Merge branch 'staging' into core-updates

[jackhill/guix/guix.git] / gnu / packages / statistics.scm

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 269e122..18ca274 100644 (file)
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -8,7 +8,7 @@
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
 ;;;
@@ -159,14 +159,14 @@ simulation not wholly unlike BUGS.  JAGS was written with three aims in mind:
 (define-public libxls
   (package
     (name "libxls")
-    (version "1.5.1")
+    (version "1.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/libxls/libxls/releases/download/"
                            "v" version "/libxls-" version ".tar.gz"))
        (sha256
-        (base32 "0dam8qgbc5ykzaxmrjhpmfm8lnlcdk6cbpzyaya91qwwa80qbj1v"))))
+        (base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld"))))
     (build-system gnu-build-system)
     (home-page "https://github.com/libxls/libxls")
     (synopsis "Read binary (.xls) Excel spreadsheet files")
@@ -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 "3.6.1")
+    (version "3.6.2")
     (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
-                "128kifbq0w25y8aq77w289ddax5i5w2djcfsqgffrb3i7syrxajv"))))
+                "0m69pfi0nxyriyb2yz74xfzaxwfkinnf9kpvf1rz727vvmfa8rdx"))))
     (build-system gnu-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -343,7 +343,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
        ("openblas" ,openblas)
        ("gfortran" ,gfortran)
        ("icu4c" ,icu4c)
-       ("libjpeg" ,libjpeg)
+       ("libjpeg" ,libjpeg-turbo)
        ("libpng" ,libpng)
        ("libtiff" ,libtiff)
        ("libxt" ,libxt)
@@ -399,14 +399,14 @@ available, greatly increasing its breadth and scope.")
 (define-public r-boot
   (package
     (name "r-boot")
-    (version "1.3-23")
+    (version "1.3-24")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "boot" version))
        (sha256
         (base32
-         "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
+         "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/boot")
     (synopsis "Bootstrap functions for R")
@@ -420,14 +420,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51.4")
+    (version "7.3-51.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "0x1ckf51y851g0kvbhsgdxb26vfpmbw3xdbcnh3ck7fjm13da4cr"))))
+         "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -504,14 +504,14 @@ code for possible problems.")
 (define-public r-foreign
   (package
     (name "r-foreign")
-    (version "0.8-72")
+    (version "0.8-75")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "foreign" version))
        (sha256
         (base32
-         "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
+         "0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/foreign")
     (synopsis "Read data stored by other statistics software")
@@ -590,13 +590,13 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-142")
+    (version "3.1-143")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
-        (base32 "0figfb1i22hfkkhzpprmpp723s01r43x725a1ab0pc9gsxqg90nx"))))
+        (base32 "13iixbs2ibldc75rl7rav5n5kx33zwm33xnfw1yvlkpcqf38bd22"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -693,14 +693,14 @@ analysis.")
 (define-public r-survival
   (package
     (name "r-survival")
-    (version "3.1-7")
+    (version "3.1-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "survival" version))
        (sha256
         (base32
-         "1ij77bgfcjx29xkx5bck0sv4ybglpcmzzv9ilkinj8fqhhclbs8p"))))
+         "15fj4y8c107bwq22amx88r5hw7qndlcbr9sapzrpkpr7iqz3kkyf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -739,14 +739,14 @@ curves, Cox models, and parametric accelerated failure time models.")
 (define-public r-bit
   (package
     (name "r-bit")
-    (version "1.1-14")
+    (version "1.1-15.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bit" version))
        (sha256
         (base32
-         "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
+         "0y351ajlrn9ywbiai46mjpwmw5pqc9ik2z24rf0bnbdcvaxdr7r8"))))
     (build-system r-build-system)
     (home-page "http://ff.r-forge.r-project.org")
     (synopsis "Class for vectors of 1-bit booleans")
@@ -933,15 +933,15 @@ in which the whole-plots or split-plots or both can be freely exchangeable.")
