gnu: julia: Update to 1.4.1.

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5058079..c91b0ee 100644 (file)
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1480,7 +1480,7 @@ applications.  That is, compute distances and related measures for angular
         (base32
          "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
     (build-system r-build-system)
-    (inputs `(("libjpeg" ,libjpeg)))
+    (inputs `(("libjpeg" ,libjpeg-turbo)))
     (home-page "https://www.rforge.net/jpeg/")
     (synopsis "Read and write JPEG images with R")
     (description "This package provides a way to read, write and display
@@ -1771,13 +1771,13 @@ processes.  Most of its code is based on the @code{psutil} Python package.")
 (define-public r-pkgbuild
   (package
     (name "r-pkgbuild")
-    (version "1.0.6")
+    (version "1.0.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgbuild" version))
        (sha256
-        (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
+        (base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -2272,14 +2272,14 @@ plot networks.")
 (define-public r-proxy
   (package
     (name "r-proxy")
-    (version "0.4-23")
+    (version "0.4-24")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proxy" version))
        (sha256
         (base32
-         "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
+         "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/proxy")
     (synopsis "Distance and similarity measures")
@@ -7084,14 +7084,14 @@ bootstrap.  Confidence intervals can be computed for (p)AUC or ROC curves.")
 (define-public r-rootsolve
   (package
     (name "r-rootsolve")
-    (version "1.8.2")
+    (version "1.8.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rootSolve" version))
        (sha256
         (base32
-         "0rj7c4zcrzgz7sb0vgvh7swpfafnw4040cxp7ypas3s8fnihn54l"))))
+         "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
     (properties `((upstream-name . "rootSolve")))
     (build-system r-build-system)
     (native-inputs `(("gfortran" ,gfortran)))
@@ -8920,14 +8920,14 @@ terminals that do not support Unicode.")
 (define-public r-usethis
   (package
     (name "r-usethis")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "usethis" version))
        (sha256
         (base32
-         "12iyimqyza752anj29wpfisl8nz5r25kfcqbssybg24nb4wyy146"))))
+         "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -9655,14 +9655,14 @@ features (e.g. local modes).")
 (define-public r-arm
   (package
     (name "r-arm")
-    (version "1.10-1")
+    (version "1.11-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "arm" version))
        (sha256
         (base32
-         "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
+         "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-abind" ,r-abind)
@@ -9900,7 +9900,7 @@ redundant complex conjugate when the input is real data.")
     (build-system r-build-system)
     (inputs
      `(("libtiff" ,libtiff)
-       ("libjpeg" ,libjpeg)
+       ("libjpeg" ,libjpeg-turbo)
        ("zlib" ,zlib)))
     (home-page "https://www.rforge.net/tiff/")
     (synopsis "Read and write TIFF images")
@@ -15435,14 +15435,14 @@ classification and regression models.")
 (define-public r-dalex
   (package
     (name "r-dalex")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "DALEX" version))
        (sha256
         (base32
-         "0mfcci54622gnk8al9fl2jhs9i2vfly7lam04y5rdacbyiam49j6"))))
+         "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
     (properties `((upstream-name . "DALEX")))
     (build-system r-build-system)
     (propagated-inputs
@@ -15510,14 +15510,14 @@ includes data sets from oceanography.")
 (define-public r-ggfortify
   (package
     (name "r-ggfortify")
-    (version "0.4.9")
+    (version "0.4.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ggfortify" version))
        (sha256
         (base32
-         "1p6knrbyaynaqwd939w09hpf1zz1gn95cb46sfgppl8l98krb2h5"))))
+         "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -16026,14 +16026,14 @@ both R code and compiled C/C++/FORTRAN code.")
 (define-public r-systemfonts
   (package
     (name "r-systemfonts")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "systemfonts" version))
        (sha256
         (base32
-         "1aba07djvxqdmnsdbwvzcsbm2fddnhrssa54xyrlviiwsv2c1qsd"))))
+         "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
     (properties `((upstream-name . "systemfonts")))
     (build-system r-build-system)
     (inputs
@@ -16055,14 +16055,14 @@ be used further by e.g. graphic devices.")
 (define-public r-graphlayouts
   (package
     (name "r-graphlayouts")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "graphlayouts" version))
        (sha256
         (base32
-         "1la016m37kp79zk8p1yx9kaha8y6d4w52w39h0mzv1mfsi6d75w0"))))
+         "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
     (properties `((upstream-name . "graphlayouts")))
     (build-system r-build-system)
     (propagated-inputs
@@ -16949,28 +16949,61 @@ for original research.  A variety of user defined options and formatting are
 included.")
     (license license:gpl3)))
 
+(define-public r-qgam
+  (package
+    (name "r-qgam")
+    (version "1.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "qgam" version))
+       (sha256
+        (base32
+         "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
+    (properties `((upstream-name . "qgam")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-mgcv" ,r-mgcv)
+       ("r-plyr" ,r-plyr)
+       ("r-shiny" ,r-shiny)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/web/packages/qgam/")
+    (synopsis "Smooth additive quantile regression models")
+    (description
+     "This package provides smooth additive quantile regression models, fitted
+using the methods of Fasiolo et al. (2017).  Differently from @code{quantreg},
+the smoothing parameters are estimated automatically by marginal loss
+minimization, while the regression coefficients are estimated using either
+PIRLS or Newton algorithm.  The learning rate is determined so that the
+Bayesian credible intervals of the estimated effects have approximately the
+correct coverage.  The main function is @code{qgam()} which is similar to
+@code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
+regression models.")
