From 7a5ed348c0073cb28dae01c10b25155e29188fdb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 7 Sep 2019 23:50:15 +0200
Subject: gnu: Add r-covr.

* gnu/packages/cran.scm (r-covr): New variable.
---
 gnu/packages/cran.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5bf37e3900..44913e53f7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15212,3 +15212,35 @@ single cell integration, described in Korsunsky et al
 @url{doi.org/10.1101/461954}.  The package includes a standalone Harmony
 function and interfaces to external frameworks.")
       (license license:gpl3))))
+
+(define-public r-covr
+  (package
+    (name "r-covr")
+    (version "3.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "covr" version))
+       (sha256
+        (base32
+         "0fvd7v53w11x6kaw61hbml8n1j2ck9l2fv2wvqdsg689xic9rqcs"))))
+    (properties `((upstream-name . "covr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-crayon" ,r-crayon)
+       ("r-digest" ,r-digest)
+       ("r-httr" ,r-httr)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-rex" ,r-rex)
+       ("r-withr" ,r-withr)
+       ("r-yaml" ,r-yaml)))
+    (home-page "https://github.com/r-lib/covr")
+    (synopsis "Test coverage for R packages")
+    (description
+     "Thisp package enables you to track and report code coverage for your
+package and (optionally) upload the results to a coverage service.  Code
+coverage is a measure of the amount of code being exercised by a set of tests.
+It is an indirect measure of test quality and completeness.  This package is
+compatible with any testing methodology or framework and tracks coverage of
+both R code and compiled C/C++/FORTRAN code.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From 6983178b06f1efe61dc513d5b3fe1673c63ff47d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:01:25 +0200
Subject: gnu: Add r-systemfonts.

* gnu/packages/cran.scm (r-systemfonts): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 44913e53f7..bdfc3fb2c9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15244,3 +15244,32 @@ It is an indirect measure of test quality and completeness.  This package is
 compatible with any testing methodology or framework and tracks coverage of
 both R code and compiled C/C++/FORTRAN code.")
     (license license:gpl3)))
+
+(define-public r-systemfonts
+  (package
+    (name "r-systemfonts")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "systemfonts" version))
+       (sha256
+        (base32
+         "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
+    (properties `((upstream-name . "systemfonts")))
+    (build-system r-build-system)
+    (inputs
+     `(("fontconfig" ,fontconfig)
+       ("freetype" ,freetype)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/r-lib/systemfonts")
+    (synopsis "System native font finding")
+    (description
+     "This package provides system native access to the font catalogue.  As
+font handling varies between systems it is difficult to correctly locate
+installed fonts across different operating systems.  The 'systemfonts' package
+provides bindings to the native libraries for finding font files that can then
+be used further by e.g. graphic devices.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 9390300915a642c08a494aa67bf970c9a6ad5ff3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:17:22 +0200
Subject: gnu: Add r-graphlayouts.

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

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bdfc3fb2c9..ac528468cb 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15273,3 +15273,30 @@ installed fonts across different operating systems.  The 'systemfonts' package
 provides bindings to the native libraries for finding font files that can then
 be used further by e.g. graphic devices.")
     (license license:expat)))
+
+(define-public r-graphlayouts
+  (package
+    (name "r-graphlayouts")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "graphlayouts" version))
+       (sha256
+        (base32
+         "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
+    (properties `((upstream-name . "graphlayouts")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://github.com/schochastics/graphlayouts")
+    (synopsis "Additional layout algorithms for network visualizations")
+    (description
+     "This package provides several layout algorithms to visualize networks
+which are not part of the igraph library.  Most are based on the concept of
+stress majorization by Gansner et al. (2004)
+<doi:10.1007/978-3-540-31843-9_25>.  Some more specific algorithms allow to
+emphasize hidden group structures in networks or focus on specific nodes.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 9567bd8dd9d092ac4bfdf9abfc35263e39146e26 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:18:03 +0200
Subject: gnu: Add r-tidygraph.

