gnu: Add emacs-sbt-mode.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index dfd26ab..03a63e6 100644 (file)
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -88,7 +88,7 @@
 (define-public pspp
   (package
     (name "pspp")
-    (version "1.2.0")
+    (version "1.4.1")
     (source
      (origin
       (method url-fetch)
@@ -96,7 +96,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
+        "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan"))))
     (build-system gnu-build-system)
     (inputs
      `(("cairo" ,cairo)
@@ -106,7 +106,7 @@
        ("pango" ,pango)
        ("readline" ,readline)
        ("gtk" ,gtk+)
-       ("gtksourceview" ,gtksourceview)
+       ("gtksourceview" ,gtksourceview-3)
        ("spread-sheet-widget" ,spread-sheet-widget)
        ("zlib" ,zlib)))
     (native-inputs
@@ -160,14 +160,14 @@ simulation not wholly unlike BUGS.  JAGS was written with three aims in mind:
 (define-public libxls
   (package
     (name "libxls")
-    (version "1.5.2")
+    (version "1.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/libxls/libxls/releases/download/"
                            "v" version "/libxls-" version ".tar.gz"))
        (sha256
-        (base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld"))))
+        (base32 "0rl513wpq5qh7wkmdk4g9c68rzffv3mcbz48p4xyg4969zrx8lnm"))))
     (build-system gnu-build-system)
     (home-page "https://github.com/libxls/libxls")
     (synopsis "Read binary (.xls) Excel spreadsheet files")
@@ -429,14 +429,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51.6")
+    (version "7.3-53")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
+         "0f2bwsbqr3nzsqxva051lg8wd068naqif3vc48hac0m3mmq4x0j1"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -599,13 +599,13 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-nlme
   (package
     (name "r-nlme")
-    (version "3.1-148")
+    (version "3.1-149")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nlme" version))
        (sha256
-        (base32 "1cmf43r82kar1hpj9dhqfi3rbjka0z5s6cbdy7fklwh99xj3phkp"))))
+        (base32 "16n39v36hdp5vy3s3xqgs6ai0vgzx6j2py7ghpljdahndbqn6qn9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)))
@@ -621,13 +621,13 @@ nonlinear mixed-effects models.")
 (define-public r-mgcv
   (package
    (name "r-mgcv")
-   (version "1.8-31")
+   (version "1.8-33")
    (source
     (origin
      (method url-fetch)
      (uri (cran-uri "mgcv" version))
      (sha256
-      (base32 "1if34mqsn9r7g0l82lxvvx0wjhi9paqdymyd73nschxcl1if8vbk"))))
+      (base32 "1x1bdzz2b2f05626xygwqp30b4rhblgg76hs15j9ab4fjan7pjwq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-matrix" ,r-matrix)
@@ -748,15 +748,17 @@ curves, Cox models, and parametric accelerated failure time models.")
 (define-public r-bit
   (package
     (name "r-bit")
-    (version "1.1-15.2")
+    (version "4.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bit" version))
        (sha256
         (base32
-         "12xjkkkmflkz8s435by4r23b57cz7z67z84907f6qg99hn1yg0qb"))))
+         "0s7isadibxp2wr62r5cpbyh9z31sczzfz4j3rm7gxgjfpqgq8174"))))
     (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "http://ff.r-forge.r-project.org")
     (synopsis "Class for vectors of 1-bit booleans")
     (description
@@ -769,14 +771,14 @@ binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
 (define-public r-bit64
   (package
     (name "r-bit64")
-    (version "0.9-7")
+    (version "4.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bit64" version))
        (sha256
         (base32
-         "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
+         "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bit" ,r-bit)))
@@ -1024,14 +1026,14 @@ solution for sending email, including attachments, from within R.")
 (define-public r-stringi
   (package
     (name "r-stringi")
-    (version "1.4.6")
+    (version "1.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringi" version))
        (sha256
         (base32
-         "1mkgxzf000zdgbbbvg2vf4md4l501n5lfksffq8vdg6pbgd6fgv3"))))
+         "0420f7zn5knyyvd3a3xa7059l4kadw0m67rfpivacqn9xn6iwkr2"))))
     (build-system r-build-system)
     (inputs `(("icu4c" ,icu4c)))
     (native-inputs `(("pkg-config" ,pkg-config)))
@@ -1133,18 +1135,19 @@ aesthetic attributes.")
