1056 lines
38 KiB
Scheme
1056 lines
38 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages statistics)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix utils)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system r)
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#:use-module (guix build-system python)
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#:use-module (gnu packages)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages icu4c)
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#:use-module (gnu packages image)
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#:use-module (gnu packages java)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages pcre)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages texlive)
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#:use-module (gnu packages texinfo)
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#:use-module (gnu packages base)
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#:use-module (gnu packages xorg)
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#:use-module (gnu packages zip)
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#:use-module (srfi srfi-1))
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(define-public r
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(package
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(name "r")
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(version "3.2.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://cran/src/base/R-"
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(version-prefix version 1) "/R-"
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version ".tar.gz"))
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(sha256
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(base32
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"07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw"))))
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(build-system gnu-build-system)
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(arguments
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`(#:make-flags
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(list (string-append "LDFLAGS=-Wl,-rpath="
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(assoc-ref %outputs "out")
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"/lib/R/lib"))
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#:phases
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(modify-phases %standard-phases
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(add-before
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'configure 'set-default-pager
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;; Set default pager to "cat", because otherwise it is "false",
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;; making "help()" print nothing at all.
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(lambda _ (setenv "PAGER" "cat") #t))
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(add-before
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'check 'set-timezone
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;; Some tests require the timezone to be set.
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(lambda _ (setenv "TZ" "UTC") #t))
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(add-after 'build 'make-info
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(lambda _ (zero? (system* "make" "info"))))
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(add-after 'build 'install-info
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(lambda _ (zero? (system* "make" "install-info")))))
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#:configure-flags
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'("--with-blas=openblas"
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"--with-lapack"
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"--with-cairo"
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"--with-libpng"
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"--with-jpeglib"
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"--with-libtiff"
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"--with-ICU"
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"--enable-R-shlib"
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"--enable-BLAS-shlib"
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"--with-system-zlib"
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"--with-system-bzlib"
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"--with-system-pcre"
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"--with-system-tre"
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"--with-system-xz")))
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;; R has some support for Java. When the JDK is available at configure
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;; time environment variables pointing to the JDK will be recorded under
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;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
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;; CMD javareconf". "R CMD javareconf" appears to only be used to update
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;; the recorded environment variables in $R_HOME/etc. Refer to
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;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
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;; for additional information.
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;; As the JDK is a rather large input with only very limited effects on R,
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;; we decided to drop it.
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(native-inputs
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`(("bzip2" ,bzip2)
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("perl" ,perl)
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("pkg-config" ,pkg-config)
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("texinfo" ,texinfo) ; for building HTML manuals
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("which" ,which) ; for tests/Examples/base-Ex.R
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("xz" ,xz)))
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(inputs
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`(("openblas" ,openblas)
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("cairo" ,cairo)
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("gfortran" ,gfortran)
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("icu4c" ,icu4c)
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("lapack" ,lapack)
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("libjpeg" ,libjpeg)
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("libpng" ,libpng)
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("libtiff" ,libtiff)
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("libxt" ,libxt)
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("pcre" ,pcre)
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("readline" ,readline)
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("zlib" ,zlib)))
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(native-search-paths
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(list (search-path-specification
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(variable "R_LIBS_SITE")
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(files (list "site-library/")))))
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(home-page "http://www.r-project.org/")
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(synopsis "Environment for statistical computing and graphics")
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(description
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"R is a language and environment for statistical computing and graphics.
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It provides a variety of statistical techniques, such as linear and nonlinear
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modeling, classical statistical tests, time-series analysis, classification
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and clustering. It also provides robust support for producing
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publication-quality data plots. A large amount of 3rd-party packages are
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available, greatly increasing its breadth and scope.")
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(license license:gpl3+)))
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(define-public r-colorspace
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(package
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(name "r-colorspace")
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(version "1.2-6")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "colorspace" version))
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(sha256
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(base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/colorspace")
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(synopsis "Color space manipulation")
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(description
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"This package carries out a mapping between assorted color spaces
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including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
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CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
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colors are provided.")
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(license license:bsd-3)))
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(define-public r-dichromat
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(package
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(name "r-dichromat")
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(version "2.0-0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "dichromat" version))
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(sha256
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(base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/dichromat")
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(synopsis "Color schemes for dichromats")
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(description
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"Dichromat collapses red-green or green-blue distinctions to simulate the
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effects of different types of color-blindness.")