* gnu/packages/cran.scm (r-tidygraph): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ac528468cb..19aa0522b1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15300,3 +15300,36 @@ stress majorization by Gansner et al. (2004)
 <doi:10.1007/978-3-540-31843-9_25>.  Some more specific algorithms allow to
 emphasize hidden group structures in networks or focus on specific nodes.")
     (license license:expat)))
+
+(define-public r-tidygraph
+  (package
+    (name "r-tidygraph")
+    (version "1.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tidygraph" version))
+       (sha256
+        (base32
+         "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
+    (properties `((upstream-name . "tidygraph")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-igraph" ,r-igraph)
+       ("r-magrittr" ,r-magrittr)
+       ("r-pillar" ,r-pillar)
+       ("r-r6" ,r-r6)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
+    (home-page "https://github.com/thomasp85/tidygraph")
+    (synopsis "Tidy API for graph manipulation")
+    (description
+     "This package provides a graph implementation that can be thought of as
+two tidy data frames describing node and edge data respectively.  It provides
+an approach to manipulate these two virtual data frames using the API defined
+in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
+common graph algorithms.")
+    (license license:expat)))
-- 
cgit v1.2.3


From 02efab6917ebb0f3e08b18a101526f2a0f1fd0b8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:05 +0200
Subject: gnu: r-feather: Update to 0.3.4.

* gnu/packages/cran.scm (r-feather): Update to 0.3.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 19aa0522b1..57765b7d85 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1059,14 +1059,14 @@ work well on small screens.")
 (define-public r-feather
   (package
     (name "r-feather")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "feather" version))
        (sha256
         (base32
-         "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa"))))
+         "1zwr2lxbzks2k1jjbnnv965j8sbwxnszl1vyrnl60ar24nykd2f3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-hms" ,r-hms)
-- 
cgit v1.2.3


From 9960ad55be0b874dc5d9fea2f8527aad47f5aab9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:09 +0200
Subject: gnu: r-geometry: Update to 0.4.4.

* gnu/packages/cran.scm (r-geometry): Update to 0.4.4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 57765b7d85..0b70df1434 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2663,14 +2663,14 @@ Optimization problems by using the simplex algorithm.")
 (define-public r-geometry
   (package
     (name "r-geometry")
-    (version "0.4.3")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "geometry" version))
        (sha256
         (base32
-         "0z4491mhfmrlbb8lazjvq55alrprx7k0abg2d39fj0lsj84cls1r"))))
+         "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magic" ,r-magic)
-- 
cgit v1.2.3


From f11920c759447679221ef483f7a06ebb9bdd6292 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:15 +0200
Subject: gnu: r-ggpubr: Update to 0.2.3.

* gnu/packages/cran.scm (r-ggpubr): Update to 0.2.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0b70df1434..bcc277e76c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5569,14 +5569,14 @@ and adds the annotation to the plot.")
 (define-public r-ggpubr
   (package
     (name "r-ggpubr")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggpubr" version))
        (sha256
         (base32
-         "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw"))))
+         "0i81mmz4qn9yzcgfa6dhkcrx4ddlflkm2c3b40isc8all43rm8rn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cowplot" ,r-cowplot)
-- 
cgit v1.2.3


From c90eebf791b063760a922f1f4de64867681b2a3a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:20 +0200
Subject: gnu: r-insight: Update to 0.5.0.

* gnu/packages/cran.scm (r-insight): Update to 0.5.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bcc277e76c..a7be239761 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6091,14 +6091,14 @@ other add-on packages.")
 (define-public r-insight
   (package
     (name "r-insight")
-    (version "0.4.1")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "insight" version))
        (sha256
         (base32
-         "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
+         "0lrh2l9n2zd9n3zzknsxz6nlasnrayx3bplxlz7m616g56gr5nfp"))))
     (build-system r-build-system)
     (home-page "https://easystats.github.io/insight/")
     (synopsis "Easy access to model information for various model objects")
-- 
cgit v1.2.3


From 9a4706828cfd01dce148c146dc710db84e538266 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:25 +0200
Subject: gnu: r-ggformula: Update to 0.9.2.