 (define-public r-ggdendro
   (package
     (name "r-ggdendro")
-    (version "0.1-20")
+    (version "0.1.22")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "ggdendro" version))
               (sha256
                (base32
-                "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
+                "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
-       ("r-mass" ,r-mass)
-       ("r-knitr" ,r-knitr)))
+       ("r-mass" ,r-mass)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/andrie/ggdendro")
     (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
     (description "This is a set of tools for dendrograms and tree plots using
@@ -1187,19 +1190,21 @@ and to generate base64 encoded string from raster matrix.")
 (define-public r-svglite
   (package
     (name "r-svglite")
-    (version "1.2.3")
+    (version "1.2.3.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "svglite" version))
        (sha256
         (base32
-         "1zivykbi1pxdxhrkc1if1ihdn5p27j0nai2q0abca1dwry3wg2yl"))))
+         "00n8bg4iligl0h24v42cka417w26zmcxrr4r6k8wdal1riwhgmi5"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bh" ,r-bh)
        ("r-gdtools" ,r-gdtools)
        ("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/svglite")
     (synopsis "SVG graphics device")
     (description
@@ -1617,13 +1622,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
     (name "r-rlang")
-    (version "0.4.6")
+    (version "0.4.7")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "rlang" version))
               (sha256
                (base32
-                "1jik4lywg4688dfi5fh8jbnmsxvq3382ii0nsw5armjzfq3v309s"))))
+                "0f4rhnhyhgrv874l0yzm80ij6vcqdykfd7bzmnqs0wbgyhkxk8vq"))))
     (build-system r-build-system)
     (home-page "http://rlang.tidyverse.org")
     (synopsis "Functions for base types, core R and Tidyverse features")
@@ -1635,14 +1640,14 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
     (name "r-tibble")
-    (version "3.0.1")
+    (version "3.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tibble" version))
        (sha256
         (base32
-         "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
+         "0f4yi87w6509lnaz1lhk9s8nm3bzx21ij3273s0zx7vpbp0qlxxz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -1667,13 +1672,13 @@ and printing capabilities than traditional data frames.")
 (define-public r-dplyr
   (package
     (name "r-dplyr")
-    (version "1.0.0")
+    (version "1.0.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "dplyr" version))
               (sha256
                (base32
-                "1wxi7pzw1mqkgay2s9hwlkpkxfzydngf56wrf7k93n14rlqm3dmz"))))
+                "0jnw18nw20gw3jvq3kvkf9mqn6b7mvgmys8g6350k5jwpygk5cbw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ellipsis" ,r-ellipsis)
@@ -1803,13 +1808,13 @@ and density estimation.")
 (define-public r-chron
   (package
     (name "r-chron")
-    (version "2.3-55")
+    (version "2.3-56")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "chron" version))
               (sha256
                (base32
-                "09gbs7c1ynlg0kl1m6nkbn75ysk16g13r17snnaws64qwywiywqg"))))
+                "0p9zz96jfyf139924hdwkzhr8knkjvx6547ac53rknm3a6wwngl6"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/chron")
     (synopsis "Chronological R objects which can handle dates and times")
@@ -1821,18 +1826,19 @@ times.")
 (define-public r-data-table
   (package
     (name "r-data-table")
-    (version "1.12.8")
+    (version "1.13.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "data.table" version))
               (sha256
                (base32
-                "1p7rf4v3ysflpgcmy9krkwmcy7z22wb08xm443649waz6lx5z9yk"))))
+                "0wihpg1syjxzsij2fmhwh30vvf2cghw2b2qi79w36qwil2s8w2gn"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
     (home-page "https://github.com/Rdatatable/data.table/wiki")
     (synopsis "Enhanced version of data.frame R object")
     (description
@@ -2094,14 +2100,14 @@ limited to R.")
 (define-public r-backports
   (package
     (name "r-backports")
-    (version "1.1.8")
+    (version "1.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "backports" version))
        (sha256
         (base32
-         "1irc9c23hwliwkky1b3hi0dkzwalhb7zgjj08562ff1k8dqv4qf6"))))
+         "1mz3r6ad484xmx0i89gvmak4wzl4cp59gxdzirrci9znw1axrrvx"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/backports")
     (synopsis "Reimplementations of functions introduced since R 3.0.0")
@@ -2282,13 +2288,13 @@ tables, autolinks and strikethrough text.")