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(license license:gpl2+)))
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(define-public r-digest
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(package
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(name "r-digest")
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(version "0.6.8")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "digest" version))
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(sha256
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(base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih"))))
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(build-system r-build-system)
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(home-page "http://dirk.eddelbuettel.com/code/digest.html")
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(synopsis "Create cryptographic hash digests of R objects")
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(description
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"This package contains an implementation of a function 'digest()' for the
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creation of hash digests of arbitrary R objects (using the md5, sha-1,
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sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
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of R language objects, as well as a function 'hmac()' to create hash-based
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message authentication code.
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Please note that this package is not meant to be deployed for cryptographic
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purposes for which more comprehensive (and widely tested) libraries such as
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OpenSSL should be used.")
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(license license:gpl2+)))
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(define-public r-gtable
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(package
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(name "r-gtable")
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(version "0.1.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "gtable" version))
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(sha256
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(base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
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(build-system r-build-system)
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(home-page "https://cran.r-project.org/web/packages/gtable")
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(synopsis "R library to arrange grobs in tables")
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(description
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"Gtable is a collection of tools to make it easier to work with
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\"tables\" of grobs.")
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(license license:gpl2+)))
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(define-public r-labeling
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(package
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(name "r-labeling")
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(version "0.3")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "labeling" version))
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(sha256
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(base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/labeling")
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(synopsis "Axis labeling algorithms")
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(description "The labeling package provides a range of axis labeling
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algorithms.")
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(license license:expat)))
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(define-public r-magrittr
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(package
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(name "r-magrittr")
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(version "1.5")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "magrittr" version))
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(sha256
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(base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
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(synopsis "A forward-pipe operator for R")
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(description
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"Magrittr provides a mechanism for chaining commands with a new
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forward-pipe operator, %>%. This operator will forward a value, or the result
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of an expression, into the next function call/expression. There is flexible
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support for the type of right-hand side expressions. For more information,
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see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
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(license license:expat)))
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(define-public r-munsell
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(package
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(name "r-munsell")
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(version "0.4.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "munsell" version))
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(sha256
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(base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
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`(("r-colorspace" ,r-colorspace)))
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(home-page "http://cran.r-project.org/web/packages/munsell")
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(synopsis "Munsell colour system")
|
|
(description
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"The Munsell package contains Functions for exploring and using the
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Munsell colour system.")
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(license license:expat)))
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(define-public r-rcpp
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(package
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(name "r-rcpp")
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(version "0.12.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "Rcpp" version))
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|
(sha256
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|
(base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38"))))
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(build-system r-build-system)
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|
(home-page "http://www.rcpp.org")
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|
(synopsis "Seamless R and C++ Integration")
|
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(description
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"The Rcpp package provides R functions as well as C++ classes which offer
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a seamless integration of R and C++. Many R data types and objects can be
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mapped back and forth to C++ equivalents which facilitates both writing of new
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code as well as easier integration of third-party libraries. Documentation
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about Rcpp is provided by several vignettes included in this package, via the
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'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
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and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
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'citation(\"Rcpp\")' for details on these last two.")
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(license license:gpl2+)))
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(define-public r-plyr
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(package
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(name "r-plyr")
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(version "1.8.3")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "plyr" version))
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|
(sha256
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|
(base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
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(build-system r-build-system)
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(native-inputs `(("r-rcpp" ,r-rcpp)))
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(home-page "http://had.co.nz/plyr")
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(synopsis "Tools for Splitting, Applying and Combining Data")
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(description
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"Plyr is a set of tools that solves a common set of problems: you need to
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break a big problem down into manageable pieces, operate on each piece and
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then put all the pieces back together. For example, you might want to fit a
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model to each spatial location or time point in your study, summarise data by
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panels or collapse high-dimensional arrays to simpler summary statistics.")
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(license license:expat)))
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(define-public r-proto
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(package
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(name "r-proto")
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(version "0.3-10")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "proto" version))
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(sha256
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(base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
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(build-system r-build-system)
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|
(home-page "http://r-proto.googlecode.com")
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(synopsis "Prototype object-based programming")
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(description
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"Proto is an object oriented system using object-based, also called
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prototype-based, rather than class-based object oriented ideas.")