* gnu/packages/cran.scm (r-ggformula): Update to 0.9.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a7be239761..dbc2ea6e60 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6873,13 +6873,13 @@ and coverage methods to tune the choice of threshold.")
 (define-public r-ggformula
   (package
     (name "r-ggformula")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggformula" version))
        (sha256
-        (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx"))))
+        (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
-- 
cgit v1.2.3


From f396d343b7779a20f2e7dc3696167c54d9869274 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:30 +0200
Subject: gnu: r-ggeffects: Update to 0.12.0.

* gnu/packages/cran.scm (r-ggeffects): Update to 0.12.0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index dbc2ea6e60..be32bdefb9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8162,14 +8162,14 @@ effects models and Bayesian models.")
 (define-public r-ggeffects
   (package
     (name "r-ggeffects")
-    (version "0.11.0")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggeffects" version))
        (sha256
         (base32
-         "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
+         "0idfycjk05gyykfp9ibmhxfcjvd01ikh1dl0fb4nqw6znw3ar0xp"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
-- 
cgit v1.2.3


From 995a20e89214049daab5026c430fe34ae4cccedb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:35 +0200
Subject: gnu: r-msigdbr: Update to 7.0.1.

* gnu/packages/cran.scm (r-msigdbr): Update to 7.0.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index be32bdefb9..224dbe8b10 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13607,14 +13607,14 @@ the XKCD web comic.")
 (define-public r-msigdbr
   (package
     (name "r-msigdbr")
-    (version "6.2.1")
+    (version "7.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "msigdbr" version))
        (sha256
         (base32
-         "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg"))))
+         "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
-- 
cgit v1.2.3


From 801dc98f1f6a99d576525c22ee40305d0cbea30c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 8 Sep 2019 00:20:46 +0200
Subject: gnu: r-ggraph: Update to 2.0.0.

* gnu/packages/cran.scm (r-ggraph): Update to 2.0.0.
[propagated-inputs]: Add r-graphlayouts, r-rlang, and r-tidygraph; remove
r-plyr.
---
 gnu/packages/cran.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 224dbe8b10..b09d46678a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -13881,14 +13881,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.")
 (define-public r-ggraph
   (package
     (name "r-ggraph")
-    (version "1.0.2")
+    (version "2.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggraph" version))
        (sha256
         (base32
-         "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c"))))
+         "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -13896,12 +13896,14 @@ databases, including ENA, PDB or ChEMBL are also accessible.")
        ("r-ggforce" ,r-ggforce)
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggrepel" ,r-ggrepel)
+       ("r-graphlayouts" ,r-graphlayouts)
        ("r-gtable" ,r-gtable)
        ("r-igraph" ,r-igraph)
        ("r-mass" ,r-mass)
-       ("r-plyr" ,r-plyr)
        ("r-rcpp" ,r-rcpp)
+       ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)
+       ("r-tidygraph" ,r-tidygraph)
        ("r-viridis" ,r-viridis)))
     (home-page "https://cran.r-project.org/web/packages/ggraph/")
     (synopsis "Implementation of grammar of graphics for graphs and networks")
-- 
cgit v1.2.3


From 3a341e822c8c73af9d8620858c66340119c5b800 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 9 Sep 2019 11:25:02 +0200
Subject: gnu: Add r-soupx.

