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5925 lines
208 KiB
5925 lines
208 KiB
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
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;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2016, 2017, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
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;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
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;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
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;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
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;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
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;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
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;;;
|
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;;; This file is part of GNU Guix.
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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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;;;
|
|
;;; 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
|
|
;;; 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)
|
|
#:use-module (guix hg-download)
|
|
#:use-module (guix git-download)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix build-system ant)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system r)
|
|
#:use-module (guix build-system python)
|
|
#:use-module (guix build-system trivial)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages algebra)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages bash)
|
|
#:use-module (gnu packages check)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages cran)
|
|
#:use-module (gnu packages curl)
|
|
#:use-module (gnu packages emacs)
|
|
#:use-module (gnu packages emacs-xyz)
|
|
#:use-module (gnu packages fontutils)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages gtk)
|
|
#:use-module (gnu packages gettext)
|
|
#:use-module (gnu packages glib)
|
|
#:use-module (gnu packages haskell-xyz)
|
|
#:use-module (gnu packages icu4c)
|
|
#:use-module (gnu packages image)
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|
#:use-module (gnu packages java)
|
|
#:use-module (gnu packages libffi)
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|
#:use-module (gnu packages machine-learning)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages multiprecision)
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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)
|
|
#:use-module (gnu packages python)
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|
#:use-module (gnu packages python-science)
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|
#:use-module (gnu packages python-xyz)
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|
#:use-module (gnu packages readline)
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|
#:use-module (gnu packages sphinx)
|
|
#:use-module (gnu packages ssh)
|
|
#:use-module (gnu packages tcl)
|
|
#:use-module (gnu packages tex)
|
|
#:use-module (gnu packages texinfo)
|
|
#:use-module (gnu packages time)
|
|
#:use-module (gnu packages tls)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages version-control)
|
|
#:use-module (gnu packages web)
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|
#:use-module (gnu packages xml)
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|
#:use-module (gnu packages xorg)
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#:use-module (srfi srfi-1))
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|
|
|
|
|
(define-public pspp
|
|
(package
|
|
(name "pspp")
|
|
(version "1.2.0")
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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://gnu/pspp/pspp-"
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version ".tar.gz"))
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(sha256
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|
(base32
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|
"07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
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(build-system gnu-build-system)
|
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(inputs
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`(("cairo" ,cairo)
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("gettext" ,gettext-minimal)
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("gsl" ,gsl)
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("libxml2" ,libxml2)
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|
("pango" ,pango)
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("readline" ,readline)
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|
("gtk" ,gtk+)
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("gtksourceview" ,gtksourceview)
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|
("spread-sheet-widget" ,spread-sheet-widget)
|
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("zlib" ,zlib)))
|
|
(native-inputs
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|
`(("autoconf" ,autoconf) ;for tests
|
|
("glib" ,glib "bin") ;for glib-genmarshal
|
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("perl" ,perl)
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("pkg-config" ,pkg-config)
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("python" ,python-2) ;for tests
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("texinfo" ,texinfo)))
|
|
(home-page "https://www.gnu.org/software/pspp/")
|
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(synopsis "Statistical analysis")
|
|
(description
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|
"GNU PSPP is a statistical analysis program. It can perform
|
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descriptive statistics, T-tests, linear regression and non-parametric tests.
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It features both a graphical interface as well as command-line input. PSPP
|
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is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
|
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can be imported from spreadsheets, text files and database sources and it can
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be output in text, PostScript, PDF or HTML.")
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(license license:gpl3+)))
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(define-public jags
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(package
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(name "jags")
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(version "4.3.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
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(version-major version) ".x/Source/"
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"JAGS-" version ".tar.gz"))
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|
(sha256
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|
(base32
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|
"1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
|
|
(build-system gnu-build-system)
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|
(home-page "http://mcmc-jags.sourceforge.net/")
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(native-inputs
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`(("gfortran" ,gfortran)
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("lapack" ,lapack)))
|
|
(synopsis "Gibbs sampler")
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(description "JAGS is Just Another Gibbs Sampler. It is a program for
|
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analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
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simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
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|
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@enumerate
|
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@item To have a cross-platform engine for the BUGS language;
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@item To be extensible, allowing users to write their own functions,
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distributions and samplers;
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@item To be a platform for experimentation with ideas in Bayesian modelling.
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@end enumerate\n")
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(license license:gpl2)))
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|
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(define-public libxls
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(package
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(name "libxls")
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(version "1.5.2")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://github.com/libxls/libxls/releases/download/"
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"v" version "/libxls-" version ".tar.gz"))
|
|
(sha256
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|
(base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld"))))
|
|
(build-system gnu-build-system)
|
|
(home-page "https://github.com/libxls/libxls")
|
|
(synopsis "Read binary (.xls) Excel spreadsheet files")
|
|
(description
|
|
"libxls is a C library to read .xls spreadsheet files in the binary OLE
|
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BIFF8 format as created by Excel 97 and later versions. It cannot write them.
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This package also provides @command{xls2csv} to export Excel files to CSV.")
|
|
(license license:bsd-2)))
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|
|
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;; Update this package together with the set of recommended packages: r-boot,
|
|
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
|
|
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
|
|
(define r-with-tests
|
|
(package
|
|
(name "r-with-tests")
|
|
(version "4.0.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://cran/src/base/R-"
|
|
(version-major version) "/R-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0ckgpihkih4b44rx48hpg9p6bv0w67j5z3qc8s4giy6qv2j29zlm"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:disallowed-references (,tzdata-for-tests)
|
|
#:make-flags
|
|
(list (string-append "LDFLAGS=-Wl,-rpath="
|
|
(assoc-ref %outputs "out")
|
|
"/lib/R/lib")
|
|
;; This affects the embedded timestamp of only the core packages.
|
|
"PKG_BUILT_STAMP=1970-01-01")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'configure 'do-not-compress-serialized-files
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
;; This ensures that Guix can detect embedded store references;
|
|
;; see bug #28157 for details.
|
|
(substitute* "src/library/base/makebasedb.R"
|
|
(("compress = TRUE") "compress = FALSE"))
|
|
#t))
|
|
(add-before 'configure 'patch-uname
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((uname-bin (string-append (assoc-ref inputs "coreutils")
|
|
"/bin/uname")))
|
|
(substitute* "src/scripts/R.sh.in"
|
|
(("uname") uname-bin)))
|
|
#t))
|
|
(add-after 'unpack 'build-reproducibly
|
|
(lambda _
|
|
;; The documentation contains time stamps to demonstrate
|
|
;; documentation generation in different phases.