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "7.1.0")
+    (version "7.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "00s1wzx5960k8pzgpz4kikjf4k061hyhnd278y65q6n0wzv3d6vy"))))
+                "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-brew" ,r-brew)
@@ -2304,6 +2310,8 @@ tables, autolinks and strikethrough text.")
        ("r-stringi" ,r-stringi)
        ("r-stringr" ,r-stringr)
        ("r-xml2" ,r-xml2)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/klutometis/roxygen")
     (synopsis "In-source documentation system for R")
     (description
@@ -2314,19 +2322,20 @@ collation, and NAMESPACE files.")
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
+         "17fkc6pr8w5z3rpadg692a689p1v4j7xl5ak0y64is7c74cxgljx"))))
     (build-system r-build-system)
     (inputs
      `(("libressl" ,libressl)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
     (propagated-inputs
      `(("r-askpass" ,r-askpass)))
     (home-page "https://github.com/jeroenooms/openssl")
@@ -2347,13 +2356,13 @@ integers.")
 (define-public r-httr
   (package
     (name "r-httr")
-    (version "1.4.1")
+    (version "1.4.2")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "httr" version))
               (sha256
                (base32
-                "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
+                "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-curl" ,r-curl)
@@ -2361,6 +2370,8 @@ integers.")
        ("r-openssl" ,r-openssl)
        ("r-mime" ,r-mime)
        ("r-r6" ,r-r6)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/hadley/httr")
     (synopsis "Tools for working with URLs and HTTP")
     (description
@@ -2415,25 +2426,21 @@ informative error messages when it's not available.")
 (define-public r-devtools
   (package
     (name "r-devtools")
-    (version "2.3.0")
+    (version "2.3.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "devtools" version))
               (sha256
                (base32
-                "1l6w765q180bg5mmdq5k2ymf6apz7ldhnknzf6ynfp1kf70pbhsg"))))
+                "100mgighf6vqsfwv2qw5rlnd5sfvcji9l9jrmx9ii28r9fd2gyas"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
        ("r-cli" ,r-cli)
        ("r-covr" ,r-covr)
-       ("r-crayon" ,r-crayon)
        ("r-desc" ,r-desc)
-       ("r-digest" ,r-digest)
        ("r-dt" ,r-dt)
        ("r-ellipsis" ,r-ellipsis)
-       ("r-glue" ,r-glue)
-       ("r-git2r" ,r-git2r)
        ("r-httr" ,r-httr)
        ("r-jsonlite" ,r-jsonlite)
        ("r-memoise" ,r-memoise)
@@ -2591,13 +2598,13 @@ well as additional utilities such as panel and axis annotation functions.")
 (define-public r-rcpparmadillo
   (package
     (name "r-rcpparmadillo")
-    (version "0.9.900.1.0")
+    (version "0.9.900.3.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "RcppArmadillo" version))
               (sha256
                (base32
-                "1zisw2yrb9qmmrs7q8y83mrm7lh1c2786h70gs8jwc0si16x0lq5"))))
+                "0x8jm6cvfvp1kyckwwqxyy5hfkr8na28fih3k0lhi55wry3ml30q"))))
     (properties `((upstream-name . "RcppArmadillo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -2703,7 +2710,7 @@ certain criterion, e.g., it contains a certain regular file.")
        ("r-tinytex" ,r-tinytex)
        ("r-xfun" ,r-xfun)
        ("r-yaml" ,r-yaml)
-       ("ghc-pandoc" ,ghc-pandoc)))
+       ("pandoc" ,pandoc)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://rmarkdown.rstudio.com")
@@ -2871,13 +2878,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
 (define-public r-xml
   (package
     (name "r-xml")
-    (version "3.99-0.3")
+    (version "3.99-0.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "XML" version))
               (sha256
                (base32
-                "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
+                "19jkpnbjx2ij0h7rxi13sqnjnwsap6wywmd4gnhfnqpic1rrnlk0"))))
     (properties
      `((upstream-name . "XML")))
     (build-system r-build-system)
@@ -3154,13 +3161,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.14")
+    (version "0.15")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "0xhinw7wasrai5wfswp3r48qfv7ppdfd9jc7py2rp63dn0bnvbab"))))
+                "1wc2aiqkn01i571h29847yaq7vb624bkf44axp4ygpn0r85hdq7k"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3451,13 +3458,13 @@ memory-mapped files.")
