;;; 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 (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 which)
  #:use-module (gnu packages xorg))

(define-public r
  (package
    (name "r")
    (version "3.1.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-prefix version 1) "/R-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0ypsm11c7n49pgh2ricyhhpfhas3famscdazzdp2zq70rapm1ldw"))))
    (build-system gnu-build-system)
    (arguments
     `(;; Tests fail probably because of locale issues:
       ;; > tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", length.out = 24)
       ;; Error in as.POSIXlt.character(x, tz, ...) :
       ;;   character string is not in a standard unambiguous format
       #:tests? #f
       #:phases
       ;; XXX This phase doesn't fix the tests.
       (alist-cons-before
        'check 'install-locales
        (lambda _
          ;; A bunch of tests require the availability of a UTF-8
          ;; locale and otherwise fail.  Give them what they want.
          (setenv "LOCPATH" (getcwd))
          (setenv "LANG" "en_US.UTF-8")
          (zero? (system* "localedef" "--no-archive"
                          "--prefix" (getcwd) "-i" "en_US"
                          "-f" "UTF-8" "./en_US.UTF-8")))
        %standard-phases)
       #:configure-flags
       '("--with-blas"
         "--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
     `(("pkg-config" ,pkg-config)))
    (inputs
     `(("atlas" ,atlas) ; --with-blas
       ("bzip2" ,bzip2)
       ("cairo" ,cairo)
       ("gfortran" ,gfortran-4.8)
       ("icu4c" ,icu4c)
       ("icedtea6" ,icedtea6)
       ("lapack" ,lapack)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libtiff" ,libtiff)
       ("libxt" ,libxt)
       ("pcre" ,pcre)
       ("perl" ,perl)
       ("readline" ,readline)
       ("texlive" ,texlive) ; needed to make vignettes
       ("texinfo" ,texinfo) ; for building HTML manuals
       ("which" ,which) ; for tests/Examples/base-Ex.R
       ("xz" ,xz)
       ("zlib" ,zlib)))
    (home-page "http://www.r-project.org/")
    (synopsis "Language and environment for statistical computing and graphics")
    (description
     "R is a language and environment for statistical computing and graphics.
R is similar to the award-winning S system, which was developed at Bell
Laboratories by John Chambers et al.  It provides a wide variety of
statistical and graphical techniques (linear and nonlinear modelling,
statistical tests, time series analysis, classification, clustering, ...).

R is designed as a true computer language with control-flow constructions for
iteration and alternation, and it allows users to add additional functionality
by defining new functions.  For computationally intensive tasks, C, C++ and
Fortran code can be linked and called at run time.")
    (license license:gpl3+)))