|
|
(substitute* "src/library/tools/man/Rd2HTML.Rd"
|
|
(("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
|
|
"(removed for reproducibility)"))
|
|
|
|
;; Remove timestamp from tracing environment. This fixes
|
|
;; reproducibility of "methods.rd{b,x}".
|
|
(substitute* "src/library/methods/R/trace.R"
|
|
(("dateCreated = Sys.time\\(\\)")
|
|
"dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
|
|
|
|
;; Ensure that gzipped files are reproducible.
|
|
(substitute* '("src/library/grDevices/Makefile.in"
|
|
"doc/manual/Makefile.in")
|
|
(("R_GZIPCMD\\)" line)
|
|
(string-append line " -n")))
|
|
|
|
;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
|
|
;; queries the mtime of a given file and records it in an object.
|
|
;; This is acceptable at runtime to detect stale source files,
|
|
;; but it destroys reproducibility at build time.
|
|
|
|
;; Similarly, the "srcfilecopy" procedure records the current
|
|
;; time. We change both of them to respect SOURCE_DATE_EPOCH.
|
|
(substitute* "src/library/base/R/srcfile.R"
|
|
(("timestamp <- (timestamp.*|file.mtime.*)" _ time)
|
|
(string-append "timestamp <- \
|
|
as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
|
|
as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
|
|
} else { " time "}, origin=\"1970-01-01\")\n")))
|
|
|
|
;; This library is installed using "install_package_description",
|
|
;; so we need to pass the "builtStamp" argument.
|
|
(substitute* "src/library/tools/Makefile.in"
|
|
(("(install_package_description\\(.*\"')\\)\"" line prefix)
|
|
(string-append prefix ", builtStamp='1970-01-01')\"")))
|
|
|
|
(substitute* "src/library/Recommended/Makefile.in"
|
|
(("INSTALL_OPTS =" m)
|
|
(string-append m " --built-timestamp=1970-01-01" m)))
|
|
|
|
;; R bundles an older version of help2man, which does not respect
|
|
;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
|
|
;; because that breaks a test.
|
|
(with-fluids ((%default-port-encoding "ISO-8859-1"))
|
|
(substitute* "tools/help2man.pl"
|
|
(("my \\$date = strftime \"%B %Y\", localtime" line)
|
|
(string-append line " 1"))))
|
|
#t))
|
|
(add-before 'build 'set-locales
|
|
(lambda _
|
|
(setlocale LC_ALL "C")
|
|
(setenv "LC_ALL" "C")
|
|
#t))
|
|
(add-before 'configure 'set-default-pager
|
|
;; Set default pager to "cat", because otherwise it is "false",
|
|
;; making "help()" print nothing at all.
|
|
(lambda _ (setenv "PAGER" "cat") #t))
|
|
(add-before 'check 'set-timezone
|
|
;; Some tests require the timezone to be set. However, the
|
|
;; timezone may not just be "UTC", or else a brittle regression
|
|
;; test in reg-tests-1d will fail.
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(setenv "TZ" "UTC+1")
|
|
(setenv "TZDIR"
|
|
(string-append (assoc-ref inputs "tzdata")
|
|
"/share/zoneinfo"))
|
|
#t))
|
|
(add-after 'build 'make-info
|
|
(lambda _ (invoke "make" "info")))
|
|
(add-after 'build 'install-info
|
|
(lambda _ (invoke "make" "install-info"))))
|
|
#:configure-flags
|
|
`(;; We build the recommended packages here, because they are needed in
|
|
;; order to run the test suite. We disable them in the r-minimal
|
|
;; package.
|
|
"--with-cairo"
|
|
"--with-blas=-lopenblas"
|
|
"--with-libpng"
|
|
"--with-jpeglib"
|
|
"--with-libtiff"
|
|
"--with-ICU"
|
|
"--with-tcltk"
|
|
,(string-append "--with-tcl-config="
|
|
(assoc-ref %build-inputs "tcl")
|
|
"/lib/tclConfig.sh")
|
|
,(string-append "--with-tk-config="
|
|
(assoc-ref %build-inputs "tk")
|
|
"/lib/tkConfig.sh")
|
|
"--enable-R-shlib"
|
|
"--enable-BLAS-shlib"
|
|
"--with-system-tre")))
|
|
;; R has some support for Java. When the JDK is available at configure
|
|
;; time environment variables pointing to the JDK will be recorded under
|
|
;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
|
|
;; CMD javareconf". "R CMD javareconf" appears to only be used to update
|
|
;; the recorded environment variables in $R_HOME/etc. Refer to
|
|
;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
|
|
;; for additional information.
|
|
|
|
;; As the JDK is a rather large input with only very limited effects on R,
|
|
;; we decided to drop it.
|
|
(native-inputs
|
|
`(("bzip2" ,bzip2)
|
|
("perl" ,perl)
|
|
("pkg-config" ,pkg-config)
|
|
("texinfo" ,texinfo) ; for building HTML manuals
|
|
("texlive" ,(texlive-union (list texlive-ae
|
|
texlive-inconsolata
|
|
texlive-fonts-ec
|
|
texlive-amsfonts
|
|
texlive-latex-base
|
|
texlive-latex-fancyvrb
|
|
texlive-latex-graphics
|
|
texlive-latex-hyperref
|
|
texlive-latex-oberdiek
|
|
texlive-latex-tools
|
|
texlive-latex-upquote
|
|
texlive-latex-url
|
|
texlive-latex-xkeyval)))
|
|
("tzdata" ,tzdata-for-tests)
|
|
("xz" ,xz)))
|
|
(inputs
|
|
`(;; We need not only cairo here, but pango to ensure that tests for the
|
|
;; "cairo" bitmapType plotting backend succeed.
|
|
("pango" ,pango)
|
|
("coreutils" ,coreutils)
|
|
("curl" ,curl)
|
|
("openblas" ,openblas)
|
|
("gfortran" ,gfortran)
|
|
("icu4c" ,icu4c)
|
|
("libjpeg" ,libjpeg-turbo)
|
|
("libpng" ,libpng)
|
|
("libtiff" ,libtiff)
|
|
("libxt" ,libxt)
|
|
("pcre2" ,pcre2)
|
|
("readline" ,readline)
|
|
;; This avoids a reference to the ungraftable static bash. R uses the
|
|
;; detected shell for the "system" procedure.