 (define-public r-plyr
   (package
     (name "r-plyr")
-    (version "1.8.4")
+    (version "1.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "plyr" version))
        (sha256
-        (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
+        (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a"))))
     (build-system r-build-system)
-    (native-inputs `(("r-rcpp" ,r-rcpp)))
+    (propagated-inputs `(("r-rcpp" ,r-rcpp)))
     (home-page "http://had.co.nz/plyr")
     (synopsis "Tools for Splitting, Applying and Combining Data")
     (description
@@ -1015,14 +1015,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.4.3")
+    (version "1.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "1vbr6g9p1iyzdj7wfw6afyizvnd1a2srfvkl72pq23vhdcwwpkhk"))))
+         "0gdmdf4i3ik8rcs7af1vlsfnilcmw3z28jx4278rpq2asigps89k"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -1240,13 +1240,13 @@ evaluation (NSE) in R.")
 (define-public r-dbi
   (package
     (name "r-dbi")
-    (version "1.0.0")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DBI" version))
               (sha256
                (base32
-                "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
+                "1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9"))))
     (build-system r-build-system)
     (home-page "https://github.com/rstats-db/DBI")
     (synopsis "R database interface")
@@ -1260,13 +1260,13 @@ R/DBMS implementations.")
 (define-public r-bh
   (package
     (name "r-bh")
-    (version "1.69.0-1")
+    (version "1.72.0-3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "BH" version))
               (sha256
                (base32
-                "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0"))))
+                "1ay8vb6i730lipg8b8g3893vqglhw2kqpc29lwdrxdkb66iw33l8"))))
     (build-system r-build-system)
     (home-page "https://github.com/eddelbuettel/bh")
     (synopsis "R package providing subset of Boost headers")
@@ -1337,13 +1337,13 @@ supported via Andre Simon's highlight package.")
 (define-public r-mime
   (package
     (name "r-mime")
-    (version "0.7")
+    (version "0.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mime" version))
               (sha256
                (base32
-                "12vpip67ajb90b8p96w43ir7mavrw2i61bwvpfnrlmlj9kj3w20i"))))
+                "18w98prfbivvygiyamsf9yg090kzbnvw2fn9b27823gmis4d08ny"))))
     (build-system r-build-system)
     (home-page "https://github.com/yihui/mime")
     (synopsis "R package to map filenames to MIME types")
@@ -1400,13 +1400,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
     (name "r-knitr")
-    (version "1.26")
+    (version "1.27")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "knitr" version))
               (sha256
                (base32
-                "08f3bdd5cnnbigybr9vmkhq12n64pbmn4layl3w5rwk8xi5kbnrq"))))
+                "02nysgnx6xv0kd351s1d59yx4g0drsd9lmcgxs0rsw5f1jiycgdg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-evaluate" ,r-evaluate)
@@ -1607,13 +1607,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.4.2")
+    (version "0.4.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "0fczcp17kaz3s4p0nd4126bppwl20vpxfybhsndpcky9h75wklgv"))))
+                "0qsqfikbsj55x5brghnkzzp7pz0japr4xnzm993f668mlls3f6i4"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1799,13 +1799,13 @@ times.")
 (define-public r-data-table
   (package
     (name "r-data-table")
-    (version "1.12.6")
+    (version "1.12.8")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "data.table" version))
               (sha256
                (base32
-                "1kgbnm5gv7ax7qn8irpz7qsry2ci21axga8y7qpkidcqkxkkndn2"))))
+                "1p7rf4v3ysflpgcmy9krkwmcy7z22wb08xm443649waz6lx5z9yk"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
@@ -1843,13 +1843,13 @@ and fast file reading.")
 (define-public python-patsy
   (package
     (name "python-patsy")
-    (version "0.4.1")
+    (version "0.5.1")
     (source (origin
               (method url-fetch)
-              (uri (pypi-uri "patsy" version ".zip"))
+              (uri (pypi-uri "patsy" version))
               (sha256
                (base32
-                "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
+                "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1861,8 +1861,7 @@ and fast file reading.")
        ("python-scipy" ,python-scipy)
        ("python-six" ,python-six)))
     (native-inputs
-     `(("python-nose" ,python-nose)
-       ("unzip" ,unzip)))
+     `(("python-nose" ,python-nose)))
     (home-page "https://github.com/pydata/patsy")
     (synopsis "Describe statistical models and build design matrices")
     (description
@@ -2032,13 +2031,13 @@ jackknifed confidence intervals are available for most estimates.")
