Merge branch 'master' into core-updates

1 files changed, 70 insertions, 5 deletions

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 3d0faf7572..7b3483206f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -98,7 +99,7 @@ be output in text, PostScript, PDF or HTML.")
 (define-public r
   (package
     (name "r")
-    (version "3.2.5")
+    (version "3.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cran/src/base/R-"
@@ -106,7 +107,7 @@ be output in text, PostScript, PDF or HTML.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1dc0iybjk9kr1nghz3fpir6mb9hb9rnrz9bgh00w5pg5vir5cx30"))))
+                "1r0i0cqs3p0vrpiwq0zg5kbrmja9rmaijyzf9f23v6d5n5ab2mlj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags
@@ -120,10 +121,14 @@ be output in text, PostScript, PDF or HTML.")
           ;; Set default pager to "cat", because otherwise it is "false",
           ;; making "help()" print nothing at all.
           (lambda _ (setenv "PAGER" "cat") #t))
-         (add-before
-          'check 'set-timezone
+         (add-before 'check 'set-timezone
           ;; Some tests require the timezone to be set.
-          (lambda _ (setenv "TZ" "UTC") #t))
+          (lambda* (#:key inputs #:allow-other-keys)
+            (setenv "TZ" "UTC")
+            (setenv "TZDIR"
+                    (string-append (assoc-ref inputs "tzdata")
+                                   "/share/zoneinfo"))
+            #t))
          (add-after 'build 'make-info
           (lambda _ (zero? (system* "make" "info"))))
          (add-after 'build 'install-info
@@ -160,6 +165,8 @@ be output in text, PostScript, PDF or HTML.")
        ("xz" ,xz)))
     (inputs
      `(("cairo" ,cairo)
+       ("curl" ,curl)
+       ("tzdata" ,tzdata)
        ("gfortran" ,gfortran)
        ("icu4c" ,icu4c)
        ("libjpeg" ,libjpeg)
@@ -252,6 +259,24 @@ purposes for which more comprehensive (and widely tested) libraries such as
 OpenSSL should be used.")
     (license license:gpl2+)))
 
+(define-public r-estimability
+  (package
+    (name "r-estimability")
+    (version "1.1-1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "estimability" version))
+              (sha256
+               (base32
+                "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w"))))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/estimability")
+    (synopsis "Tools for assessing estimability of linear predictions")
+    (description "Provides tools for determining estimability of linear
+functions of regression coefficients, and 'epredict' methods that handle
+non-estimable cases correctly.")
+    (license license:gpl2+)))
+
 (define-public r-gtable
   (package
     (name "r-gtable")
@@ -1239,6 +1264,27 @@ inference for statistical models.")
        `(("python2-setuptools" ,python2-setuptools)
          ,@(package-native-inputs stats))))))
 
+(define-public r-coda
+  (package
+    (name "r-coda")
+    (version "0.18-1")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "coda" version))
+              (sha256
+               (base32
+                "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lattice" ,r-lattice)))
+    (home-page "http://cran.r-project.org/web/packages/coda")
+    (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
+    (description "This package provides functions for summarizing and plotting
+the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
+diagnostic tests of convergence to the equilibrium distribution of the Markov
+chain.")
+    (license license:gpl2+)))
+
 (define-public r-xml2
   (package
     (name "r-xml2")
@@ -2393,6 +2439,25 @@ things.  RSP is ideal for self-contained scientific reports and R package
 vignettes.")
     (license license:lgpl2.1+)))
 
+(define-public r-mvtnorm
+  (package
+    (name "r-mvtnorm")
+    (version "1.0-5")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "mvtnorm" version))
+              (sha256
+               (base32
+                "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh"))))
+    (build-system r-build-system)
+    (inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "http://mvtnorm.R-forge.R-project.org")
+    (synopsis "Package for multivariate normal and t-distributions")
+    (description "This package can compute multivariate normal and
+t-probabilities, quantiles, random deviates and densities.")
+    (license license:gpl2)))
+
 (define-public r-matrixstats
   (package
     (name "r-matrixstats")