|
|
("bash" ,bash-minimal)
|
|
("tcl" ,tcl)
|
|
("tk" ,tk)
|
|
("which" ,which)
|
|
("zlib" ,zlib)))
|
|
(native-search-paths
|
|
(list (search-path-specification
|
|
(variable "R_LIBS_SITE")
|
|
(files (list "site-library/")))))
|
|
(home-page "https://www.r-project.org/")
|
|
(synopsis "Environment for statistical computing and graphics")
|
|
(description
|
|
"R is a language and environment for statistical computing and graphics.
|
|
It provides a variety of statistical techniques, such as linear and nonlinear
|
|
modeling, classical statistical tests, time-series analysis, classification
|
|
and clustering. It also provides robust support for producing
|
|
publication-quality data plots. A large amount of 3rd-party packages are
|
|
available, greatly increasing its breadth and scope.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-minimal
|
|
(package (inherit r-with-tests)
|
|
(name "r-minimal")
|
|
(arguments
|
|
`(#:tests? #f
|
|
,@(substitute-keyword-arguments (package-arguments r-with-tests)
|
|
((#:configure-flags flags)
|
|
;; Do not build the recommended packages. The build system creates
|
|
;; random temporary directories and embeds their names in some
|
|
;; package files. We build these packages with the r-build-system
|
|
;; instead.
|
|
`(cons "--without-recommended-packages" ,flags)))))))
|
|
|
|
(define-public rmath-standalone
|
|
(package (inherit r-minimal)
|
|
(name "rmath-standalone")
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'configure 'chdir
|
|
(lambda _ (chdir "src/nmath/standalone/") #t)))))
|
|
(synopsis "Standalone R math library")
|
|
(description
|
|
"This package provides the R math library as an independent package.")))
|
|
|
|
(define-public r-boot
|
|
(package
|
|
(name "r-boot")
|
|
(version "1.3-25")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "boot" version))
|
|
(sha256
|
|
(base32
|
|
"1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/boot")
|
|
(synopsis "Bootstrap functions for R")
|
|
(description
|
|
"This package provides functions and datasets for bootstrapping from the
|
|
book \"Bootstrap Methods and Their Application\" by A.C. Davison and
|
|
D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
|
|
;; Unlimited distribution
|
|
(license (license:non-copyleft "file://R/bootfuns.q"))))
|
|
|
|
(define-public r-mass
|
|
(package
|
|
(name "r-mass")
|
|
(version "7.3-51.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "MASS" version))
|
|
(sha256
|
|
(base32
|
|
"1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
|
|
(properties `((upstream-name . "MASS")))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
|
(synopsis "Support functions and datasets for Venables and Ripley's MASS")
|
|
(description
|
|
"This package provides functions and datasets for the book \"Modern
|
|
Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
|
|
;; Either version may be picked.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-class
|
|
(package
|
|
(name "r-class")
|
|
(version "7.3-17")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "class" version))
|
|
(sha256
|
|
(base32
|
|
"04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)))
|
|
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
|
(synopsis "R functions for classification")
|
|
(description
|
|
"This package provides various functions for classification, including
|
|
k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
|
|
;; Either of the two versions can be picked.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-cluster
|
|
(package
|
|
(name "r-cluster")
|
|
(version "2.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cluster" version))
|
|
(sha256
|
|
(base32
|
|
"055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/cluster")
|
|
(synopsis "Methods for cluster analysis")
|
|
(description
|
|
"This package provides methods for cluster analysis. It is a much
|
|
extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
|
|
Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-codetools
|
|
(package
|
|
(name "r-codetools")
|
|
(version "0.2-16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "codetools" version))
|
|
(sha256
|
|
(base32
|
|
"00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/codetools")
|
|
(synopsis "Code analysis tools for R")
|
|
(description "This package provides code analysis tools for R to check R
|
|
code for possible problems.")
|
|
;; Any version of the GPL.
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-foreign
|
|
(package
|
|
(name "r-foreign")
|
|
(version "0.8-80")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "foreign" version))
|
|
(sha256
|
|
(base32
|
|
"0wjdi3qn9famsxmpdyyahidaid0yhxlpx4ad9k8vrxhxd6xspasp"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/foreign")
|
|
(synopsis "Read data stored by other statistics software")
|
|
(description
|
|
"This package provides functions for reading and writing data stored by
|
|
some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
|
|
for reading and writing some dBase files.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-kernsmooth
|
|
(package
|
|
(name "r-kernsmooth")
|
|
(version "2.23-17")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "KernSmooth" version))
|
|
(sha256
|
|
(base32
|
|
"11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
|
|
(properties `((upstream-name . "KernSmooth")))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/KernSmooth")
|
|
(synopsis "Functions for kernel smoothing")
|
|
(description
|
|
"This package provides functions for kernel smoothing (and density
|
|
estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
|
|
\"Kernel Smoothing\".")
|
|
;; Unlimited use and distribution
|
|
(license (license:non-copyleft "file://LICENCE.note"))))
|
|
|
|
(define-public r-lattice
|
|
(package
|
|
(name "r-lattice")
|
|
(version "0.20-41")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lattice" version))
|
|
(sha256
|
|
(base32
|
|
"1dapkmh4jlb9sxfrpvapvlfhczl4s8p3r20bn47gcgdk1izmbjjl"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://lattice.r-forge.r-project.org/")
|
|
(synopsis "High-level data visualization system")
|
|
(description
|
|
"The lattice package provides a powerful and elegant high-level data
|
|
visualization system inspired by Trellis graphics, with an emphasis on
|
|
multivariate data. Lattice is sufficient for typical graphics needs, and is
|
|
also flexible enough to handle most nonstandard requirements.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-matrix
|
|
(package
|
|
(name "r-matrix")
|
|
(version "1.2-18")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Matrix" version))
|
|
(sha256
|
|
(base32
|
|
"06b1rc1vq65b271f2wpzhqkvhng8hwwnvjflzxkng50i52603zzp"))))
|
|
(properties `((upstream-name . "Matrix")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "http://Matrix.R-forge.R-project.org/")
|
|
(synopsis "Sparse and dense matrix classes and methods")
|
|
(description
|
|
"This package provides classes and methods for dense and sparse matrices
|
|
and operations on them using LAPACK and SuiteSparse.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-nlme
|
|
(package
|
|
(name "r-nlme")
|
|
(version "3.1-148")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nlme" version))
|
|
(sha256
|
|
(base32 "1cmf43r82kar1hpj9dhqfi3rbjka0z5s6cbdy7fklwh99xj3phkp"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/nlme")
|
|
(synopsis "Linear and nonlinear mixed effects models")
|
|
(description
|
|
"This package provides tools to fit and compare Gaussian linear and
|
|
nonlinear mixed-effects models.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-mgcv
|
|
(package
|
|
(name "r-mgcv")
|
|
(version "1.8-31")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mgcv" version))
|
|
(sha256
|
|
(base32 "1if34mqsn9r7g0l82lxvvx0wjhi9paqdymyd73nschxcl1if8vbk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)
|
|
("r-nlme" ,r-nlme)))
|
|
(home-page "https://cran.r-project.org/web/packages/mgcv")
|
|
(synopsis "Mixed generalised additive model computation")
|
|
(description
|
|
"GAMs, GAMMs and other generalized ridge regression with multiple smoothing
|
|
parameter estimation by GCV, REML or UBRE/AIC. The library includes a
|
|
@code{gam()} function, a wide variety of smoothers, JAGS support and
|
|
distributions beyond the exponential family.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-nnet
|
|
(package
|
|
(name "r-nnet")
|
|
(version "7.3-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nnet" version))
|
|
(sha256
|
|
(base32
|
|
"1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
|
(synopsis "Feed-forward neural networks and multinomial log-linear models")
|
|
(description
|
|
"This package provides functions for feed-forward neural networks with a
|
|
single hidden layer, and for multinomial log-linear models.")