* gnu/packages/cran.scm (r-soupx): New variable.
---
 gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b09d46678a..6ef2066429 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15335,3 +15335,33 @@ an approach to manipulate these two virtual data frames using the API defined
 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
 common graph algorithms.")
     (license license:expat)))
+
+(define-public r-soupx
+  (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
+        (revision "1"))
+    (package
+      (name "r-soupx")
+      (version (git-version "0.3.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/constantAmateur/SoupX")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
+      (properties `((upstream-name . "SoupX")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-ggplot2" ,r-ggplot2)
+         ("r-matrix" ,r-matrix)
+         ("r-seurat" ,r-seurat)))
+      (home-page "https://github.com/constantAmateur/SoupX")
+      (synopsis "Single cell mRNA Soup eXterminator")
+      (description
+       "This package provides a package for quantifying, profiling and
+removing cell free mRNA contamination (the \"soup\") from droplet based single
+cell RNA-seq experiments.")
+      (license license:gpl2))))
-- 
cgit v1.2.3


From 16fddf17f5ba90cd1b3c203a5fd8ec5b652fddb7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Wiktor=20=C5=BBelazny?= <wzelazny@vurv.cz>
Date: Thu, 12 Sep 2019 18:44:57 +0200
Subject: gnu: Add r-assertr.

* gnu/packages/cran.scm (r-assertr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 6ef2066429..aa1135d0e4 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15,6 +15,7 @@
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
+;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -15365,3 +15366,30 @@ common graph algorithms.")
 removing cell free mRNA contamination (the \"soup\") from droplet based single
 cell RNA-seq experiments.")
       (license license:gpl2))))
+
+(define-public r-assertr
+  (package
+    (name "r-assertr")
+    (version "2.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "assertr" version))
+       (sha256
+        (base32
+         "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-mass" ,r-mass)
+       ("r-rlang" ,r-rlang)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))           ; needed for vignette
+    (home-page "https://github.com/ropensci/assertr")
+    (synopsis "Assertive programming for R analysis pipelines")
+    (description
+     "This package provides functionality to assert conditions that have to be
+met so that errors in data used in analysis pipelines can fail quickly.  It is
+similar to @code{stopifnot()} but more powerful, friendly, and easier for use
+in pipelines.")
+    (license license:expat)))
-- 
cgit v1.2.3


From a5a79dd0b88c0d9da09be7823c6158fa80ac5acd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:23:14 +0200
Subject: gnu: Add r-parameters.

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

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index aa1135d0e4..732028601f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15393,3 +15393,30 @@ met so that errors in data used in analysis pipelines can fail quickly.  It is
 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
 in pipelines.")
     (license license:expat)))
+
+(define-public r-parameters
+  (package
+    (name "r-parameters")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "parameters" version))
+       (sha256
+        (base32
+         "12v301va1l3xydicbf0k04anxlmyjclbbjfg0riprryhkxwwk8g5"))))
+    (properties `((upstream-name . "parameters")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bayestestr" ,r-bayestestr)
+       ("r-insight" ,r-insight)))
+    (home-page "https://cran.r-project.org/web/packages/parameters")
+    (synopsis "Processing of model parameters")
+    (description
+     "This package provides utilities for processing the parameters of various
+statistical models.  Beyond computing p values, CIs, and other indices for a
+wide variety of models, this package implements features like standardization
+or bootstrapping of parameters and models, feature reduction (feature
+extraction and variable selection) as well as conversion between indices of
+effect size.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From a0244ef0008dd3c45ede84d5692c4be4327b60d0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:31:21 +0200
Subject: gnu: Add r-rgdal.

* gnu/packages/cran.scm (r-rgdal): New variable.
---
 gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 732028601f..3c300a39a6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15420,3 +15420,32 @@ or bootstrapping of parameters and models, feature reduction (feature
 extraction and variable selection) as well as conversion between indices of
 effect size.")
     (license license:gpl3)))
+
+(define-public r-rgdal
+  (package
+    (name "r-rgdal")
+    (version "1.4-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rgdal" version))
+       (sha256
+        (base32
+         "1my56hdc9x40ynxx1qwqwqxjvjxybmm00w4xg5gi8zgj19pffci5"))))
+    (properties `((upstream-name . "rgdal")))
+    (build-system r-build-system)
+    (inputs
+     `(("gdal" ,gdal)
+       ("proj.4" ,proj.4)
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-sp" ,r-sp)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://rgdal.r-forge.r-project.org")
+    (synopsis "Bindings for the Geospatial Data Abstraction Library")
+    (description
+     "This package provides bindings to the Geospatial Data Abstraction
+Library (GDAL) and access to projection/transformation operations from the
+PROJ.4 library.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From 5ad9da9ab32761181ace8e41d7af9798e7ce9ea9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:31:57 +0200
Subject: gnu: Add r-insol.