 (define-public r-rversions
   (package
     (name "r-rversions")
-    (version "2.0.0")
+    (version "2.0.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rversions" version))
               (sha256
                (base32
-                "0mkg9zrjxlbwqzijiysivrs523x48syqj30xdfp88clpkqfk435m"))))
+                "1ic6sxnyya24d5xsxjg3fba73fhya9fhs0kaf66yha6nwxj1zv2i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -2260,13 +2259,13 @@ tables, autolinks and strikethrough text.")
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "7.0.1")
+    (version "7.0.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "07v7f7may3vr80f4m1w1ll41qdahszycyx4c1yf8pw7asx73d77j"))))
+                "162xag27hwwyadfwm5zpyy15nxwhw2vbhwapx3jmi9cfyryr68sq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-brew" ,r-brew)
@@ -2456,14 +2455,14 @@ were originally a part of the r-devtools package.")
 (define-public r-hms
   (package
     (name "r-hms")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "hms" version))
        (sha256
         (base32
-         "0h24dsagn4kcr65arn73mpqapcg002kw4kyxfqyff95j6s6cjifl"))))
+         "1baki0qw5ijgiflvsdvqj3apg4yanf12vx14kwbqdzk5rz46fasf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rlang" ,r-rlang)
@@ -2505,13 +2504,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7-6")
+    (version "3.7-7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "0ijfjlr7ls5hvfyzdmwab6bx0w3nvp0c8fgynj4355cj8mbzgmc3"))))
+                "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -2540,18 +2539,20 @@ scaling functions for R.")
 (define-public r-latticeextra
   (package
     (name "r-latticeextra")
-    (version "0.6-28")
+    (version "0.6-29")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "latticeExtra" version))
        (sha256
         (base32
-         "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
+         "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
     (properties `((upstream-name . "latticeExtra")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-lattice" ,r-lattice)
+     `(("r-jpeg" ,r-jpeg)
+       ("r-lattice" ,r-lattice)
+       ("r-png" ,r-png)
        ("r-rcolorbrewer" ,r-rcolorbrewer)))
     (home-page "http://latticeextra.r-forge.r-project.org/")
     (synopsis "Extra graphical utilities based on lattice")
@@ -2564,13 +2565,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.800.1.0")
+    (version "0.9.800.4.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1frg7y3fb571jf9dp1kkc75x0nxvw8j3qccsrm1brg5l1z2jmlaz"))))
+                "1csh54v4d0ccwmk4bqj4rca1d5rqpafvb4459x3q6k9sys0charx"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     ;; All needed for vignettes
@@ -2616,13 +2617,13 @@ vectors.")
 (define-public r-catools
   (package
     (name "r-catools")
-    (version "1.17.1.3")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "caTools" version))
               (sha256
                (base32
-                "04m7vbydxb1nipday97w29p2miykyzxw572j9lda6jxmmp2kb1yp"))))
+                "0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
     (properties `((upstream-name . "caTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2662,13 +2663,13 @@ certain criterion, e.g., it contains a certain regular file.")
 (define-public r-rmarkdown
   (package
     (name "r-rmarkdown")
-    (version "1.18")
+    (version "2.1")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "rmarkdown" version))
         (sha256
-          (base32 "0fykzbb5kjsqc8v6gjcdma7rmq0gailp30qij6plgna4d8nhjw3w"))))
+          (base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg"))))
     (properties `((upstream-name . "rmarkdown")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2754,17 +2755,16 @@ that package, other packages are unaffected.")
 (define-public r-blob
   (package
     (name "r-blob")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "blob" version))
               (sha256
                (base32
-                "08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
+                "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-prettyunits" ,r-prettyunits)
-       ("r-rlang" ,r-rlang)
+     `(("r-rlang" ,r-rlang)
        ("r-vctrs" ,r-vctrs)))
     (home-page "https://github.com/hadley/blob")
     (synopsis "Simple S3 Class for representing vectors of binary data")
@@ -2777,13 +2777,13 @@ a column in data frame.")