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-rpart
|
|
(package
|
|
(name "r-rpart")
|
|
(version "4.1-15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rpart" version))
|
|
(sha256
|
|
(base32
|
|
"0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rpart")
|
|
(synopsis "Recursive partitioning and regression trees")
|
|
(description
|
|
"This package provides recursive partitioning functions for
|
|
classification, regression and survival trees.")
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-spatial
|
|
(package
|
|
(name "r-spatial")
|
|
(version "7.3-12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "spatial" version))
|
|
(sha256
|
|
(base32
|
|
"0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
|
(synopsis "Functions for kriging and point pattern analysis")
|
|
(description
|
|
"This package provides functions for kriging and point pattern
|
|
analysis.")
|
|
;; Either version may be picked.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-survival
|
|
(package
|
|
(name "r-survival")
|
|
(version "3.2-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "survival" version))
|
|
(sha256
|
|
(base32
|
|
"07h76r2y23w889257krlijcw4n4d7ssx92x7i5qb1xyv5gyvl3rx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)))
|
|
(home-page "https://github.com/therneau/survival")
|
|
(synopsis "Survival analysis")
|
|
(description
|
|
"This package contains the core survival analysis routines, including
|
|
definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
|
|
curves, Cox models, and parametric accelerated failure time models.")
|
|
(license license:lgpl2.0+)))
|
|
|
|
(define-public r
|
|
(package (inherit r-minimal)
|
|
(name "r")
|
|
(source #f)
|
|
(build-system trivial-build-system)
|
|
(arguments '(#:builder (begin (mkdir %output) #t)))
|
|
(propagated-inputs
|
|
`(("r-minimal" ,r-minimal)
|
|
("r-boot" ,r-boot)
|
|
("r-class" ,r-class)
|
|
("r-cluster" ,r-cluster)
|
|
("r-codetools" ,r-codetools)
|
|
("r-foreign" ,r-foreign)
|
|
("r-kernsmooth" ,r-kernsmooth)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-nlme" ,r-nlme)
|
|
("r-nnet" ,r-nnet)
|
|
("r-rpart" ,r-rpart)
|
|
("r-spatial" ,r-spatial)
|
|
("r-survival" ,r-survival)))))
|
|
|
|
(define-public r-bit
|
|
(package
|
|
(name "r-bit")
|
|
(version "1.1-15.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bit" version))
|
|
(sha256
|
|
(base32
|
|
"12xjkkkmflkz8s435by4r23b57cz7z67z84907f6qg99hn1yg0qb"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://ff.r-forge.r-project.org")
|
|
(synopsis "Class for vectors of 1-bit booleans")
|
|
(description
|
|
"This package provides bitmapped vectors of booleans (no @code{NA}s),
|
|
coercion from and to logicals, integers and integer subscripts, fast boolean
|
|
operators and fast summary statistics. With @code{bit} class vectors of true
|
|
binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-bit64
|
|
(package
|
|
(name "r-bit64")
|
|
(version "0.9-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bit64" version))
|
|
(sha256
|
|
(base32
|
|
"07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bit" ,r-bit)))
|
|
(home-page "http://ff.r-forge.r-project.org/")
|
|
(synopsis "S3 class for vectors of 64 bit integers")
|
|
(description
|
|
"The bit64 package provides serializable S3 atomic 64 bit (signed)
|
|
integers that can be used in vectors, matrices, arrays and @code{data.frames}.
|
|
Methods are available for coercion from and to logicals, integers, doubles,
|
|
characters and factors as well as many elementwise and summary functions.
|
|
Many fast algorithmic operations such as @code{match} and @code{order} support
|
|
interactive data exploration and manipulation and optionally leverage
|
|
caching.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-dichromat
|
|
(package
|
|
(name "r-dichromat")
|
|
(version "2.0-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dichromat" version))
|
|
(sha256
|
|
(base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/dichromat")
|
|
(synopsis "Color schemes for dichromats")
|
|
(description
|
|
"Dichromat collapses red-green or green-blue distinctions to simulate the
|
|
effects of different types of color-blindness.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-digest
|
|
(package
|
|
(name "r-digest")
|
|
(version "0.6.25")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "digest" version))
|
|
(sha256
|
|
(base32 "1r9dkq0kxkps54gkmgcdngsd068p054va2vhnqhs5jmwp2vsvk0m"))))
|
|
(build-system r-build-system)
|
|
;; Vignettes require r-knitr, which requires r-digest, so we have to
|
|
;; disable them and the tests.
|
|
(arguments
|
|
`(#:tests? #f
|
|
#:configure-flags (list "--no-build-vignettes")))
|
|
(home-page "http://dirk.eddelbuettel.com/code/digest.html")
|
|
(synopsis "Create cryptographic hash digests of R objects")
|
|
(description
|
|
"This package contains an implementation of a function @code{digest()} for
|
|
the creation of hash digests of arbitrary R objects (using the md5, sha-1,
|
|
sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
|
|
of R language objects, as well as a function @code{hmac()} to create hash-based
|
|
message authentication code.