 (define-public r-r-methodss3
   (package
     (name "r-r-methodss3")
-    (version "1.8.0")
+    (version "1.8.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.methodsS3" version))
               (sha256
                (base32
-                "19c5870v7b59fs6xk58bh3rfkmhfralmgsax86zzpdmz47pga1g0"))))
+                "16v1br7lf7vxv40z65giv9jnqkpnyqagcmgqa0s1jy7spj0zp64a"))))
     (properties `((upstream-name . "R.methodsS3")))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
@@ -3475,13 +3482,13 @@ want to migrate to S4.")
 (define-public r-r-oo
   (package
     (name "r-r-oo")
-    (version "1.23.0")
+    (version "1.24.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.oo" version))
               (sha256
                (base32
-                "189fb7mmyzwg6nn8rza8iip7fbyws7i2vkmzy672x9mhvgilq4pm"))))
+                "1divisff26fmiqg6vmabnwlrx079c066r8qvkakfp336vnwdm89p"))))
     (properties `((upstream-name . "R.oo")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3498,13 +3505,13 @@ maintenance for package developers.")
 (define-public r-r-utils
   (package
     (name "r-r-utils")
-    (version "2.9.2")
+    (version "2.10.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.utils" version))
               (sha256
                (base32
-                "1krj1ny7y43lpm2q8c7swxfdc3ngy2j8knzv71f8bfsgh673nsxc"))))
+                "1gssnk73nhisc20by9kvfl4byfsmwrk6597na0x40ycck58lyylm"))))
     (properties `((upstream-name . "R.utils")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3546,13 +3553,13 @@ persistent (on the file system).")
 (define-public r-r-rsp
   (package
     (name "r-r-rsp")
-    (version "0.43.2")
+    (version "0.44.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.rsp" version))
               (sha256
                (base32
-                "128zqyvbq9hm9gy86jzhj609lkfw57vr24mdxgh46ncmx66ag4gj"))))
+                "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9"))))
     (properties `((upstream-name . "R.rsp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3705,17 +3712,18 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "1.1.0")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "0vqj5dakb35axv4l0yrihpa16vnz2b5bhaaqg7l0gsqbb04qcb00"))))
+         "0v7x1pgmwmjypzdr4j2ig2klgrrgryi3qvw8hwqv65a5h9kwpz08"))))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-dplyr" ,r-dplyr)
+     `(("r-cpp11" ,r-cpp11)
+       ("r-dplyr" ,r-dplyr)
        ("r-ellipsis" ,r-ellipsis)
        ("r-magrittr" ,r-magrittr)
        ("r-glue" ,r-glue)
@@ -3723,8 +3731,6 @@ selection.")
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
        ("r-tidyselect" ,r-tidyselect)
-       ("r-rcpp" ,r-rcpp)
-       ("r-stringi" ,r-stringi)
        ("r-tibble" ,r-tibble)
        ("r-vctrs" ,r-vctrs)))
     (native-inputs
@@ -3994,20 +4000,19 @@ package instead.")
 (define-public r-hmisc
   (package
     (name "r-hmisc")
-    (version "4.4-0")
+    (version "4.4-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Hmisc" version))
        (sha256
-        (base32 "1ivfamwghd2z408fkhs7jy5zl3q0z1a2la16yi8js872br6cyvpi"))))
+        (base32 "0mm3r2kv0kgrhg7salk2hw0s37d4i2mghwk0l0qxaw2ny0w8w5z6"))))
     (properties `((upstream-name . "Hmisc")))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
     (propagated-inputs
-     `(("r-acepack" ,r-acepack)
-       ("r-base64enc" ,r-base64enc)
+     `(("r-base64enc" ,r-base64enc)
        ("r-cluster" ,r-cluster)
        ("r-data-table" ,r-data-table)
        ("r-foreign" ,r-foreign)
@@ -4074,27 +4079,6 @@ framework, with additional code inspection and report generation tools.")
 hierarchical clustering dendrograms.")
     (license license:gpl2+)))
 
-(define-public r-preprocesscore
-  (package
-    (name "r-preprocesscore")
-    (version "1.50.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "preprocessCore" version))
-       (sha256
-        (base32
-         "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
-    (properties
-     `((upstream-name . "preprocessCore")))
-    (build-system r-build-system)
-    (home-page "https://github.com/bmbolstad/preprocessCore")
-    (synopsis "Collection of pre-processing functions")
-    (description
-     "This package provides a library of core pre-processing and normalization
-routines.")