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(license license:gpl2+)))
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(define-public r-rcolorbrewer
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(package
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(name "r-rcolorbrewer")
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(version "1.1-2")
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(source
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|
(origin
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|
(method url-fetch)
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|
(uri (cran-uri "RColorBrewer" version))
|
|
(sha256
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|
(base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/RColorBrewer")
|
|
(synopsis "ColorBrewer palettes")
|
|
(description
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|
"This package provides color schemes for maps (and other graphics)
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designed by Cynthia Brewer as described at http://colorbrewer2.org")
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;; Includes code licensed under bsd-4
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(license license:asl2.0)))
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(define-public r-stringi
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(package
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(name "r-stringi")
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|
(version "0.5-5")
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|
(source
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|
(origin
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|
(method url-fetch)
|
|
(uri (cran-uri "stringi" version))
|
|
(sha256
|
|
(base32
|
|
"183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("icu4c" ,icu4c)))
|
|
(native-inputs `(("pkg-config" ,pkg-config)))
|
|
(home-page "http://stringi.rexamine.com/")
|
|
(synopsis "Character string processing facilities")
|
|
(description
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|
"This package allows for fast, correct, consistent, portable, as well as
|
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convenient character string/text processing in every locale and any native
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|
encoding. Owing to the use of the ICU library, the package provides R users
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|
with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
|
|
programmers. Among available features there are: pattern searching
|
|
(e.g. via regular expressions), random string generation, string collation,
|
|
transliteration, concatenation, date-time formatting and parsing, etc.")
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|
(license license:bsd-3)))
|
|
|
|
(define-public r-stringr
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|
(package
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|
(name "r-stringr")
|
|
(version "1.0.0")
|
|
(source
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|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stringr" version))
|
|
(sha256
|
|
(base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-magrittr" ,r-magrittr)
|
|
("r-stringi" ,r-stringi)))
|
|
(home-page "https://github.com/hadley/stringr")
|
|
(synopsis "Simple, consistent wrappers for common string operations")
|
|
(description
|
|
"Stringr is a consistent, simple and easy to use set of wrappers around
|
|
the fantastic 'stringi' package. All function and argument names (and
|
|
positions) are consistent, all functions deal with \"NA\"'s and zero length
|
|
vectors in the same way, and the output from one function is easy to feed into
|
|
the input of another.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-reshape2
|
|
(package
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|
(name "r-reshape2")
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|
(version "1.4.1")
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|
(source
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|
(origin
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|
(method url-fetch)
|
|
(uri (cran-uri "reshape2" version))
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|
(sha256
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|
(base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
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|
`(("r-plyr" ,r-plyr)
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|
("r-rcpp" ,r-rcpp)
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|
("r-stringr" ,r-stringr)))
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|
(home-page "https://github.com/hadley/reshape")
|
|
(synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
|
|
(description
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|
"Reshape2 is an R library to flexibly restructure and aggregate data
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using just two functions: melt and dcast (or acast).")