|
|
|
|
Please note that this package is not meant to be deployed for cryptographic
|
|
purposes for which more comprehensive (and widely tested) libraries such as
|
|
OpenSSL should be used.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-estimability
|
|
(package
|
|
(name "r-estimability")
|
|
(version "1.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "estimability" version))
|
|
(sha256
|
|
(base32
|
|
"0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/estimability")
|
|
(synopsis "Tools for assessing estimability of linear predictions")
|
|
(description "Provides tools for determining estimability of linear
|
|
functions of regression coefficients, and @code{epredict} methods that handle
|
|
non-estimable cases correctly.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-labeling
|
|
(package
|
|
(name "r-labeling")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "labeling" version))
|
|
(sha256
|
|
(base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/labeling")
|
|
(synopsis "Axis labeling algorithms")
|
|
(description "The labeling package provides a range of axis labeling
|
|
algorithms.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-magrittr
|
|
(package
|
|
(name "r-magrittr")
|
|
(version "1.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "magrittr" version))
|
|
(sha256
|
|
(base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
|
|
(synopsis "A forward-pipe operator for R")
|
|
(description
|
|
"Magrittr provides a mechanism for chaining commands with a new
|
|
forward-pipe operator, %>%. This operator will forward a value, or the result
|
|
of an expression, into the next function call/expression. There is flexible
|
|
support for the type of right-hand side expressions. For more information,
|
|
see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
|
|
(license license:expat)))
|
|
|
|
(define-public r-munsell
|
|
(package
|
|
(name "r-munsell")
|
|
(version "0.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "munsell" version))
|
|
(sha256
|
|
(base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-colorspace" ,r-colorspace)))
|
|
(home-page "https://cran.r-project.org/web/packages/munsell")
|
|
(synopsis "Munsell colour system")
|
|
(description
|
|
"The Munsell package contains Functions for exploring and using the
|
|
Munsell colour system.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-permute
|
|
(package
|
|
(name "r-permute")
|
|
(version "0.9-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "permute" version))
|
|
(sha256
|
|
(base32
|
|
"0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
|
|
(build-system r-build-system)
|
|
;; Tests do not run correctly, but running them properly would entail a
|
|
;; circular dependency with vegan.
|
|
(home-page "https://github.com/gavinsimpson/permute")
|
|
(synopsis "Functions for Generating Restricted Permutations of Data")
|
|
(description
|
|
"This package provides a set of restricted permutation designs for freely
|
|
exchangeable, line transects (time series), spatial grid designs and permutation
|
|
of blocks (groups of samples). @code{permute} also allows split-plot designs,
|
|
in which the whole-plots or split-plots or both can be freely exchangeable.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-plyr
|
|
(package
|
|
(name "r-plyr")
|
|
(version "1.8.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plyr" version))
|
|
(sha256
|
|
(base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://had.co.nz/plyr")
|
|
(synopsis "Tools for Splitting, Applying and Combining Data")
|
|
(description
|
|
"Plyr is a set of tools that solves a common set of problems: you need to
|
|
break a big problem down into manageable pieces, operate on each piece and
|
|
then put all the pieces back together. For example, you might want to fit a
|
|
model to each spatial location or time point in your study, summarise data by
|
|
panels or collapse high-dimensional arrays to simpler summary statistics.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-proto
|
|
(package
|
|
(name "r-proto")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "proto" version))
|
|
(sha256
|
|
(base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/hadley/proto")
|
|
(synopsis "Prototype object-based programming")
|
|
(description
|
|
"Proto is an object oriented system using object-based, also called
|
|
prototype-based, rather than class-based object oriented ideas.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rcolorbrewer
|
|
(package
|
|
(name "r-rcolorbrewer")
|
|
(version "1.1-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RColorBrewer" version))
|
|
(sha256
|
|
(base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/RColorBrewer")
|
|
(synopsis "ColorBrewer palettes")
|
|
(description
|
|
"This package provides color schemes for maps (and other graphics)
|
|
designed by Cynthia Brewer as described at http://colorbrewer2.org")
|
|
;; Includes code licensed under bsd-4
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-sendmailr
|
|
(package
|
|
(name "r-sendmailr")
|
|
(version "1.2-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sendmailR" version))
|
|
(sha256
|
|
(base32
|
|
"0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
|
|
(properties `((upstream-name . "sendmailR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)))
|
|
(home-page
|
|
"https://cran.r-project.org/web/packages/sendmailR")
|
|
(synopsis "Send email using R")
|
|
(description
|
|
"This package contains a simple SMTP client which provides a portable
|
|
solution for sending email, including attachments, from within R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-stringi
|
|
(package
|
|
(name "r-stringi")
|
|
(version "1.4.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stringi" version))
|
|
(sha256
|
|
(base32
|
|
"1mkgxzf000zdgbbbvg2vf4md4l501n5lfksffq8vdg6pbgd6fgv3"))))
|
|
(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
|
|
"This package allows for fast, correct, consistent, portable, as well as
|
|
convenient character string/text processing in every locale and any native
|
|
encoding. Owing to the use of the ICU library, the package provides R users
|
|
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.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-stringr
|
|
(package
|
|
(name "r-stringr")
|
|
(version "1.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stringr" version))
|
|
(sha256
|
|
(base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-glue" ,r-glue)
|
|
("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 @code{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
|
|
(name "r-reshape2")
|
|
(version "1.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reshape2" version))
|
|
(sha256
|
|
(base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-plyr" ,r-plyr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-stringr" ,r-stringr)))
|
|
(home-page "https://github.com/hadley/reshape")
|
|
(synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
|
|
(description
|
|
"Reshape2 is an R library to flexibly restructure and aggregate data
|
|
using just two functions: melt and dcast (or acast).")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggplot2
|
|
(package
|
|
(name "r-ggplot2")
|
|
(version "3.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggplot2" version))
|
|
(sha256
|
|
(base32 "0wsib5qpzn4d0w1ss3x158xmrawkms8vvsfvr3mh40pvd8g2ibad"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-glue" ,r-glue)
|
|
("r-gtable" ,r-gtable)
|
|
("r-isoband" ,r-isoband)
|
|
("r-mass" ,r-mass)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-tibble" ,r-tibble)
|
|
("r-rlang" ,r-rlang)
|
|
("r-scales" ,r-scales)
|
|
("r-svglite" ,r-svglite) ; Needed for 'ggsave'
|
|
("r-withr" ,r-withr)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://ggplot2.tidyverse.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-ggdendro
|
|
(package
|
|
(name "r-ggdendro")
|
|
(version "0.1-20")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggdendro" version))
|
|
(sha256
|
|
(base32
|
|
"1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-mass" ,r-mass)
|
|
("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/andrie/ggdendro")
|
|
(synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
|
|
(description "This is a set of tools for dendrograms and tree plots using
|
|
ggplot2. The ggplot2 philosophy is to clearly separate data from the
|
|
presentation. Unfortunately the plot method for dendrograms plots directly
|
|
to a plot device with out exposing the data. The ggdendro package resolves
|
|
this by making available functions that extract the dendrogram plot data.