-    (license license:lgpl2.0+)))
-
 (define-public r-fastcluster
   (package
     (name "r-fastcluster")
@@ -4212,20 +4196,22 @@ including:
 (define-public r-gplots
   (package
     (name "r-gplots")
-    (version "3.0.3")
+    (version "3.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gplots" version))
        (sha256
         (base32
-         "0hs6mk48i9yd43rg9wfjc2nxsjjwrnpifxqvxkv8ah18kvpd6xnp"))))
+         "15ip3v4xiqzbanf8bc5fj90cbwdgixr72aj5jrp34jfdzdx0gxwg"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-catools" ,r-catools)
        ("r-gdata" ,r-gdata)
        ("r-gtools" ,r-gtools)
        ("r-kernsmooth" ,r-kernsmooth)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://cran.r-project.org/web/packages/gplots")
     (synopsis "Various R programming tools for plotting data")
     (description
@@ -4515,20 +4501,22 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
 (define-public r-cowplot
   (package
     (name "r-cowplot")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cowplot" version))
        (sha256
         (base32
-         "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
+         "04d5pg4xi9nhgcbam71b5mp3q1g804ng864v90add1kddfyl3f9h"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ggplot2" ,r-ggplot2)
        ("r-gtable" ,r-gtable)
        ("r-rlang" ,r-rlang)
        ("r-scales" ,r-scales)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "https://github.com/wilkelab/cowplot")
     (synopsis "Streamlined plot theme and plot annotations for ggplot2")
     (description
@@ -4815,14 +4803,14 @@ analysis} (PCA) by projection pursuit.")
 (define-public r-rrcov
   (package
     (name "r-rrcov")
-    (version "1.5-2")
+    (version "1.5-5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rrcov" version))
        (sha256
         (base32
-         "0m62k58nabw7hjz1qyyf9a0d6lvcz5vcvpksjnq93zcfra9inr57"))))
+         "0ag6q16ajkqwj28dk9vp4xkvqw26fqqqdxnz38gpszilirahfzqz"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-lattice" ,r-lattice)
@@ -4841,14 +4829,14 @@ estimation and robust multivariate analysis with high breakdown point.")
 (define-public r-fit-models
   (package
     (name "r-fit-models")
-    (version "0.63")
+    (version "0.64")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fit.models" version))
        (sha256
         (base32
-         "0wrrfsgngsfrqnm247f0h6g01807i7lbf5chpyx7hkfdfmm4xbxn"))))
+         "1nk4x2q8cv79zcls61saf627ac0fci6jcrd6lmzk61asm2zhc27p"))))
     (properties `((upstream-name . "fit.models")))
     (build-system r-build-system)
     (propagated-inputs
@@ -4918,14 +4906,14 @@ of the points.")
 (define-public r-fpc
   (package
     (name "r-fpc")
-    (version "2.2-6")
+    (version "2.2-7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fpc" version))
        (sha256
         (base32
-         "0lpn951gy58039gk2wh8nsw6qss8m3flkawv55yq3l6373ly79if"))))
+         "1xnp3j36hggfg675v39mnr6rgvp7i11pfng7nmyy3k2ldgklz0j9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -4974,14 +4962,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
 (define-public r-pbapply
   (package
     (name "r-pbapply")
-    (version "1.4-2")
+    (version "1.4-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pbapply" version))
        (sha256
         (base32
-         "1xmk4p006v8gij26rs6kp5prjyf2n32nqjxiyp8a6kvgyc4z46dc"))))
+         "08gb6c8p1r9z8wrfidj2dfn6irm43k6f4448d1d6nxmy6msjirlg"))))
     (build-system r-build-system)
     (home-page "https://github.com/psolymos/pbapply")
     (synopsis "Adding progress bar to apply functions")
@@ -5087,18 +5075,19 @@ using modular prediction and response module classes.")
 (define-public r-quantreg
   (package
     (name "r-quantreg")
-    (version "5.55")
+    (version "5.67")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "quantreg" version))
        (sha256
-        (base32 "1zjc8p95kb0ypxa6nxp0lkdq8armkjmmhf8484m25n5f14a59qfb"))))
+        (base32 "09hgch8x6x2k7wm17c0njp7l0r6rrrlcji60afrv19dm9r4596wr"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
     (propagated-inputs
-     `(("r-matrix" ,r-matrix)
+     `(("r-conquer" ,r-conquer)
+       ("r-matrix" ,r-matrix)
        ("r-matrixmodels" ,r-matrixmodels)
        ("r-sparsem" ,r-sparsem)))
     (home-page "https://www.r-project.org")
@@ -5114,14 +5103,14 @@ expected shortfall risk are also included.")