+    (license license:gpl2+)))
+
 (define-public r-abtest
   (package
     (name "r-abtest")
-    (version "0.2.0")
+    (version "0.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "abtest" version))
        (sha256
         (base32
-         "1ky3cf827kj24bhcpk00v5zl5jdkii1gca0x81ay1cjkzfispgws"))))
+         "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
     (properties `((upstream-name . "abtest")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)
        ("r-mvtnorm" ,r-mvtnorm)
        ("r-plotrix" ,r-plotrix)
+       ("r-qgam" ,r-qgam)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
        ("r-sn" ,r-sn)
-       ("r-truncnorm" ,r-truncnorm)
-       ("r-vgam" ,r-vgam)))
+       ("r-truncnorm" ,r-truncnorm)))
     (home-page "https://cran.r-project.org/web/packages/abtest/")
     (synopsis "Bayesian A/B testing")
     (description
@@ -18300,14 +18333,14 @@ actigraphy-measured activity counts data.")
 (define-public r-fda
   (package
     (name "r-fda")
-    (version "2.4.8.1")
+    (version "5.1.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "fda" version))
        (sha256
         (base32
-         "0g50kj1dx7zarjv0lgwyzd2c7bv6di7nkndmywday5vjywgl8m7a"))))
+         "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
     (properties `((upstream-name . "fda")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18597,7 +18630,7 @@ currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
     (properties `((upstream-name . "readbitmap")))
     (build-system r-build-system)
     (inputs
-     `(("libjpeg" ,libjpeg)
+     `(("libjpeg" ,libjpeg-turbo)
        ("libpng" ,libpng)))
     (propagated-inputs
      `(("r-bmp" ,r-bmp)
@@ -18762,14 +18795,14 @@ functions.")
 (define-public r-univoutl
   (package
     (name "r-univoutl")
-    (version "0.1-5")
+    (version "0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "univOutl" version))
        (sha256
         (base32
-         "193wrpkvgmlrx43nag8w3ivrlqm37nm6g86wcvd3bgw3hchs70gi"))))
+         "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
     (properties `((upstream-name . "univOutl")))
     (build-system r-build-system)
     (propagated-inputs
@@ -19706,17 +19739,20 @@ character codes as well as the UN M.49 area codes.")
 (define-public r-stopwords
   (package
     (name "r-stopwords")
-    (version "1.0")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stopwords" version))
        (sha256
         (base32
-         "1nmi0bpd0c238g5b8ch1v034m5ng9llhs519cgxdrj3sh9fplwlv"))))
+         "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
     (properties `((upstream-name . "stopwords")))
     (build-system r-build-system)
-    (propagated-inputs `(("r-isocodes" ,r-isocodes)))
+    (propagated-inputs
+     `(("r-desc" ,r-desc)
+       ("r-isocodes" ,r-isocodes)
+       ("r-usethis" ,r-usethis)))
     (home-page "https://github.com/quanteda/stopwords")
     (synopsis "Multilingual stopword lists")
     (description
@@ -19820,14 +19856,14 @@ machine learning, visually representing text and text analyses, and more.")
 (define-public r-topicmodels
   (package
     (name "r-topicmodels")
-    (version "0.2-9")
+    (version "0.2-11")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "topicmodels" version))
        (sha256
         (base32
-         "1757r5x8bsl4dk106xg6481mvdkdz9vwg87n7rpbvdkavsvhyxs0"))))
+         "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
     (properties `((upstream-name . "topicmodels")))
     (build-system r-build-system)
     (native-inputs
@@ -20183,19 +20219,18 @@ estimate parameters given observed data.")
 (define-public r-kutils
   (package
     (name "r-kutils")
-    (version "1.69")
+    (version "1.70")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "kutils" version))
        (sha256
         (base32
-         "12pg26a85h0jxlfcyai68dbh4bq1gnq8v1ngi8k9qvafbrpc6gx8"))))
+         "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
     (properties `((upstream-name . "kutils")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
-       ("r-lavaan" ,r-lavaan)
        ("r-openxlsx" ,r-openxlsx)
        ("r-plyr" ,r-plyr)
        ("r-runit" ,r-runit)
@@ -21597,3 +21632,40 @@ infinite-precision rational arithmetic.")
 Archive Toolkit.  Rxnat uses the XNAT REST API to perform data queries and
 download images.")
     (license license:gpl2)))
+
+(define-public r-rserve
+  (package
+    (name "r-rserve")
+    (version "1.8-6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-checkmate" ,r-checkmate)
+       ("r-mime" ,r-mime)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-knitr" ,r-knitr)
+       ("r-r6" ,r-r6)
+       ("r-rcpp" ,r-rcpp)
+       ("r-uuid" ,r-uuid)))
+    (inputs
+     `(("openssl" ,openssl)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/s-u/Rserve")
+    (synopsis
+     "Server providing access to R from many languages and systems")
+    (description
+     "Rserve acts as a socket server (TCP/IP or local sockets) which allows
+binary requests to be sent to R.  Every connection has a separate workspace
+and working directory.  Client-side implementations are available for popular
+languages such as C/C++ and Java, allowing any application to use facilities
+of R without the need of linking to R code.  Rserve supports remote
+connection, user authentication and file transfer.  A simple R client is
+included in this package as well.")
+    (license license:gpl2)))