* gnu/packages/cran.scm (r-insol): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3c300a39a6..8228f2d988 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15449,3 +15449,31 @@ effect size.")
 Library (GDAL) and access to projection/transformation operations from the
 PROJ.4 library.")
     (license license:gpl2+)))
+
+(define-public r-insol
+  (package
+    (name "r-insol")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "insol" version))
+       (sha256
+        (base32
+         "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
+    (properties `((upstream-name . "insol")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-raster" ,r-raster)
+       ("r-rgdal" ,r-rgdal)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://meteoexploration.com/R/insol/index.html")
+    (synopsis "Tools for calculating solar radiation")
+    (description
+     "This package provides functions to compute insolation on tilted
+surfaces, computes atmospheric transmittance and related parameters such as:
+Earth radius vector, declination, sunset and sunrise, daylength, equation of
+time, vector in the direction of the sun, vector normal to surface, and some
+atmospheric physics.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From a1f439943802eb45ec9c1c8da9e439079722ced5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:34:29 +0200
Subject: gnu: r-httpuv: Update to 1.5.2.

* gnu/packages/cran.scm (r-httpuv): Update to 1.5.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8228f2d988..0fc017d007 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -448,13 +448,13 @@ into a pipeline of data manipulation and visualisation.")
 (define-public r-httpuv
   (package
     (name "r-httpuv")
-    (version "1.5.1")
+    (version "1.5.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httpuv" version))
               (sha256
                (base32
-                "042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm"))))
+                "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
-- 
cgit v1.2.3


From 4557f44755530be1675ea92437665f00b34c40fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:34:34 +0200
Subject: gnu: r-circlize: Update to 0.4.8.

* gnu/packages/cran.scm (r-circlize): Update to 0.4.8.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0fc017d007..635d295701 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1650,14 +1650,14 @@ validation and filtering on the values, making options invisible or private.")
 (define-public r-circlize
   (package
     (name "r-circlize")
-    (version "0.4.7")
+    (version "0.4.8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "circlize" version))
        (sha256
         (base32
-         "07y1bchkslpz2wl43yg5j5h1nl9z0i425a07jdmfd5avrynd8p3m"))))
+         "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-colorspace" ,r-colorspace)
-- 
cgit v1.2.3


From 3ab3f7f3bb80951cf1456589c2918163884f257b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:34:39 +0200
Subject: gnu: r-sjlabelled: Update to 1.1.1.

* gnu/packages/cran.scm (r-sjlabelled): Update to 1.1.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 635d295701..fbf0f8c4ec 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6118,14 +6118,14 @@ information are missing.")
 (define-public r-sjlabelled
   (package
     (name "r-sjlabelled")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjlabelled" version))
        (sha256
         (base32
-         "0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
+         "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-haven" ,r-haven)
-- 
cgit v1.2.3


From 28110e684275282e3a980b09e0cf04ef840a7485 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:34:48 +0200
Subject: gnu: r-emmeans: Update to 1.4.1.

* gnu/packages/cran.scm (r-emmeans): Update to 1.4.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fbf0f8c4ec..1f4f5e2f9d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -7879,14 +7879,14 @@ Hothorn, Westfall, 2010, CRC Press).")
 (define-public r-emmeans
   (package
     (name "r-emmeans")
-    (version "1.4")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "emmeans" version))
        (sha256
         (base32
-         "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
+         "1fpawaxnmj67md169a9mzrnnh2d0c973xydfg6hw865933jil9lq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-estimability" ,r-estimability)
-- 
cgit v1.2.3


From 664e15ed8fcb255c60ba2e7fbe807cafe36e3961 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:34:55 +0200
Subject: gnu: r-sjstats: Update to 0.17.6.