|
|
The package provides implementations for tree, rpart, as well as diana and
|
|
agnes cluster diagrams.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-gdtools
|
|
(package
|
|
(name "r-gdtools")
|
|
(version "0.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gdtools" version))
|
|
(sha256
|
|
(base32
|
|
"08njzin0c6biw62j5w30r9j85vr1m2cg4hmv5d76nym860yrlqjf"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("cairo" ,cairo)
|
|
("freetype2" ,freetype)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-systemfonts" ,r-systemfonts)))
|
|
(home-page "https://cran.r-project.org/web/packages/gdtools")
|
|
(synopsis "Utilities for graphical rendering")
|
|
(description
|
|
"The @code{gdtools} package provides functionalities to get font metrics
|
|
and to generate base64 encoded string from raster matrix.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-svglite
|
|
(package
|
|
(name "r-svglite")
|
|
(version "1.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "svglite" version))
|
|
(sha256
|
|
(base32
|
|
"1zivykbi1pxdxhrkc1if1ihdn5p27j0nai2q0abca1dwry3wg2yl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-gdtools" ,r-gdtools)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/hadley/svglite")
|
|
(synopsis "SVG graphics device")
|
|
(description
|
|
"@code{svglite} is a graphics device that produces clean
|
|
@dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
|
|
hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
|
|
considerably faster, produces smaller files, and leaves text as is.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-assertthat
|
|
(package
|
|
(name "r-assertthat")
|
|
(version "0.2.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertthat" version))
|
|
(sha256
|
|
(base32
|
|
"17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
|
|
(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 "0.2.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lazyeval" version))
|
|
(sha256
|
|
(base32
|
|
"1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
|
|
(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 "1.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DBI" version))
|
|
(sha256
|
|
(base32
|
|
"1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9"))))
|
|
(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 "1.72.0-3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BH" version))
|
|
(sha256
|
|
(base32
|
|
"1ay8vb6i730lipg8b8g3893vqglhw2kqpc29lwdrxdkb66iw33l8"))))
|
|
(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 "0.14")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "evaluate" version))
|
|
(sha256
|
|
(base32
|
|
"0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
|
|
(build-system r-build-system)
|
|
(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 "1.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "formatR" version))
|
|
(sha256
|
|
(base32
|
|
"1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://yihui.org/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 "0.8")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "highr" version))
|
|
(sha256
|
|
(base32
|
|
"0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
|
|
(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 "0.9")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mime" version))
|
|
(sha256
|
|
(base32
|
|
"107sqarmyhxlch5nrg796i5z03p9mshskisiq2fm628ajk99gkrc"))))
|
|
(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 "1.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "markdown" version))
|
|
(sha256
|
|
(base32
|
|
"06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
|
|
(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)
|
|
("r-xfun" ,r-xfun)))
|
|
(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 "2.2.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "yaml" version))
|
|
(sha256
|
|
(base32
|
|
"10r7g26x73am45niigm3k466030nymnr3v3fjljafzrr5aybf58i"))))
|
|
(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 "1.28")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "knitr" version))
|
|
(sha256
|
|
(base32
|
|
"0ai382fmpz25qrhdgchs3vph2cdvyd73xyryg4jby5fp67d03vh5"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-evaluate" ,r-evaluate)
|
|
("r-highr" ,r-highr)
|
|
("r-markdown" ,r-markdown)
|
|
("r-stringr" ,r-stringr)
|
|
("r-xfun" ,r-xfun)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "https://yihui.org/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-knitrbootstrap
|
|
(package
|
|
(name "r-knitrbootstrap")
|
|
(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "knitrBootstrap" version))
|
|
(sha256
|
|
(base32
|
|
"1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
|
|
(properties `((upstream-name . "knitrBootstrap")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-knitr" ,r-knitr)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-markdown" ,r-markdown)))
|
|
(home-page "https://github.com/jimhester/knitrBootstrap")
|
|
(synopsis "Knitr bootstrap framework")
|
|
(description
|
|
"This package provides a framework to create Bootstrap 3 HTML reports
|
|
from knitr Rmarkdown.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-microbenchmark
|
|
(package
|
|
(name "r-microbenchmark")
|
|
(version "1.4-7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "microbenchmark" version))
|
|
(sha256
|
|
(base32
|
|
"1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6"))))
|
|
(build-system r-build-system)
|
|
(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-pryr
|
|
(package
|
|
(name "r-pryr")
|
|
(version "0.1.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pryr" version))
|
|
(sha256
|
|
(base32
|
|
"06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
|
|
(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 "1.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "memoise" version))
|
|
(sha256
|
|
(base32
|
|
"034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)))
|
|
(home-page "https://github.com/hadley/memoise")
|
|
(synopsis "Memoise functions for R")
|
|
(description
|
|
"This R package caches 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 "1.3.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "crayon" version))
|
|
(sha256
|
|
(base32
|
|
"0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
|
|
(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-praise
|
|
(package
|
|
(name "r-praise")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "praise" version))
|
|
(sha256
|
|
(base32
|
|
"1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/gaborcsardi/praise")
|
|
(synopsis "Functions to praise users")
|
|
(description
|
|
"This package provides template functions to assist in building friendly
|
|
R packages that praise their users.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-testthat
|
|
(package
|
|
(name "r-testthat")
|
|
(version "2.3.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "testthat" version))
|
|
(sha256
|
|
(base32
|
|
"0v70v2fs0f2ir962z9csbjlj8snrq9mbjfyhhb9dhz3zy26qs9hs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-digest" ,r-digest)
|
|
("r-ellipsis" ,r-ellipsis)
|
|
("r-evaluate" ,r-evaluate)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-pkgload" ,r-pkgload)
|
|
("r-praise" ,r-praise)
|
|
("r-r6" ,r-r6)
|
|
("r-rlang" ,r-rlang)
|
|
("r-withr" ,r-withr)))
|
|