 (define-public r-nloptr
   (package
     (name "r-nloptr")
-    (version "1.2.2.1")
+    (version "1.2.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "nloptr" version))
        (sha256
         (base32
-         "1bhh2v14phzndjhiq7yw9vych6vzn5yy3vk9q35zcp3jhjjbwdyh"))))
+         "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr) ; for building vignettes
@@ -5220,13 +5209,13 @@ Companion to Applied Regression, Third Edition, Sage.")
 (define-public r-car
   (package
     (name "r-car")
-    (version "3.0-8")
+    (version "3.0-9")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "car" version))
        (sha256
-        (base32 "0ig1691kxbzkrsq8xi5a6fq2f0vq22j1dn54jxdkldqr5vri1m57"))))
+        (base32 "1clh8c7mj87i4hz27l16w76dpw7k4mlnjbgm9mbrhrfkv0lpb63c"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
@@ -5302,14 +5291,14 @@ normals.")
 (define-public r-mnormt
   (package
     (name "r-mnormt")
-    (version "2.0.0")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
         (uri (cran-uri "mnormt" version))
         (sha256
           (base32
-           "1gxhma0zqsx5pkc0871vszq1y7akwdmpm8rhws5b3gr6w9mx4agf"))))
+           "0d7ka4l4fl1wi77r2r81dc91n6cbj2xrb3lsizz5y0ziscva0sjw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-tmvnsim" ,r-tmvnsim)))
@@ -5442,14 +5431,14 @@ genome-wide association studies can be analyzed efficiently.")
 (define-public r-cairo
   (package
     (name "r-cairo")
-    (version "1.5-12")
+    (version "1.5-12.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Cairo" version))
        (sha256
         (base32
-         "02v29am4fac3fyq6y1w6r89zwbqqkxjsxrafcwb5s124ikxyl22f"))))
+         "14hgz5wmnhlbqkd1g662n1agmjnlj3pq69gfng1vb0ivr02l2lnx"))))
     (properties `((upstream-name . "Cairo")))
     (build-system r-build-system)
     (inputs
@@ -5627,7 +5616,7 @@ parameters.")
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://github.com/Gibbsdavidl/CatterPlots.git")
+                      (url "https://github.com/Gibbsdavidl/CatterPlots")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
@@ -5650,7 +5639,7 @@ shaped points?  Now you can!")
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/jalvesaq/colorout.git")
+             (url "https://github.com/jalvesaq/colorout")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
@@ -5675,76 +5664,87 @@ to any arbitrary string.  In this case, it is up to you to set valid values.")
     (license license:gpl3+)))
 
 (define-public python-rpy2
-  ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
-  ;; it fixes a regression when using ggplot 3.2.0.
-  (let ((changeset "19868a8")
-        (revision "1"))
-    (package
-      (name "python-rpy2")
-      (version (git-version "3.0.4" revision changeset))
-      (source
-       (origin
-         (method hg-fetch)
-         (uri (hg-reference
-               (url "https://bitbucket.org/rpy2/rpy2")
-               (changeset changeset)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
-      (build-system python-build-system)
-      (arguments
-       '(#:modules ((ice-9 ftw)
-                    (srfi srfi-1)
-                    (srfi srfi-26)
-                    (guix build utils)
-                    (guix build python-build-system))
-         #:phases
-         (modify-phases %standard-phases
-           (replace 'check
-             (lambda* (#:key outputs inputs #:allow-other-keys)
-               (let ((cwd (getcwd)))
-                 (setenv "TZ" "UTC")
-                 (setenv "PYTHONPATH"
-                         (string-append cwd "/build/"
-                                        (find (cut string-prefix? "lib" <>)
-                                              (scandir (string-append cwd "/build")))
-                                        ":"
-                                        (getenv "PYTHONPATH"))))
-               (invoke "pytest" "-v" "rpy/tests/"))))))
-      (propagated-inputs
-       `(("python-cffi" ,python-cffi)
-         ("python-six" ,python-six)
-         ("python-jinja2" ,python-jinja2)
-         ("python-numpy" ,python-numpy)
-         ("python-pandas" ,python-pandas)
-         ("python-pytz" ,python-pytz)
-         ("python-ipython" ,python-ipython)
-         ("python-tzlocal" ,python-tzlocal)))
-      (inputs
-       `(("readline" ,readline)
-         ("icu4c" ,icu4c)
-         ("pcre" ,pcre)
-         ("r-minimal" ,r-minimal)
-         ("r-survival" ,r-survival)
-         ("r-ggplot2" ,r-ggplot2)
-         ("r-rsqlite" ,r-rsqlite)
-         ("r-dplyr" ,r-dplyr)
-         ("r-dbplyr" ,r-dbplyr)
-         ("python-numpy" ,python-numpy)))
-      (native-inputs
-       `(("zlib" ,zlib)
-         ("python-pytest" ,python-pytest)))
-      (home-page "https://rpy2.bitbucket.io/")
-      (synopsis "Python interface to the R language")
-      (description "rpy2 is a redesign and rewrite of rpy.  It is providing a
+  (package
+    (name "python-rpy2")
+    (version "3.3.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "rpy2" version))
+        (sha256
+         (base32
+          "1bs36rds5fq8821l5q85q2b25161rs9ppw5c26x0hjwj487gpcfj"))
+        ;; These patches should be removed with the next release.