* gnu/packages/cran.scm (r-sjstats): Update to 0.17.6.
[propagated-inputs]: Add r-parameters.
---
 gnu/packages/cran.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1f4f5e2f9d..fac81d5e86 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8037,14 +8037,14 @@ detection, parallelism through BLAS and parallel user templates.")
 (define-public r-sjstats
   (package
     (name "r-sjstats")
-    (version "0.17.5")
+    (version "0.17.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjstats" version))
        (sha256
         (base32
-         "1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
+         "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bayestestr" ,r-bayestestr)
@@ -8056,6 +8056,7 @@ detection, parallelism through BLAS and parallel user templates.")
        ("r-magrittr" ,r-magrittr)
        ("r-mass" ,r-mass)
        ("r-modelr" ,r-modelr)
+       ("r-parameters" ,r-parameters)
        ("r-performance" ,r-performance)
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
-- 
cgit v1.2.3


From d72da21d54a6836668b7405743f25d34bc871877 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:35:07 +0200
Subject: gnu: r-sjplot: Update to 2.7.1.

* gnu/packages/cran.scm (r-sjplot): Update to 2.7.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fac81d5e86..946ee5b7aa 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -8198,14 +8198,14 @@ results using @code{ggplot2}.")
 (define-public r-sjplot
   (package
     (name "r-sjplot")
-    (version "2.7.0")
+    (version "2.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjPlot" version))
        (sha256
         (base32
-         "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
+         "14shypabpahf68hd66rb1dpqhiyl3i0yx1yc85wamdvljh9fdymb"))))
     (properties `((upstream-name . "sjPlot")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From aef5e2aaddfddd6c574853928236f4e37efe9827 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:35:12 +0200
Subject: gnu: r-activity: Update to 1.3.

* gnu/packages/cran.scm (r-activity): Update to 1.3.
[propagated-inputs]: Add r-insol.
---
 gnu/packages/cran.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 946ee5b7aa..436e545e00 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9124,17 +9124,18 @@ Scientific.")
 (define-public r-activity
   (package
     (name "r-activity")
-    (version "1.2")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "activity" version))
        (sha256
         (base32
-         "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs"))))
+         "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-circular" ,r-circular)
+       ("r-insol" ,r-insol)
        ("r-pbapply" ,r-pbapply)))
     (home-page "https://cran.r-project.org/web/packages/activity/")
     (synopsis "Animal activity statistics")
-- 
cgit v1.2.3


From ac50956f319106315df8263dabcf3dd3705d0ef1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:35:22 +0200
Subject: gnu: r-tidytree: Update to 0.2.7.

* gnu/packages/cran.scm (r-tidytree): Update to 0.2.7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 436e545e00..fa03c3a0c8 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9447,14 +9447,14 @@ maps.")
 (define-public r-tidytree
   (package
     (name "r-tidytree")
-    (version "0.2.6")
+    (version "0.2.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidytree" version))
        (sha256
         (base32
-         "13mhizbsawmfqjpnzb73yw6kn1f1wlz0vhyzj3g0rj6ry880rw89"))))
+         "15ky7hj7w08jx94wm0yikckca0apwv3jy5svd77dpzgb2lr9ff9a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
-- 
cgit v1.2.3


From cd3ba9c8c7952567d4524f67d57046f08b7ad48a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:35:27 +0200
Subject: gnu: r-huge: Update to 1.3.3.

* gnu/packages/cran.scm (r-huge): Update to 1.3.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fa03c3a0c8..d85712df2c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11155,14 +11155,14 @@ regression coefficients can be conducted via jackknifing.")
 (define-public r-huge
   (package
     (name "r-huge")
-    (version "1.3.2")
+    (version "1.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "huge" version))
        (sha256
         (base32
-         "1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd"))))
+         "18f8w4hdp9fdi2k5ip6fnrn5z47w4ybgxs2m6a7jdvd2v4wfdr69"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-igraph" ,r-igraph)
-- 
cgit v1.2.3


From f5b1354fdb963586bb3cf0411c8bb2a3e8e7fd84 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:35:37 +0200
Subject: gnu: Add r-lifecycle.

