Merge branch 'master' into core-updates

 Conflicts:
	gnu/local.mk
	gnu/packages/backup.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/guile.scm
	gnu/packages/lisp.scm
	gnu/packages/openldap.scm
	gnu/packages/package-management.scm
	gnu/packages/web.scm
	gnu/packages/xorg.scm

1 files changed, 51 insertions, 36 deletions

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 38d75941d6..fe8c731a1a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -183,7 +183,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
 (define r-with-tests
   (package
     (name "r-with-tests")
-    (version "3.6.3")
+    (version "4.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -191,7 +191,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49"))))
+                "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -269,6 +269,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                  (("my \\$date = strftime \"%B %Y\", localtime" line)
                   (string-append line " 1"))))
              #t))
+         (add-before 'build 'set-locales
+           (lambda _
+             (setlocale LC_ALL "C")
+             (setenv "LC_ALL" "C")
+             #t))
          (add-before 'configure 'set-default-pager
           ;; Set default pager to "cat", because otherwise it is "false",
           ;; making "help()" print nothing at all.
@@ -322,7 +327,9 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo) ; for building HTML manuals
-       ("texlive" ,(texlive-union (list texlive-fonts-ec
+       ("texlive" ,(texlive-union (list texlive-ae
+                                        texlive-inconsolata
+                                        texlive-fonts-ec
                                         texlive-amsfonts
                                         texlive-latex-base
                                         texlive-latex-fancyvrb
@@ -331,7 +338,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                                         texlive-latex-oberdiek
                                         texlive-latex-tools
                                         texlive-latex-upquote
-                                        texlive-latex-url)))
+                                        texlive-latex-url
+                                        texlive-latex-xkeyval)))
        ("tzdata" ,tzdata-for-tests)
        ("xz" ,xz)))
     (inputs
@@ -347,7 +355,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
        ("libxt" ,libxt)
-       ("pcre" ,pcre)
+       ("pcre2" ,pcre2)
        ("readline" ,readline)
        ;; This avoids a reference to the ungraftable static bash.  R uses the
        ;; detected shell for the "system" procedure.
@@ -399,14 +407,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-24")
+    (version "1.3-25")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
+         "1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
@@ -420,14 +428,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51.5")
+    (version "7.3-51.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
+         "1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -441,14 +449,14 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
 (define-public r-class
   (package
     (name "r-class")
-    (version "7.3-16")
+    (version "7.3-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "class" version))
        (sha256
         (base32
-         "1jpdgj0lsi60q0mqbhfw809w8d66whix27y6wpdzll6775g3j3ll"))))
+         "04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)))
@@ -504,14 +512,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-76")
+    (version "0.8-79")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "1z6x2x1z12wnv0z4p74d91r5wfaq30sdz4ynwx0lncz1q45mhbh5"))))
+         "1d5rk4k3khjrir1b4ciridd6vdpcgzi35r7p7ra4ky7vbaabcdmg"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -524,14 +532,14 @@ for reading and writing some dBase files.")
 (define-public r-kernsmooth
   (package
     (name "r-kernsmooth")
-    (version "2.23-16")
+    (version "2.23-17")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "KernSmooth" version))
        (sha256
         (base32
-         "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
+         "11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
     (properties `((upstream-name . "KernSmooth")))
     (build-system r-build-system)
     (native-inputs
@@ -635,14 +643,14 @@ distributions beyond the exponential family.")
 (define-public r-nnet
   (package
     (name "r-nnet")
-    (version "7.3-13")
+    (version "7.3-14")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nnet" version))
        (sha256
         (base32
-         "1z0rj5cm4ycw1y0gd5wwwg8c2298v90iybgqdqh17967jbi2125f"))))
+         "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Feed-forward neural networks and multinomial log-linear models")
@@ -673,14 +681,14 @@ classification, regression and survival trees.")
 (define-public r-spatial
   (package
     (name "r-spatial")
-    (version "7.3-11")
+    (version "7.3-12")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "spatial" version))
        (sha256
         (base32
-         "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
+         "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
     (synopsis "Functions for kriging and point pattern analysis")
@@ -1624,14 +1632,14 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "3.0.0")
+    (version "3.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "0s84h8ls5qwixbs1n5safr3xqmg3p0llzdrd9sp4vs2572mwzqzi"))))
+         "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -1694,25 +1702,28 @@ database.")
 (define-public r-dbplyr
   (package
     (name "r-dbplyr")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbplyr" version))
        (sha256
         (base32
-         "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
+         "1si8sahr1kwq1xgjzi9klkahad07pyrsngy75y1f74f64907pb39"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
        ("r-dbi" ,r-dbi)
        ("r-dplyr" ,r-dplyr)
        ("r-glue" ,r-glue)
+       ("r-lifecycle" ,r-lifecycle)
        ("r-purrr" ,r-purrr)
        ("r-r6" ,r-r6)
        ("r-rlang" ,r-rlang)
        ("r-tibble" ,r-tibble)
        ("r-tidyselect" ,r-tidyselect)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/tidyverse/dbplyr")
     (synopsis "Dplyr back end for databases")
     (description
@@ -1989,14 +2000,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
 (define-public r-xml2
   (package
     (name "r-xml2")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xml2" version))
        (sha256
         (base32
-         "0r7rxp922785dcryghbb3wxqgdav7mafwnmxjqfx8zaj3v1q2j3z"))))
+         "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
     (build-system r-build-system)
     (inputs
      `(("libxml2" ,libxml2)
@@ -2446,14 +2457,16 @@ tools to simplify the devolpment of R packages.")
 (define-public r-withr
   (package
     (name "r-withr")
-    (version "2.1.2")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "withr" version))
               (sha256
                (base32
-                "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
+                "10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/jimhester/withr")
     (synopsis "Run code with temporarily modified global state")
     (description
@@ -2514,13 +2527,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-7")
+    (version "3.7-8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
+                "104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -2575,13 +2588,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.860.2.0")
+    (version "0.9.870.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1rg9ak0zbv8d9cyj10jq52nrcbk1pvfz28kbkhpx79mpjhrl7pb5"))))
+                "1r7iajxvbyvslsy16rqacc95azmjciw9lvcq31xl97fl09kmsq5v"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3743,18 +3756,20 @@ It uses and relies on grid graphics and formal (S4) classes and methods.")
 (define-public r-purrr
   (package
     (name "r-purrr")
-    (version "0.3.3")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "purrr" version))
        (sha256
         (base32
-         "17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g"))))
+         "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-magrittr" ,r-magrittr)
        ("r-rlang" ,r-rlang)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/purrr")
     (synopsis "Functional programming tools")
     (description
@@ -4942,16 +4957,16 @@ groupings.")
 (define-public r-vgam
   (package
     (name "r-vgam")
-    (version "1.1-2")
+    (version "1.1-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "VGAM" version))
        (sha256
-        (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
+        (base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc"))))
     (properties `((upstream-name . "VGAM")))
     (build-system r-build-system)
-    (inputs
+    (native-inputs
      `(("gfortran" ,gfortran)))
     (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
     (synopsis "Vector generalized linear and additive models")