501 lines
18 KiB
Scheme
501 lines
18 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
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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 (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 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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(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 (string-append "mirror://cran/src/contrib/colorspace_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/dichromat_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/digest_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/gtable_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/labeling_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/magrittr_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/munsell_"
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version ".tar.gz"))
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(sha256
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(base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
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(build-system r-build-system)
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(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")
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(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 (string-append "mirror://cran/src/contrib/Rcpp_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/plyr_"
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version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/proto_" version ".tar.gz"))
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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 (string-append "mirror://cran/src/contrib/RColorBrewer_"
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version ".tar.gz"))
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(sha256
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(base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/RColorBrewer")
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(synopsis "ColorBrewer palettes")
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(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)
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(uri (string-append
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"mirror://cran/src/contrib/stringi_"
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version
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".tar.gz"))
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(sha256
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(base32
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"183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
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(build-system r-build-system)
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(inputs `(("icu4c" ,icu4c)))
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(native-inputs `(("pkg-config" ,pkg-config)))
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(home-page "http://stringi.rexamine.com/")
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(synopsis "Character string processing facilities")
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(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
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programmers. Among available features there are: pattern searching
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(e.g. via regular expressions), random string generation, string collation,
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transliteration, concatenation, date-time formatting and parsing, etc.")
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(license license:bsd-3)))
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(define-public r-stringr
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(package
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(name "r-stringr")
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(version "1.0.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://cran/src/contrib/stringr_"
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version ".tar.gz"))
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(sha256
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(base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-magrittr" ,r-magrittr)
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("r-stringi" ,r-stringi)))
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(home-page "https://github.com/hadley/stringr")
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(synopsis "Simple, consistent wrappers for common string operations")
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(description
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"Stringr is a consistent, simple and easy to use set of wrappers around
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the fantastic 'stringi' package. All function and argument names (and
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positions) are consistent, all functions deal with \"NA\"'s and zero length
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vectors in the same way, and the output from one function is easy to feed into
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the input of another.")
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(license license:gpl2+)))
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(define-public r-reshape2
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(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)
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(uri (string-append "mirror://cran/src/contrib/reshape2_"
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version ".tar.gz"))
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(sha256
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(base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
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(build-system r-build-system)
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(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")
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(synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
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(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 "0.2.5")
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(source
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|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://cran/src/contrib/scales_"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32 "12xrmn1vh64dl46bq7n7pa427aicb2ifjrby9in3m32nyvir0kac"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dichromat" ,r-dichromat)
|
|
("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 (string-append "mirror://cran/src/contrib/ggplot2_"
|
|
version ".tar.gz"))
|
|
(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+)))
|