 (define-public r-rsqlite
   (package
     (name "r-rsqlite")
-    (version "2.1.2")
+    (version "2.2.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RSQLite" version))
               (sha256
                (base32
-                "1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
+                "1m38sj8rwbf3p2lhqabcp7c7djk7s9ng37cz39yxk706v9pi4380"))))
     (properties `((upstream-name . "RSQLite")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2849,13 +2849,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.98-1.20")
+    (version "3.99-0.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
+                "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)
@@ -2972,14 +2972,14 @@ statements.")
 (define-public r-segmented
   (package
     (name "r-segmented")
-    (version "1.0-0")
+    (version "1.1-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "segmented" version))
        (sha256
         (base32
-         "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf"))))
+         "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/segmented")
     (synopsis "Regression models with breakpoints estimation")
@@ -3013,16 +3013,16 @@ worker processes and collect and return the results on the master.")
 (define-public r-sparsem
   (package
     (name "r-sparsem")
-    (version "1.77")
+    (version "1.78")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "SparseM" version))
               (sha256
                (base32
-                "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
+                "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn"))))
     (properties
      `((upstream-name . "SparseM")))
-    (inputs
+    (native-inputs
      `(("gfortran" ,gfortran)))
     (build-system r-build-system)
     (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
@@ -3130,13 +3130,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.10")
+    (version "0.11")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "0vwhn1mcwv0hkbxnppf6vip23iiib0szvp1h3prawlkvd74xziiw"))))
+                "09k9s07aah1apc308sj1abvr27mky6fkpl9j6lxl2x55n4immvkg"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3207,13 +3207,13 @@ analysis of large sparse or dense matrices.")
 (define-public r-glmnet
   (package
    (name "r-glmnet")
-   (version "3.0-1")
+   (version "3.0-2")
    (source
     (origin
      (method url-fetch)
      (uri (cran-uri "glmnet" version))
      (sha256
-      (base32 "04wa926mnss53p1fhx0mjgxnmwmmqls12sc0sy7w09kbmyqa3fq7"))))
+      (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl"))))
    (build-system r-build-system)
    (native-inputs
     `(("gfortran" ,gfortran)))
@@ -3234,17 +3234,18 @@ path-wise fashion.")
 (define-public r-pkgmaker
   (package
     (name "r-pkgmaker")
-    (version "0.27")
+    (version "0.31")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgmaker" version))
        (sha256
         (base32
-         "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
+         "0cc6v6kpwxwwh7k7zyw13wqdp0f9qzzr1a7vv02lskgii54aa4nb"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-bibtex" ,r-bibtex)
+     `(("r-assertthat" ,r-assertthat)
+       ("r-bibtex" ,r-bibtex)
        ("r-codetools" ,r-codetools)
        ("r-digest" ,r-digest)
        ("r-magrittr" ,r-magrittr)
@@ -3283,19 +3284,17 @@ package registries.")
 (define-public r-rngtools
   (package
     (name "r-rngtools")
-    (version "1.4")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rngtools" version))
        (sha256
         (base32
-         "1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
+         "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-digest" ,r-digest)
-       ("r-pkgmaker" ,r-pkgmaker)
-       ("r-stringr" ,r-stringr)))
+     `(("r-digest" ,r-digest)))
     (home-page "https://renozao.github.io/rngtools")
     (synopsis "Utility functions for working with random number generators")
     (description
@@ -3400,14 +3399,14 @@ message passing.")
 (define-public r-bigmemory
   (package
     (name "r-bigmemory")
-    (version "4.5.33")
+    (version "4.5.36")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bigmemory" version))
        (sha256
         (base32
-         "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
+         "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
@@ -3511,13 +3510,13 @@ maintenance for package developers.")
 (define-public r-r-utils
   (package
     (name "r-r-utils")
-    (version "2.9.0")
+    (version "2.9.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.utils" version))
               (sha256
                (base32
-                "1w4zn2db15bggfnh64fbyi2z2sj47rcd4xn53b28dsnkamdcramj"))))
+                "1krj1ny7y43lpm2q8c7swxfdc3ngy2j8knzv71f8bfsgh673nsxc"))))
     (properties `((upstream-name . "R.utils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3533,13 +3532,13 @@ developing R packages.")
