-public r-adaptivesparsity
 (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")

From 99b225f3ebe815ec95584ad64136d81b1e16ce96 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:34:21 +0200
Subject: [PATCH 36/60] gnu: r-bit: Update to 1.1-14.

* gnu/packages/statistics.scm (r-bit): Update to 1.1-14.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e333d7558f..9e45c48bf3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -649,14 +649,14 @@ (define-public r
 (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")

From 22cdc16fa410c4d4a9279e3d16e4de5b1961f298 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:34:29 +0200
Subject: [PATCH 37/60] gnu: r-pheatmap: Update to 1.0.10.

* gnu/packages/statistics.scm (r-pheatmap): Update to 1.0.10.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 9e45c48bf3..674e4e9936 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -762,14 +762,14 @@ (define-public r-estimability
 (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)

From 624283a1072c628ab9e0ac6f9c3a0d03aaf36391 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:34:39 +0200
Subject: [PATCH 38/60] gnu: r-knitrbootstrap: Update to 1.0.2.

* gnu/packages/statistics.scm (r-knitrbootstrap): Update to 1.0.2.
[propagated-inputs]: Add r-markdown.
---
 gnu/packages/statistics.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 674e4e9936..410747be6c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1386,19 +1386,20 @@ (define-public r-knitr
 (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

From 2d7758c1d67fe8ff2fd30f115ece76060131b5a4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:34:56 +0200
Subject: [PATCH 39/60] gnu: r-rlang: Update to 0.2.1.

* gnu/packages/statistics.scm (r-rlang): Update to 0.2.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 410747be6c..09d6ee8693 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1562,13 +1562,13 @@ (define-public r-r6
 (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")

From 1ce6be5ee2a8a254be958ce49c1d38d0342913d9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:35:06 +0200
Subject: [PATCH 40/60] gnu: r-data-table: Update to 1.11.4.

* gnu/packages/statistics.scm (r-data-table): Update to 1.11.4.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 09d6ee8693..4487e8a395 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1754,13 +1754,13 @@ (define-public r-chron
 (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")

From a52bb97a799c28de77e57e003f42f4c196f610a1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:35:16 +0200
Subject: [PATCH 41/60] gnu: r-plotrix: Update to 3.7-2.

* gnu/packages/statistics.scm (r-plotrix): Update to 3.7-2.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4487e8a395..8d6da4751e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2439,13 +2439,13 @@ (define-public r-readr
 (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")

From b4ca0076bde81e53b2706ae0d0997ef728fa4ce0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:35:30 +0200
Subject: [PATCH 42/60] gnu: r-lambda-r: Update to 1.2.3.

* gnu/packages/statistics.scm (r-lambda-r): Update to 1.2.3.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8d6da4751e..64b71b6dd2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2836,13 +2836,13 @@ (define-public r-xnomial
 (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

From 3a6051659d7a944df68d560a1974db115ac43542 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:35:42 +0200
Subject: [PATCH 43/60] gnu: r-pkgmaker: Update to 0.27.

* gnu/packages/statistics.scm (r-pkgmaker): Update to 0.27.
[propagated-inputs]: Add r-bibtex, r-magrittr, r-stringi, and r-withr.
---
 gnu/packages/statistics.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 64b71b6dd2..5b5ebbe0f3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3165,20 +3165,24 @@ (define-public r-glmnet
 (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")

From 7da0790e2a4020aad60ba69f7e1059bbe3ed11a7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:36:13 +0200
Subject: [PATCH 44/60] gnu: r-rngtools: Update to 1.3.1.

* gnu/packages/statistics.scm (r-rngtools): Update to 1.3.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5b5ebbe0f3..a522bf6b92 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3214,14 +3214,14 @@ (define-public r-registry
 (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)

From 1957c20e0c824a39d6a1272757d076b6fc1f8c79 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:36:22 +0200
Subject: [PATCH 45/60] gnu: r-synchronicity: Update to 1.3.4.

* gnu/packages/statistics.scm (r-synchronicity): Update to 1.3.4.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index a522bf6b92..d741c77a23 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3306,14 +3306,14 @@ (define-public r-bigmemory-sri
 (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)

From e94d827440dcbb858f221e9ed5749673d0bff068 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:36:32 +0200
Subject: [PATCH 46/60] gnu: r-tidyr: Update to 0.8.1.

* gnu/packages/statistics.scm (r-tidyr): Update to 0.8.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d741c77a23..e49f33403d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3643,14 +3643,14 @@ (define-public r-tidyselect
 (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)

From edb29f298613ec75ef12a56ddb4d495e6a69e793 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:36:42 +0200
Subject: [PATCH 47/60] gnu: r-purrr: Update to 0.2.5.

* gnu/packages/statistics.scm (r-purrr): Update to 0.2.5.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e49f33403d..d02ce34dee 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3699,14 +3699,14 @@ (define-public r-hexbin
 (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)

From 366dd8d7cb46b28ec15ecd311603e9f71ae73735 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:36:52 +0200
Subject: [PATCH 48/60] gnu: r-runit: Update to 0.4.32.