(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 "2.4.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R6" version))
|
|
(sha256
|
|
(base32
|
|
"0gma5z41mx02ka9h96xdyf3p6i1rx0izczrzj26c4mbnh9jgvc16"))))
|
|
(build-system r-build-system)
|
|
(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-rlang
|
|
(package
|
|
(name "r-rlang")
|
|
(version "0.4.6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rlang" version))
|
|
(sha256
|
|
(base32
|
|
"1jik4lywg4688dfi5fh8jbnmsxvq3382ii0nsw5armjzfq3v309s"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://rlang.tidyverse.org")
|
|
(synopsis "Functions for base types, core R and Tidyverse features")
|
|
(description "This package provides a toolbox for working with base types,
|
|
core R features like the condition system, and core @code{Tidyverse} features
|
|
like tidy evaluation.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-tibble
|
|
(package
|
|
(name "r-tibble")
|
|
(version "3.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tibble" version))
|
|
(sha256
|
|
(base32
|
|
"17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-ellipsis" ,r-ellipsis)
|
|
("r-fansi" ,r-fansi)
|
|
("r-lifecycle" ,r-lifecycle)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-pkgconfig" ,r-pkgconfig)
|
|
("r-pillar" ,r-pillar)
|
|
("r-rlang" ,r-rlang)
|
|
("r-vctrs" ,r-vctrs)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/hadley/tibble")
|
|
(synopsis "Simple data frames")
|
|
(description
|
|
"This package provides a @code{tbl_df} class that offers better checking
|
|
and printing capabilities than traditional data frames.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-dplyr
|
|
(package
|
|
(name "r-dplyr")
|
|
(version "1.0.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dplyr" version))
|
|
(sha256
|
|
(base32
|
|
"1wxi7pzw1mqkgay2s9hwlkpkxfzydngf56wrf7k93n14rlqm3dmz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ellipsis" ,r-ellipsis)
|
|
("r-generics" ,r-generics)
|
|
("r-glue" ,r-glue)
|
|
("r-lifecycle" ,r-lifecycle)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-r6" ,r-r6)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyselect" ,r-tidyselect)
|
|
("r-vctrs" ,r-vctrs)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(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-dbplyr
|
|
(package
|
|
(name "r-dbplyr")
|
|
(version "1.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dbplyr" version))
|
|
(sha256
|
|
(base32
|
|
"1v0p0557n6bz84nq9jc4182k00mdd1hvz7h4w3bbg81z0fmpj0d8"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-blob" ,r-blob)
|
|
("r-dbi" ,r-dbi)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-glue" ,r-glue)
|
|
("r-lifecycle" ,r-lifecycle)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-r6" ,r-r6)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyselect" ,r-tidyselect)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/tidyverse/dbplyr")
|
|
(synopsis "Dplyr back end for databases")
|
|
(description
|
|
"This package provides a dplyr back end for databases that allows you to
|
|
work with remote database tables as if they are in-memory data frames. Basic
|
|
features works with any database that has a @code{DBI} back end; more advanced
|
|
features require SQL translation to be provided by the package author.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-acepack
|
|
(package
|
|
(name "r-acepack")
|
|
(version "1.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "acepack" version))
|
|
(sha256
|
|
(base32
|
|
"1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/acepack")
|
|
(synopsis "Functions for regression transformations")
|
|
(description
|
|
"This package provides ACE and AVAS methods for choosing regression
|
|
transformations.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-formula
|
|
(package
|
|
(name "r-formula")
|
|
(version "1.2-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Formula" version))
|
|
(sha256
|
|
(base32
|
|
"0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
|
|
(properties `((upstream-name . "Formula")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/Formula")
|
|
(synopsis "Extended model formulas")
|
|
(description
|
|
"This package provides a new class @code{Formula}, which extends the base
|
|
class @code{formula}. It supports extended formulas with multiple parts of
|
|
regressors on the right-hand side and/or multiple responses on the left-hand
|
|
side.")
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-locfit
|
|
(package
|
|
(name "r-locfit")
|
|
(version "1.5-9.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "locfit" version))
|
|
(sha256
|
|
(base32
|
|
"1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "https://cran.r-project.org/web/packages/locfit")
|
|
(synopsis "Local regression, likelihood and density estimation")
|
|
(description
|
|
"This package provides functions used for local regression, likelihood
|
|
and density estimation.")
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-chron
|
|
(package
|
|
(name "r-chron")
|
|
(version "2.3-55")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "chron" version))
|
|
(sha256
|
|
(base32
|
|
"09gbs7c1ynlg0kl1m6nkbn75ysk16g13r17snnaws64qwywiywqg"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://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 "1.12.8")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "data.table" version))
|
|
(sha256
|
|
(base32
|
|
"1p7rf4v3ysflpgcmy9krkwmcy7z22wb08xm443649waz6lx5z9yk"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://github.com/Rdatatable/data.table/wiki")
|
|
(synopsis "Enhanced version of data.frame R object")
|
|
(description
|
|
"The R package @code{data.table} is an extension of @code{data.frame}
|
|
providing 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:gpl3+)))
|
|
|
|
(define-public r-xtable
|
|
(package
|
|
(name "r-xtable")
|
|
(version "1.8-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xtable" version))
|
|
(sha256
|
|
(base32
|
|
"077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(home-page "http://xtable.r-forge.r-project.org/")
|
|
(synopsis "Export R tables to LaTeX or HTML")
|
|
(description
|
|
"This package provides tools to export R data as LaTeX and HTML tables.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public python-patsy
|
|
(package
|
|
(name "python-patsy")
|
|
(version "0.5.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "patsy" version))
|
|
(sha256
|
|
(base32
|
|
"149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda _ (invoke "nosetests" "-v"))))))
|
|
(propagated-inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-scipy" ,python-scipy)
|
|
("python-six" ,python-six)))
|
|
(native-inputs
|
|
`(("python-nose" ,python-nose)))
|
|
(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
|
|
(package-with-python2 python-patsy))
|
|
|
|
(define-public python-statsmodels
|
|
(package
|
|
(name "python-statsmodels")
|
|
(version "0.11.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "statsmodels" version))
|
|
(sha256
|
|
(base32
|
|
"1w6mf8b86vizi2895j11szqryr2v1ckjig3wp9fv94aslfh3zpjv"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(;; The test suite is very large and rather brittle. Tests often fail
|
|
;; because of minor changes in dependencies that upstream hasn't fixed
|
|
;; in a new release.