 (define-public r-r-cache
   (package
     (name "r-r-cache")
-    (version "0.13.0")
+    (version "0.14.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.cache" version))
               (sha256
                (base32
-                "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
+                "1n8n5ihkryrbxv630dwhz4r048nyv676qd3i9f5z5fa04hvlxbqq"))))
     (properties `((upstream-name . "R.cache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3591,15 +3590,15 @@ vignettes.")
 (define-public r-mvtnorm
   (package
     (name "r-mvtnorm")
-    (version "1.0-11")
+    (version "1.0-12")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "mvtnorm" version))
               (sha256
                (base32
-                "0lkjph661blc1nwfzg9w48a60wvj6ffh4zjwlisvracsx4nn2883"))))
+                "03rfmii9j8x8fjv7hp8qd28z0svl4w0x54k2f4jpwv4qa7079i24"))))
     (build-system r-build-system)
-    (inputs
+    (native-inputs
      `(("gfortran" ,gfortran)))
     (home-page "http://mvtnorm.R-forge.R-project.org")
     (synopsis "Package for multivariate normal and t-distributions")
@@ -3713,14 +3712,14 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "1.0.0")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "1403j0xd93l0r7qj738ryd5zc79hbcghrzybib3c3hrnaq5s78cj"))))
+         "0safj8bcf8libwr0jx4059bmarngvhfddrcv8k5iw39m9lpxs0r4"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -4080,14 +4079,14 @@ hierarchical clustering dendrograms.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.46.0")
+    (version "1.48.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0"))))
+         "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -4215,14 +4214,14 @@ including:
 (define-public r-gplots
   (package
     (name "r-gplots")
-    (version "3.0.1.1")
+    (version "3.0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gplots" version))
        (sha256
         (base32
-         "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx"))))
+         "0vrm7wqrmqsmfrc070r9chpzb0vv60pay2lyar9qxfry6bsrvx86"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-catools" ,r-catools)
@@ -4285,13 +4284,13 @@ mechanism.")
 (define-public r-zoo
   (package
     (name "r-zoo")
-    (version "1.8-6")
+    (version "1.8-7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "zoo" version))
               (sha256
                (base32
-                "1k1pmzr9nfwbxq1xf0jzn3nawv4sgnkxkgzxnm1i887jcbrs85r2"))))
+                "1w4542zs53bm261g95086a60576v334g1jrhnbgdqni4izf2s1wy"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -4441,13 +4440,13 @@ Wall Street Journal, among others.  This package also provides
 (define-public r-statmod
   (package
     (name "r-statmod")
-    (version "1.4.32")
+    (version "1.4.33")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "statmod" version))
               (sha256
                (base32
-                "083yyp84xj85zg4bhz7i90bqzl3p6155ch4abwsfc9k1lv7s2rrg"))))
+                "1fbi5m4c0lingm2vvi0g6jf8f2mg1h01xwyz5rnymrq7gs0ibiks"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/statmod")
     (native-inputs
@@ -4742,14 +4741,14 @@ and resampling-based inference.")
 (define-public r-prabclus
   (package
     (name "r-prabclus")
-    (version "2.3-1")
+    (version "2.3-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "prabclus" version))
        (sha256
         (base32
-         "1h5k13w8mmmdy74l145zh64f339wy78z1nlg8xr3zg23gmv98cpg"))))
+         "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-mass" ,r-mass)
@@ -4834,18 +4833,17 @@ analysis} (PCA) by projection pursuit.")
 (define-public r-rrcov
   (package
     (name "r-rrcov")
-    (version "1.4-9")
+    (version "1.5-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rrcov" version))
        (sha256
         (base32
-         "11zvxidlb1pr2j5dzvmbjqdgsmmicsq8ppjf5wcfykfyf2fkcmz7"))))
+         "0m62k58nabw7hjz1qyyf9a0d6lvcz5vcvpksjnq93zcfra9inr57"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-cluster" ,r-cluster)
-       ("r-lattice" ,r-lattice)
+     `(("r-lattice" ,r-lattice)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-pcapp" ,r-pcapp)
        ("r-robustbase" ,r-robustbase)))
@@ -4889,14 +4887,14 @@ generally.")