* gnu/packages/cran.scm (r-lifecycle): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d85712df2c..f40d00fc94 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15479,3 +15479,31 @@ Earth radius vector, declination, sunset and sunrise, daylength, equation of
 time, vector in the direction of the sun, vector normal to surface, and some
 atmospheric physics.")
     (license license:gpl2+)))
+
+(define-public r-lifecycle
+  (package
+    (name "r-lifecycle")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "lifecycle" version))
+       (sha256
+        (base32
+         "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
+    (properties `((upstream-name . "lifecycle")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-glue" ,r-glue)
+       ("r-rlang" ,r-rlang)))
+    (home-page "https://github.com/r-lib/lifecycle")
+    (synopsis "Manage the life cycle of your package functions")
+    (description
+     "Manage the life cycle of your exported functions with shared
+conventions, documentation badges, and non-invasive deprecation warnings.  The
+lifecycle package defines four development stages (experimental, maturing,
+stable, and questioning) and three deprecation stages (soft-deprecated,
+deprecated, and defunct).  It makes it easy to insert badges corresponding to
+these stages in your documentation.  Usage of deprecated functions are
+signalled with increasing levels of non-invasive verbosity.")
+    (license license:gpl3)))
-- 
cgit v1.2.3


From fd399b7a83c2e804a68eb83b67055ad752713f0e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 14 Sep 2019 00:35:42 +0200
Subject: gnu: r-seqinr: Update to 3.6-1.

* gnu/packages/cran.scm (r-seqinr): Update to 3.6-1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index f40d00fc94..84b3b1dab6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -12593,14 +12593,14 @@ barplots or heatmaps.")
 (define-public r-seqinr
   (package
     (name "r-seqinr")
-    (version "3.4-5")
+    (version "3.6-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqinr" version))
        (sha256
         (base32
-         "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
+         "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)
-- 
cgit v1.2.3


From e48e476f41319736297a67699b9eb26d40f6d0af Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Sep 2019 16:13:15 +0200
Subject: gnu: r-feather: Update to 0.3.5.

* gnu/packages/cran.scm (r-feather): Update to 0.3.5.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 84b3b1dab6..4f1e9bcdbd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1060,14 +1060,14 @@ work well on small screens.")
 (define-public r-feather
   (package
     (name "r-feather")
-    (version "0.3.4")
+    (version "0.3.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "feather" version))
        (sha256
         (base32
-         "1zwr2lxbzks2k1jjbnnv965j8sbwxnszl1vyrnl60ar24nykd2f3"))))
+         "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-hms" ,r-hms)
-- 
cgit v1.2.3


From d77e69e9e1fd1f9e3810e20749f9888d26090906 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Sep 2019 16:13:22 +0200
Subject: gnu: r-spam: Update to 2.3-0.

* gnu/packages/cran.scm (r-spam): Update to 2.3-0.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4f1e9bcdbd..5398b4dca3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -10770,14 +10770,14 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.")
 (define-public r-spam
   (package
     (name "r-spam")
-    (version "2.2-2")
+    (version "2.3-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spam" version))
        (sha256
         (base32
-         "024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi"))))
+         "194n5mgvyms9ckjqixl3h33apii8h9kqspqg2si9k741k578qb3w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dotcall64" ,r-dotcall64)))
-- 
cgit v1.2.3


From 41b8b05c9e515e43753ddbed24b70e27b5c3be31 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Sep 2019 22:33:50 +0200
Subject: gnu: Add r-shinytree.