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|
(license license:expat)))
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|
|
|
(define-public r-scales
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|
(package
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|
(name "r-scales")
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|
(version "0.3.0")
|
|
(source
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|
(origin
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|
(method url-fetch)
|
|
(uri (cran-uri "scales" version))
|
|
(sha256
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|
(base32 "1kkgpqzb0a6lnpblhcprr4qzyfk5lhicdv4639xs5cq16n7bkqgl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dichromat" ,r-dichromat)
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|
("r-labeling" ,r-labeling)
|
|
("r-munsell" ,r-munsell)
|
|
("r-plyr" ,r-plyr)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/hadley/scales")
|
|
(synopsis "Scale functions for visualization")
|
|
(description
|
|
"This package provides graphical scales that map data to aesthetics, and
|
|
provides methods for automatically determining breaks and labels for axes and
|
|
legends.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggplot2
|
|
(package
|
|
(name "r-ggplot2")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggplot2" version))
|
|
(sha256
|
|
(base32 "0794kjqi3lrxb33lr1mykd58959hlgkhdn259vj8fxrh65mqw920"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-gtable" ,r-gtable)
|
|
("r-plyr" ,r-plyr)
|
|
("r-proto" ,r-proto)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "http://ggplot2.org")
|
|
(synopsis "An implementation of the grammar of graphics")
|
|
(description
|
|
"Ggplot2 is an implementation of the grammar of graphics in R. It
|
|
combines the advantages of both base and lattice graphics: conditioning and
|
|
shared axes are handled automatically, and you can still build up a plot step
|
|
by step from multiple data sources. It also implements a sophisticated
|
|
multidimensional conditioning system and a consistent interface to map data to
|
|
aesthetic attributes.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-assertthat
|
|
(package
|
|
(name "r-assertthat")
|
|
(version "0.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertthat" version))
|
|
(sha256
|
|
(base32
|
|
"0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/hadley/assertthat")
|
|
(synopsis "Easy pre and post assertions")
|
|
(description
|
|
"Assertthat is an extension to stopifnot() that makes it easy to declare
|
|
the pre and post conditions that your code should satisfy, while also
|
|
producing friendly error messages so that your users know what they've done
|
|
wrong.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-lazyeval
|
|
(package
|
|
(name "r-lazyeval")
|
|
(version "0.1.10")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lazyeval" version))
|
|
(sha256
|
|
(base32
|
|
"02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/hadley/lazyeval")
|
|
(synopsis "Lazy (non-standard) evaluation in R")
|
|
(description
|
|
"This package provides the tools necessary to do non-standard
|
|
evaluation (NSE) in R.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-dbi
|
|
(package
|
|
(name "r-dbi")
|
|
(version "0.3.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DBI" version))
|
|
(sha256
|
|
(base32
|
|
"0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/rstats-db/DBI")
|
|
(synopsis "R database interface")
|
|
(description
|
|
"The DBI package provides a database interface (DBI) definition for
|
|
communication between R and relational database management systems. All
|
|
classes in this package are virtual and need to be extended by the various
|
|
R/DBMS implementations.")
|
|
(license license:lgpl2.0+)))
|
|
|
|
(define-public r-bh
|
|
(package
|
|
(name "r-bh")
|
|
(version "1.58.0-1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BH" version))
|
|
(sha256
|
|
(base32
|
|
"17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/eddelbuettel/bh")
|
|
(synopsis "R package providing subset of Boost headers")
|
|
(description
|
|
"This package aims to provide the most useful subset of Boost libraries
|
|
for template use among CRAN packages.")
|
|
(license license:boost1.0)))
|
|
|
|
(define-public r-evaluate
|
|
(package
|
|
(name "r-evaluate")
|
|
(version "0.8")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "evaluate" version))
|
|
(sha256
|
|
(base32
|
|
"137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringr" ,r-stringr)))
|
|
(home-page "https://github.com/hadley/evaluate")
|
|
(synopsis "Parsing and evaluation tools for R")
|
|
(description
|
|
"This package provides tools that allow you to recreate the parsing,
|
|
evaluation and display of R code, with enough information that you can
|
|
accurately recreate what happens at the command line. The tools can easily be
|
|
adapted for other output formats, such as HTML or LaTeX.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-formatr
|
|
(package
|
|
(name "r-formatr")
|
|
(version "1.2.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "formatR" version))
|
|
(sha256
|
|
(base32
|
|
"0f4cv2zv5wayyqx99ybfyl0p83kgjvnsv8dhcwa4s49kw6jsx1lr"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://yihui.name/formatR")
|
|
(synopsis "Format R code automatically")
|
|
(description
|
|
"This package provides a function to format R source code. Spaces and
|
|
indent will be added to the code automatically, and comments will be preserved
|
|
under certain conditions, so that R code will be more human-readable and tidy.