 (define-public r-robust
   (package
     (name "r-robust")
-    (version "0.4-18.1")
+    (version "0.4-18.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "robust" version))
        (sha256
         (base32
-         "0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy"))))
+         "02x7d6dgx3skiadvx5m3c44b4bhz37ycpfhc25dhhv50y1db6l3k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-fit-models" ,r-fit-models)
@@ -4938,14 +4936,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.2-3")
+    (version "2.2-4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
+         "1gsnl5sbdg86b2wdrsy6wq83xj6mrziiq7rxa8cqksgljc7gp6yf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -5062,14 +5060,14 @@ decompositions of such matrices, and solutions of linear systems.")
 (define-public r-modelmetrics
   (package
     (name "r-modelmetrics")
-    (version "1.2.2")
+    (version "1.2.2.1")
     (source
      (origin
        (method url-fetch)
         (uri (cran-uri "ModelMetrics" version))
         (sha256
          (base32
-          "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
+          "17yw46yr0n9hddvlhh73jdpmpdlpa581n5xjpwkr6cpr2f7xxpqc"))))
     (properties `((upstream-name . "ModelMetrics")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5107,13 +5105,13 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.52")
+    (version "5.54")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
-        (base32 "0rq9as31wiz41lmi9hmdq3gknpcbpwqzfcn065ysjdxzjdb57dcy"))))
+        (base32 "19nh79qrkb75q348nk148l8wqjwnq5jgq29wpzqym5cfv1kjqfvh"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -5236,13 +5234,13 @@ Companion to Applied Regression, Third Edition, Sage.")
 (define-public r-car
   (package
     (name "r-car")
-    (version "3.0-5")
+    (version "3.0-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "car" version))
        (sha256
-        (base32 "0w7fm81pn0wqrwzbjyddnrkpjl8gavg7ijh7rab9f21rkgkzgm3y"))))
+        (base32 "0yv5mwaa0ymrbis9590mx0zcj3w6j4drhs6ab13zhx4zc3x1b7b6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
@@ -5263,35 +5261,6 @@ Companion to Applied Regression, Third Edition, Sage.")
 to Applied regression, Second Edition, Sage, 2011.")
     (license license:gpl2+)))
 
-(define-public r-caret
-  (package
-    (name "r-caret")
-    (version "6.0-84")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "caret" version))
-       (sha256
-        (base32
-         "03898irgb70q0p01kq99yb6q6xji0jx4jmj0yxlv8wcwd841r0x1"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-lattice" ,r-lattice)
-       ("r-modelmetrics" ,r-modelmetrics)
-       ("r-nlme" ,r-nlme)
-       ("r-plyr" ,r-plyr)
-       ("r-recipes" ,r-recipes)
-       ("r-reshape2" ,r-reshape2)
-       ("r-withr" ,r-withr)))
-    (home-page "https://github.com/topepo/caret")
-    (synopsis "Classification and regression training")
-    (description
-     "This package provides misc functions for training and plotting
-classification and regression models.")
-    (license license:gpl2+)))
-
 (define-public r-rcppprogress
   (package
     (name "r-rcppprogress")
@@ -5413,14 +5382,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
 (define-public r-ranger
   (package
     (name "r-ranger")
-    (version "0.11.2")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ranger" version))
        (sha256
         (base32
-         "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k"))))
+         "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-rcpp" ,r-rcpp)
@@ -5656,20 +5625,20 @@ inferring an appropriate positioning method.")
     (license license:gpl3)))
 
 (define-public r-catterplots
-  (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
-        (revision "2"))
+  (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
+        (revision "3"))
     (package
       (name "r-catterplots")
-      (version (string-append "0-" revision "." (string-take commit 9)))
+      (version (git-version "0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
                       (url "https://github.com/Gibbsdavidl/CatterPlots.git")
                       (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
+                  "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
       (build-system r-build-system)
       (propagated-inputs
        `(("r-png" ,r-png)))