* gnu/packages/cran.scm (r-shinytree): New variable.
---
 gnu/packages/cran.scm | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5398b4dca3..d33eb20a37 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -797,6 +797,84 @@ extensive prebuilt widgets make it possible to build beautiful,
 responsive, and powerful applications with minimal effort.")
     (license license:artistic2.0)))
 
+;; This package includes minified JavaScript files.  When upgrading please
+;; check that there are no new minified JavaScript files.
+(define-public r-shinytree
+  (package
+    (name "r-shinytree")
+    (version "0.2.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinyTree" version))
+       (sha256
+        (base32
+         "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Delete minified JavaScript
+           (for-each delete-file
+                     '("inst/www/jsTree-3.3.7/libs/require.js"
+                       "inst/www/jsTree-3.3.7/libs/jquery.js"
+                       "inst/www/jsTree-3.3.7/jstree.min.js"))
+           #t))))
+    (properties `((upstream-name . "shinyTree")))
+    (build-system r-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build r-build-system)
+                  (srfi srfi-1)
+                  (ice-9 popen))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'replace-minified-javascript
+           (lambda* (#:key inputs #:allow-other-keys)
+             (with-directory-excursion "inst/www/jsTree-3.3.7/"
+               (symlink (string-append (assoc-ref inputs "js-requirejs")
+                                       "/share/javascript/require.min.js")
+                        "libs/require.js")
+               (call-with-values
+                   (lambda ()
+                     (unzip2
+                      `((,(assoc-ref inputs "js-jquery")
+                         "libs/jquery.js")
+                        ("jstree.js"
+                         "jstree.min.js"))))
+                 (lambda (sources targets)
+                   (for-each (lambda (source target)
+                               (format #t "Processing ~a --> ~a~%"
+                                       source target)
+                               (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
+                                 (call-with-output-file target
+                                   (lambda (port)
+                                     (dump-port minified port)))))
+                             sources targets))))
+             #t)))))
+    (propagated-inputs
+     `(("r-htmlwidgets" ,r-htmlwidgets)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-promises" ,r-promises)
+       ("r-shiny" ,r-shiny)
+       ("r-stringr" ,r-stringr)))
+    (inputs
+     `(("js-requirejs" ,js-requirejs)))
+    (native-inputs
+     `(("uglify-js" ,uglify-js)
+       ("js-jquery"
+        ,(origin
+           (method url-fetch)
+           (uri "https://code.jquery.com/jquery-3.3.1.js")
+           (sha256
+            (base32
+             "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
+    (home-page "https://cran.r-project.org/web/packages/shinyTree/")
+    (synopsis "jsTree bindings for Shiny")
+    (description
+     "This package exposes R bindings to jsTree, a JavaScript library that
+supports interactive trees, to enable rich, editable trees in Shiny.")
+    (license license:expat)))
+
 (define-public r-shinydashboard
   (package
     (name "r-shinydashboard")
-- 
cgit v1.2.3


From fc3719cc0f91644b56e7572a81669398b5fd1c8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 15 Sep 2019 22:40:25 +0200
Subject: gnu: Add r-shinythemes.

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

(limited to 'gnu/packages/cran.scm')

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d33eb20a37..cb0be4aedd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -946,6 +946,31 @@ this gives the user direct access to the file system without the need to
 well as file saving is available.")
     (license license:gpl2+)))
 
+(define-public r-shinythemes
+  (package
+    (name "r-shinythemes")
+    (version "1.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "shinythemes" version))
+       (sha256
+        (base32
+         "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
+    (properties `((upstream-name . "shinythemes")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-shiny" ,r-shiny)))
+    (home-page "http://rstudio.github.io/shinythemes/")
+    (synopsis "Themes for Shiny")
+    (description
+     "This package provides themes for use with Shiny.  It includes several
+Bootstrap themes, which are packaged for use with Shiny applications.")
+    ;; The package is released under version 3 of the GPL, but it includes
+    ;; source files that are covered by the Expat license.  It also includes
+    ;; fonts under SIL or the ASL.
+    (license (list license:gpl3 license:expat
+                   license:silofl1.1 license:asl2.0))))
+
 ;; The package sources include minified variants of d3.js and non-minified
 ;; source code of d3-jetpack.
 (define-public r-d3r
-- 
cgit v1.2.3