;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages statistics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system r)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages icu4c)
  #:use-module (gnu packages image)
  #:use-module (gnu packages java)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages texlive)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages base)
  #:use-module (gnu packages xorg))

(define-public r
  (package
    (name "r")
    (version "3.2.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-prefix version 1) "/R-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (list (string-append "LDFLAGS=-Wl,-rpath="
                            (assoc-ref %outputs "out")
                            "/lib/R/lib"))
       #:phases
       (modify-phases %standard-phases
         (add-before
          'configure 'set-default-pager
          ;; 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
          ;; Some tests require the timezone to be set.
          (lambda _ (setenv "TZ" "UTC") #t)))
       #:configure-flags
       '("--with-blas=openblas"
         "--with-lapack"
         "--with-cairo"
         "--with-libpng"
         "--with-jpeglib"
         "--with-libtiff"
         "--with-ICU"
         "--enable-R-shlib"
         "--enable-BLAS-shlib"
         "--with-system-zlib"
         "--with-system-bzlib"
         "--with-system-pcre"
         "--with-system-tre"
         "--with-system-xz")))
    (native-inputs
     `(("bzip2" ,bzip2)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)
       ("texlive" ,texlive) ; needed to make vignettes
       ("texinfo" ,texinfo) ; for building HTML manuals
       ("which" ,which) ; for tests/Examples/base-Ex.R
       ("xz" ,xz)))
    (inputs
     `(("openblas" ,openblas)
       ("cairo" ,cairo)
       ("gfortran" ,gfortran)
       ("icu4c" ,icu4c)
       ("icedtea6" ,icedtea6 "jdk")
       ("lapack" ,lapack)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libtiff" ,libtiff)
       ("libxt" ,libxt)
       ("pcre" ,pcre)
       ("readline" ,readline)
       ("zlib" ,zlib)))
    (native-search-paths
     (list (search-path-specification
            (variable "R_LIBS_SITE")
            (files (list "site-library/")))))
    (home-page "http://www.r-project.org/")
    (synopsis "Environment for statistical computing and graphics")
    (description
     "R is a language and environment for statistical computing and graphics.
It provides a variety of statistical techniques, such as linear and nonlinear
modeling, classical statistical tests, time-series analysis, classification
and clustering.  It also provides robust support for producing
publication-quality data plots.  A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
    (license license:gpl3+)))

(define-public r-colorspace
  (package
    (name "r-colorspace")
    (version "1.2-6")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/colorspace_"
                           version ".tar.gz"))
       (sha256
        (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/colorspace")
    (synopsis "Color space manipulation")
    (description
     "This package carries out a mapping between assorted color spaces
including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
CIELAB.  Qualitative, sequential, and diverging color palettes based on HCL
colors are provided.")
    (license license:bsd-3)))