|
|
There is also a Shiny app as a user interface in this package.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-highr
|
|
(package
|
|
(name "r-highr")
|
|
(version "0.5.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "highr" version))
|
|
(sha256
|
|
(base32
|
|
"11hyawzhaw3ph5y5xphi7alx6df1d0i6wh0a2n5m4sxxhdrzswnb"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/yihui/highr")
|
|
(synopsis "Syntax highlighting for R source code")
|
|
(description
|
|
"This package provides syntax highlighting for R source code. Currently
|
|
it supports LaTeX and HTML output. Source code of other languages is
|
|
supported via Andre Simon's highlight package.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-mime
|
|
(package
|
|
(name "r-mime")
|
|
(version "0.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mime" version))
|
|
(sha256
|
|
(base32
|
|
"145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/yihui/mime")
|
|
(synopsis "R package to map filenames to MIME types")
|
|
(description
|
|
"This package guesses the MIME type from a filename extension using the
|
|
data derived from /etc/mime.types in UNIX-type systems.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-markdown
|
|
(package
|
|
(name "r-markdown")
|
|
(version "0.7.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "markdown" version))
|
|
(sha256
|
|
(base32
|
|
"00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
|
|
(build-system r-build-system)
|
|
;; Skip check phase because the tests require the r-knitr package to be
|
|
;; installed. This prevents installation failures. Knitr normally
|
|
;; shouldn't be available since r-markdown is a dependency of the r-knitr
|
|
;; package.
|
|
(arguments `(#:tests? #f))
|
|
(propagated-inputs
|
|
`(("r-mime" ,r-mime)))
|
|
(home-page "https://github.com/rstudio/markdown")
|
|
(synopsis "Markdown rendering for R")
|
|
(description
|
|
"This package provides R bindings to the Sundown Markdown rendering
|
|
library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
|
|
syntax that can be converted to XHTML or other formats.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-yaml
|
|
(package
|
|
(name "r-yaml")
|
|
(version "2.1.13")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "yaml" version))
|
|
(sha256
|
|
(base32
|
|
"18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/yaml/")
|
|
(synopsis "Methods to convert R data to YAML and back")
|
|
(description
|
|
"This package implements the libyaml YAML 1.1 parser and
|
|
emitter (http://pyyaml.org/wiki/LibYAML) for R.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-knitr
|
|
(package
|
|
(name "r-knitr")
|
|
(version "1.11")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "knitr" version))
|
|
(sha256
|
|
(base32
|
|
"1ikjla0hnpjfkdbydqhhqypc0aiizbi4nyn8c694sdk9ca4jasdd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-evaluate" ,r-evaluate)
|
|
("r-digest" ,r-digest)
|
|
("r-formatr" ,r-formatr)
|
|
("r-highr" ,r-highr)
|
|
("r-markdown" ,r-markdown)
|
|
("r-stringr" ,r-stringr)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "http://yihui.name/knitr/")
|
|
(synopsis "General-purpose package for dynamic report generation in R")
|
|
(description
|
|
"This package provides a general-purpose tool for dynamic report
|
|
generation in R using Literate Programming techniques.")
|
|
;; The code is released under any version of the GPL. As it is used by
|
|
;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
|
|
;; here.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-microbenchmark
|
|
(package
|
|
(name "r-microbenchmark")
|
|
(version "1.4-2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "microbenchmark" version))
|
|
(sha256
|
|
(base32
|
|
"05yxvdnkxr2ll94h6f2m5sn3gg7vrlm9nbdxgmj2g8cp8gfxpfkg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)))
|
|
(home-page "https://cran.r-project.org/web/packages/microbenchmark/")
|
|
(synopsis "Accurate timing functions for R")
|
|
(description
|
|
"This package provides infrastructure to accurately measure and compare
|
|
the execution time of R expressions.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public r-codetools
|
|
(package
|
|
(name "r-codetools")
|
|
(version "0.2-14")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "codetools" version))
|
|
(sha256
|
|
(base32
|
|
"0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/codetools/index.html")
|
|
(synopsis "Code analysis tools for R")
|
|
(description "This package provides code analysis tools for R.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-pryr
|
|
(package
|
|
(name "r-pryr")
|
|
(version "0.1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pryr" version))
|
|
(sha256
|
|
(base32
|
|
"1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringr" ,r-stringr)
|
|
("r-codetools" ,r-codetools)))
|
|
(native-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/hadley/pryr")
|
|
(synopsis "Tools for computing on the R language")
|
|
(description
|
|
"This package provides useful tools to pry back the covers of R and
|
|
understand the language at a deeper level.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-memoise
|
|
(package
|
|
(name "r-memoise")
|
|
(version "0.2.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "memoise" version))
|
|
(sha256
|
|
(base32
|
|
"19wm4b3kq6xva43kga3xydnl7ybl5mq7b4y2fczgzzjz63jd75y4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)))
|
|
(home-page "http://github.com/hadley/memoise")
|
|
(synopsis "Memoise functions for R")
|
|
(description
|
|
"This R package allows to cache the results of a function so that when
|
|
you call it again with the same arguments it returns the pre-computed value.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-crayon
|
|
(package
|
|
(name "r-crayon")
|
|
(version "1.3.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "crayon" version))
|
|
(sha256
|
|
(base32
|
|
"0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-memoise" ,r-memoise)))
|
|
(home-page "https://github.com/gaborcsardi/crayon")
|
|
(synopsis "Colored terminal output for R")
|
|
(description
|
|
"Colored terminal output on terminals that support ANSI color and
|
|
highlight codes. It also works in Emacs ESS. ANSI color support is
|
|
automatically detected. Colors and highlighting can be combined and nested.