+        (patches
+          (list
+            (origin
+              (method url-fetch)
+              (uri "https://github.com/rpy2/rpy2/commit/04c57598f00145d868ea8da31ac1b1e7c49f7570.patch")
+              (file-name "python-rpy2-fix-test-failure.patch")
+              (sha256
+               (base32
+                "1lqd3yxjfx1rxrybcmnapy0r6ambg9myrb98q4nlfhpxanwfdbbh")))
+            (origin
+              (method url-fetch)
+              (uri "https://github.com/rpy2/rpy2/commit/685f67d0a6b47ea80e718116a10755019446aef7.patch")
+              (file-name "python-rpy2-r-console-test-fix.patch")
+              (sha256
+               (base32
+                "18wpvfaa4c13d44cb4sw88c3c7403xdy5m8h82wfq8fjmcq3cmzn")))))))
+    (build-system python-build-system)
+    (arguments
+     '(#:modules ((ice-9 ftw)
+                  (srfi srfi-1)
+                  (srfi srfi-26)
+                  (guix build utils)
+                  (guix build python-build-system))
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let ((cwd (getcwd)))
+               (setenv "TZ" "UTC")
+               (setenv "PYTHONPATH"
+                       (string-append cwd "/build/"
+                                      (find (cut string-prefix? "lib" <>)
+                                            (scandir (string-append cwd "/build")))
+                                      ":"
+                                      (getenv "PYTHONPATH"))))
+             ;; test_vector_complex has issues when run in our environment.
+             (invoke "pytest" "-v" "rpy2/tests/" "-k" "not test_vector_complex"))))))
+    (propagated-inputs
+     `(("python-cffi" ,python-cffi)
+       ("python-six" ,python-six)
+       ("python-jinja2" ,python-jinja2)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-pytz" ,python-pytz)
+       ("python-ipython" ,python-ipython)
+       ("python-tzlocal" ,python-tzlocal)))
+    (inputs
+     `(("readline" ,readline)
+       ("icu4c" ,icu4c)
+       ("pcre" ,pcre)
+       ("r-minimal" ,r-minimal)
+       ("r-survival" ,r-survival)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-dplyr" ,r-dplyr)
+       ("r-dbplyr" ,r-dbplyr)
+       ("python-numpy" ,python-numpy)))
+    (native-inputs
+     `(("zlib" ,zlib)
+       ("python-pytest" ,python-pytest)))
+    (home-page "https://rpy2.github.io")
+    (synopsis "Python interface to the R language")
+    (description "rpy2 is a redesign and rewrite of rpy.  It is providing a
 low-level interface to R from Python, a proposed high-level interface,
 including wrappers to graphical libraries, as well as R-like structures and
 functions.")
-      ;; Any of these licenses can be picked for the R interface.  The whole
-      ;; project is released under GPLv2+ according to the license declaration
-      ;; in "setup.py".
-      (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
+    ;; Any of these licenses can be picked for the R interface.  The whole
+    ;; project is released under GPLv2+ according to the license declaration
+    ;; in "setup.py".
+    (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
 
 (define-public java-jdistlib
   (package