Merge branch 'master' into core-updates

 Conflicts:
	gnu/packages/admin.scm
	gnu/packages/commencement.scm
	gnu/packages/guile.scm
	gnu/packages/linux.scm
	gnu/packages/package-management.scm
	gnu/packages/pulseaudio.scm
	gnu/packages/web.scm

1 files changed, 24 insertions, 14 deletions

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 129c5c07c8..9d71502017 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -677,7 +677,11 @@ LaTeX.")
                (("if \\(!grepl\\(\"mingw\".*")
                 "if (FALSE)\n"))
              (substitute* "src/handle.c"
-               (("#ifdef _WIN32") "#if 1"))
+               (("/\\* Only set" m)
+                (string-append "\
+const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
+if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
+" m)))
              #t)))))
     (inputs
      `(("libcurl" ,curl)
@@ -2107,14 +2111,14 @@ package also provides a C++ API, that works with or without Rcpp.")
 (define-public r-ggally
   (package
     (name "r-ggally")
-    (version "1.4.0")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "GGally" version))
        (sha256
         (base32
-         "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
+         "082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
     (properties `((upstream-name . "GGally")))
     (build-system r-build-system)
     (inputs
@@ -6086,14 +6090,14 @@ results to the user.")
 (define-public r-hdf5r
   (package
     (name "r-hdf5r")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hdf5r" version))
        (sha256
         (base32
-         "0hvi2cvyv6zlxgpawnmsihxclp2ln88slbrnmaxagmjswskxsrpx"))))
+         "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
     (build-system r-build-system)
     (inputs
      `(("hdf5" ,hdf5)
@@ -6101,6 +6105,8 @@ results to the user.")
     (propagated-inputs
      `(("r-bit64" ,r-bit64)
        ("r-r6" ,r-r6)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://hhoeflin.github.io/hdf5r")
     (synopsis "Interface to the HDF5 binary data format")
     (description
@@ -8512,18 +8518,20 @@ differentiation.")
 (define-public r-bayestestr
   (package
     (name "r-bayestestr")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bayestestR" version))
        (sha256
         (base32
-         "1l0kqw793d8fnk0745fllmqwjwnj9srvqzv4baq5s05ls1gbi2mw"))))
+         "1q24qh5p6bz4nbf4546kckh7d518x5pm1yhhbc8fwcnbca4kgqjz"))))
     (properties `((upstream-name . "bayestestR")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-insight" ,r-insight)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/easystats/bayestestR")
     (synopsis "Describe Bayesian models and posterior distributions")
     (description
@@ -13178,14 +13186,14 @@ tessellation.")
 (define-public r-sf
   (package
     (name "r-sf")
-    (version "0.8-1")
+    (version "0.9-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sf" version))
        (sha256
         (base32
-         "17wyv74m1ppc3s5jdv60r74jj23nidxpzl46vjhfclfhnpvm7sx9"))))
+         "117r9l3v7nkdj9bfy6qr0yz0gd5bv0pwnkc9vk2gv3xqj0h1fpf6"))))
     (build-system r-build-system)
     (inputs
      `(("gdal" ,gdal)
@@ -13198,7 +13206,9 @@ tessellation.")
        ("r-magrittr" ,r-magrittr)
        ("r-rcpp" ,r-rcpp)
        ("r-units" ,r-units)))
-    (native-inputs `(("pkg-config" ,pkg-config)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
     (home-page "https://github.com/r-spatial/sf/")
     (synopsis "Simple features for R")
     (description
@@ -13848,14 +13858,14 @@ the corresponding outputs (tables and graphs).")
 (define-public r-rjava
   (package
     (name "r-rjava")
-    (version "0.9-11")
+    (version "0.9-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rJava" version))
        (sha256
         (base32
-         "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
+         "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
     (properties `((upstream-name . "rJava")))
     (build-system r-build-system)
     (arguments
@@ -15355,14 +15365,14 @@ the current document.")
 (define-public r-xgboost
   (package
     (name "r-xgboost")
-    (version "1.0.0.1")
+    (version "1.0.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xgboost" version))
        (sha256
         (base32
-         "0fx5qjpjjirzhplddqmxlysyqszp79w74x00b5shp6p2lzy6yd9a"))))
+         "1ld2w51c5fy3bl0kvjn1iplffc4lmin9s9zz5xx7xsm44d6j6kzd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-data-table" ,r-data-table)