|
|
New styles can also be created easily. This package was inspired by the
|
|
\"chalk\" JavaScript project.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-testthat
|
|
(package
|
|
(name "r-testthat")
|
|
(version "0.10.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "testthat" version))
|
|
(sha256
|
|
(base32
|
|
"0b3akwcx5mv9dmi8vssbk91hr3yrrdxd2fm6zhr31fnyz8kjx4pw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-crayon" ,r-crayon)))
|
|
(home-page "https://github.com/hadley/testthat")
|
|
(synopsis "Unit testing for R")
|
|
(description
|
|
"This package provides a unit testing system for R designed to be fun,
|
|
flexible and easy to set up.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-r6
|
|
(package
|
|
(name "r-r6")
|
|
(version "2.1.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R6" version))
|
|
(sha256
|
|
(base32
|
|
"16qq35bgxgswf989yvsqkb6fv7srpf8n8dv2s2c0z9n6zgmwq66m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-knitr" ,r-knitr)
|
|
("r-microbenchmark" ,r-microbenchmark)
|
|
("r-pryr" ,r-pryr)
|
|
("r-testthat" ,r-testthat)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://github.com/wch/R6/")
|
|
(synopsis "Classes with reference semantics in R")
|
|
(description
|
|
"The R6 package allows the creation of classes with reference semantics,
|
|
similar to R's built-in reference classes. Compared to reference classes, R6
|
|
classes are simpler and lighter-weight, and they are not built on S4 classes
|
|
so they do not require the methods package. These classes allow public and
|
|
private members, and they support inheritance, even when the classes are
|
|
defined in different packages.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-dplyr
|
|
(package
|
|
(name "r-dplyr")
|
|
(version "0.4.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dplyr" version))
|
|
(sha256
|
|
(base32
|
|
"1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-r6" ,r-r6)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-dbi" ,r-dbi)))
|
|
(native-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-bh" ,r-bh)))
|
|
(home-page "https://github.com/hadley/dplyr")
|
|
(synopsis "Tools for working with data frames in R")
|
|
(description
|
|
"dplyr is the next iteration of plyr. It is focussed on tools for
|
|
working with data frames. It has three main goals: 1) identify the most
|
|
important data manipulation tools needed for data analysis and make them easy
|
|
to use in R; 2) provide fast performance for in-memory data by writing key
|
|
pieces of code in C++; 3) use the same code interface to work with data no
|
|
matter where it is stored, whether in a data frame, a data table or
|
|
database.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-chron
|
|
(package
|
|
(name "r-chron")
|
|
(version "2.3-47")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "chron" version))
|
|
(sha256
|
|
(base32
|
|
"1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/chron")
|
|
(synopsis "Chronological R objects which can handle dates and times")
|
|
(description
|
|
"This package provides chronological R objects which can handle dates and
|
|
times.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-data.table
|
|
(package
|
|
(name "r-data.table")
|
|
(version "1.9.6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "data.table" version))
|
|
(sha256
|
|
(base32
|
|
"0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-chron" ,r-chron)))
|
|
(home-page "https://github.com/Rdatatable/data.table/wiki")
|
|
(synopsis "Enhanced version of data.frame R object")
|
|
(description
|
|
"The R data.table package provides functions for fast aggregation of
|
|
large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of
|
|
columns by group, column listing and fast file reading.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public python-patsy
|
|
(package
|
|
(name "python-patsy")
|
|
(version "0.4.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://pypi.python.org/packages/source/"
|
|
"p/patsy/patsy-" version ".zip"))
|
|
(sha256
|
|
(base32
|
|
"1kbs996xc2haxalmhd19rr1wh5fa4gbbxf81czkf5w4kam7h7wz4"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))
|
|
(add-after 'unpack 'prevent-generation-of-egg-archive
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("from setuptools import setup")
|
|
"from distutils.core import setup"))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-scipy" ,python-scipy)
|
|
("python-six" ,python-six)))
|
|
(native-inputs
|
|
`(("python-nose" ,python-nose)
|
|
("unzip" ,unzip)))
|
|
(home-page "https://github.com/pydata/patsy")
|
|
(synopsis "Describe statistical models and build design matrices")
|
|
(description
|
|
"Patsy is a Python package for describing statistical models and for
|
|
building design matrices.")