* gnu/packages/statistics.scm (r-runit): Update to 0.4.32.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d02ce34dee..7585306336 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3965,14 +3965,14 @@ (define-public r-hmisc
 (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")

From 6f96c2d89ea815b37eddf84f5431aef1831cb0f2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:37:03 +0200
Subject: [PATCH 49/60] gnu: r-ggthemes: Update to 3.5.0.

* gnu/packages/statistics.scm (r-ggthemes): Update to 3.5.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7585306336..fc3628f11f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4333,13 +4333,13 @@ (define-public r-ggbeeswarm
 (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)

From 13dc49243511d1aa3f018355d5dcdb59f01c6219 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:37:14 +0200
Subject: [PATCH 50/60] gnu: r-rrcov: Update to 1.4-4.

* gnu/packages/statistics.scm (r-rrcov): Update to 1.4-4.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index fc3628f11f..0642860779 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4751,14 +4751,14 @@ (define-public r-pcapp
 (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)

From 9bcc68fbf678bd7252561e43b5716c22004b971c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:37:26 +0200
Subject: [PATCH 51/60] gnu: r-quantreg: Update to 5.36.

* gnu/packages/statistics.scm (r-quantreg): Update to 5.36.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0642860779..1738844016 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5026,14 +5026,14 @@ (define-public r-matrixmodels
 (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)))

From 9fad62743c43906b87a521d0285878ab881daa37 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:37:36 +0200
Subject: [PATCH 52/60] gnu: r-caret: Update to 6.0-80.

* gnu/packages/statistics.scm (r-caret): Update to 6.0-80.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1738844016..47d306107a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5186,14 +5186,14 @@ (define-public r-car
 (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)

From 14bb6f5f83efb52fec8ec0aa31f677ec862fa001 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:37:47 +0200
Subject: [PATCH 53/60] gnu: r-tclust: Update to 1.4-1.

* gnu/packages/statistics.scm (r-tclust): Update to 1.4-1.
---
 gnu/packages/statistics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 47d306107a..5e64448ac3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5307,15 +5307,16 @@ (define-public r-sn
 (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)

From 089e03763834d0e3b2c2ef884ffcdabc990e889e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:37:56 +0200
Subject: [PATCH 54/60] gnu: r-ranger: Update to 0.10.0.

* gnu/packages/statistics.scm (r-ranger): Update to 0.10.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5e64448ac3..44285fff6a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5333,14 +5333,14 @@ (define-public r-tclust
 (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)

From beb0878fe56d905da93845627afb53804182740c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:38:06 +0200
Subject: [PATCH 55/60] gnu: r-directlabels: Update to 2018.05.22.

* gnu/packages/statistics.scm (r-directlabels): Update to 2018.05.22.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 44285fff6a..7d5c552a3e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5552,14 +5552,14 @@ (define-public r-tgconfig
 (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)))

From 71644c0ee81de00170045ecf732d9a8e38e2156f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:38:20 +0200
Subject: [PATCH 56/60] gnu: r-htmltable: Update to 1.12.

* gnu/packages/web.scm (r-htmltable): Update to 1.12.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 1d47aae09f..e9c27ed146 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3909,14 +3909,14 @@ (define-public r-htmlwidgets
 (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

From eb0d599a676caaccdcb76430abfd484f11757cb8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:38:33 +0200
Subject: [PATCH 57/60] gnu: r-rjson: Update to 0.2.19.

* gnu/packages/web.scm (r-rjson): Update to 0.2.19.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index e9c27ed146..3b28e1f7fe 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4000,14 +4000,14 @@ (define-public r-hwriter
 (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")

From 508dd24abe3659c8a819189d73000478c52320cf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:38:54 +0200
Subject: [PATCH 58/60] gnu: r-shiny: Update to 1.1.0.

* gnu/packages/web.scm (r-shiny): Update to 1.1.0.
[source]: Fetch from git.
[propagated-inputs]: Add r-crayon.
---
 gnu/packages/web.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 3b28e1f7fe..8b74bb4926 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5326,16 +5326,17 @@ (define-public python2-clf
 (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)
@@ -5400,7 +5401,8 @@ (define-public r-shiny
                               "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)

From ce8b9e3b1c82e0a179b6baeec0faeb1f3456e84c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 12:53:24 +0200
Subject: [PATCH 59/60] gnu: r-seurat: Update to 2.3.1.

* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.1.
[propagated-inputs]: Remove r-gridextra; add r-reticulate.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d1db06f398..e0bfaac06e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9687,13 +9687,13 @@ (define-public r-msnid
 (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")
@@ -9737,7 +9737,6 @@ (define-public r-seurat
        ("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)
@@ -9758,6 +9757,7 @@ (define-public r-seurat
        ("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)

From 404e5c7d7d2f6fc80eebec831283c2f4161b6582 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 31 May 2018 13:09:44 +0200
Subject: [PATCH 60/60] gnu: r-servr: Update to 0.10.

* gnu/packages/web.scm (r-servr): Update to 0.10.
[native-inputs]: Remove r-rcpp.
---
 gnu/packages/web.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 8b74bb4926..e06247a7cc 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3826,21 +3826,19 @@ (define-public r-jsonlite
 (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