|
|
;; The majority of the code is distributed under BSD-2. The module
|
|
;; patsy.compat contains code derived from the Python standard library,
|
|
;; and is covered by the PSFL.
|
|
(license (list license:bsd-2 license:psfl))))
|
|
|
|
(define-public python2-patsy
|
|
(let ((patsy (package-with-python2 python-patsy)))
|
|
(package (inherit patsy)
|
|
(native-inputs
|
|
`(("python2-setuptools" ,python2-setuptools)
|
|
,@(package-native-inputs patsy)))
|
|
(propagated-inputs
|
|
`(("python2-numpy" ,python2-numpy)
|
|
("python2-scipy" ,python2-scipy)
|
|
,@(alist-delete "python-numpy"
|
|
(alist-delete "python-scipy"
|
|
(package-propagated-inputs patsy))))))))
|
|
|
|
(define-public python-statsmodels
|
|
(package
|
|
(name "python-statsmodels")
|
|
(version "0.6.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://pypi.python.org/packages/source/"
|
|
"s/statsmodels/statsmodels-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
;; tests must be run after installation
|
|
(delete 'check)
|
|
(add-after 'unpack 'set-matplotlib-backend-to-agg
|
|
(lambda _
|
|
;; Set the matplotlib backend to Agg to avoid problems using the
|
|
;; GTK backend without a display.
|
|
(substitute* (find-files "statsmodels/graphics/tests" "\\.py")
|
|
(("import matplotlib\\.pyplot as plt" line)
|
|
(string-append "import matplotlib;matplotlib.use('Agg');"
|
|
line)))
|
|
#t))
|
|
(add-after 'install 'check
|
|
(lambda _
|
|
(with-directory-excursion "/tmp"
|
|
(zero? (system* "nosetests"
|
|
"--stop"
|
|
"-v" "statsmodels"))))))))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-scipy" ,python-scipy)
|
|
("python-pandas" ,python-pandas)
|
|
("python-patsy" ,python-patsy)
|
|
("python-matplotlib" ,python-matplotlib)))
|
|
(native-inputs
|
|
`(("python-cython" ,python-cython)
|
|
("python-nose" ,python-nose)
|
|
("python-sphinx" ,python-sphinx)))
|
|
(home-page "http://statsmodels.sourceforge.net/")
|
|
(synopsis "Statistical modeling and econometrics in Python")
|
|
(description
|
|
"Statsmodels is a Python package that provides a complement to scipy for
|
|
statistical computations including descriptive statistics and estimation and
|
|
inference for statistical models.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python2-statsmodels
|
|
(let ((stats (package-with-python2 python-statsmodels)))
|
|
(package (inherit stats)
|
|
(propagated-inputs
|
|
`(("python2-numpy" ,python2-numpy)
|
|
("python2-scipy" ,python2-scipy)
|
|
("python2-pandas" ,python2-pandas)
|
|
("python2-patsy" ,python2-patsy)
|
|
("python2-matplotlib" ,python2-matplotlib)))
|
|
(native-inputs
|
|
`(("python2-setuptools" ,python2-setuptools)
|
|
,@(package-native-inputs stats))))))
|