|
|
#:tests? #f
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(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* (append (find-files "statsmodels/graphics/tests" "\\.py")
|
|
'("statsmodels/tsa/vector_ar/tests/test_var.py"
|
|
"statsmodels/duration/tests/test_survfunc.py"))
|
|
(("import matplotlib\\.pyplot as plt" line)
|
|
(string-append "import matplotlib;matplotlib.use('Agg');"
|
|
line)))
|
|
#t)))))
|
|
(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-pytz" ,python2-pytz)
|
|
("python2-numpy" ,python2-numpy)
|
|
("python2-scipy" ,python2-scipy)
|
|
("python2-pandas" ,python2-pandas)
|
|
("python2-patsy" ,python2-patsy)
|
|
("python2-matplotlib" ,python2-matplotlib))))))
|
|
|
|
(define-public r-coda
|
|
(package
|
|
(name "r-coda")
|
|
(version "0.19-3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "coda" version))
|
|
(sha256
|
|
(base32
|
|
"1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "https://cran.r-project.org/web/packages/coda")
|
|
(synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
|
|
(description "This package provides functions for summarizing and plotting
|
|
the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
|
|
diagnostic tests of convergence to the equilibrium distribution of the Markov
|
|
chain.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ade4
|
|
(package
|
|
(name "r-ade4")
|
|
(version "1.7-15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ade4" version))
|
|
(sha256
|
|
(base32
|
|
"1xpxznlqm8wb4d5z2dcrl0wi3jjciq2hr5rcx2b5aaipiiyzm1ij"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-pixmap" ,r-pixmap)
|
|
("r-sp" ,r-sp)))
|
|
(home-page "http://pbil.univ-lyon1.fr/ADE-4")
|
|
(synopsis "Multivariate data analysis and graphical display")
|
|
(description
|
|
"The ade4 package contains data analysis functions to analyze ecological
|
|
and environmental data in the framework of Euclidean exploratory methods.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-xml2
|
|
(package
|
|
(name "r-xml2")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xml2" version))
|
|
(sha256
|
|
(base32
|
|
"1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libxml2" ,libxml2)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)
|
|
("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/hadley/xml2")
|
|
(synopsis "Parse XML with R")
|
|
(description
|
|
"This package provides a simple, consistent interface to working with XML
|
|
files in R. It is built on top of the libxml2 C library.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-multitaper
|
|
(package
|
|
(name "r-multitaper")
|
|
(version "1.0-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "multitaper" version))
|
|
(sha256
|
|
(base32
|
|
"04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://github.com/wesleyburr/multitaper/")
|
|
(synopsis "Multitaper spectral analysis tools")
|
|
(description
|
|
"This package implements multitaper spectral estimation
|
|
techniques using prolate spheroidal sequences (Slepians) and sine
|
|
tapers for time series analysis. It includes an adaptive weighted
|
|
multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
|
|
F-test, and complex demodulation. The Slepians sequences are
|
|
generated efficiently using a tridiagonal matrix solution, and
|
|
jackknifed confidence intervals are available for most estimates.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rversions
|
|
(package
|
|
(name "r-rversions")
|
|
(version "2.0.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rversions" version))
|
|
(sha256
|
|
(base32
|
|
"0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://github.com/metacran/rversions")
|
|
(synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
|
|
(description
|
|
"This package provides functions to query the main R repository to find
|
|
the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
|
|
previous R versions and their release dates.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-whisker
|
|
(package
|
|
(name "r-whisker")
|
|
(version "0.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "whisker" version))
|
|
(sha256
|
|
(base32
|
|
"1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/edwindj/whisker")
|
|
(synopsis "Logicless mustache templating for R")
|
|
(description
|
|
"This package provides logicless templating, with a syntax that is not
|
|
limited to R.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-backports
|
|
(package
|
|
(name "r-backports")
|
|
(version "1.1.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "backports" version))
|
|
(sha256
|
|
(base32
|
|
"1irc9c23hwliwkky1b3hi0dkzwalhb7zgjj08562ff1k8dqv4qf6"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/backports")
|
|
(synopsis "Reimplementations of functions introduced since R 3.0.0")
|
|
(description
|
|
"Provides implementations of functions which have been introduced in R
|
|
since version 3.0.0. The backports are conditionally exported which results
|
|
in R resolving the function names to the version shipped with R (if available)
|
|
and uses the implemented backports as fallback. This way package developers
|
|
can make use of the new functions without worrying about the minimum required
|
|
R version.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-checkmate
|
|
(package
|
|
(name "r-checkmate")
|
|
(version "2.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "checkmate" version))
|
|
(sha256
|
|
(base32
|
|
"193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)))
|
|
(home-page "https://github.com/mllg/checkmate")
|
|
(synopsis "Fast and versatile argument checks")
|
|
(description
|
|
"This package provides tests and assertions to perform frequent argument
|
|
checks. A substantial part of the package was written in C to minimize any
|
|
worries about execution time overhead.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-bbmisc
|
|
(package
|
|
(name "r-bbmisc")
|
|
(version "1.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BBmisc" version))
|
|
(sha256
|
|
(base32
|
|
"1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
|
|
(properties `((upstream-name . "BBmisc")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-checkmate" ,r-checkmate)))
|
|
(home-page "https://github.com/berndbischl/BBmisc")
|
|
(synopsis "Miscellaneous functions for R package development")
|
|
(description
|
|
"This package provides miscellaneous helper functions for the development
|
|
of R packages.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-fail
|
|
(package
|
|
(name "r-fail")
|
|
(version "1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fail" version))
|
|
(sha256
|
|
(base32
|
|
"0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bbmisc" ,r-bbmisc)
|
|
("r-checkmate" ,r-checkmate)))
|
|
(home-page "https://github.com/mllg/fail")
|
|
(synopsis "File abstraction interface layer (FAIL)")
|
|
(description
|
|
"This package provides a more comfortable interface to work with R data
|
|
or source files in a key-value fashion.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-batchjobs
|
|
(package
|
|
(name "r-batchjobs")
|
|
(version "1.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BatchJobs" version))
|
|
(sha256
|
|
(base32
|
|
"1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
|
|
(properties `((upstream-name . "BatchJobs")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)
|
|
("r-bbmisc" ,r-bbmisc)
|
|
("r-brew" ,r-brew)
|
|
("r-checkmate" ,r-checkmate)
|
|
("r-data-table" ,r-data-table)
|
|
("r-dbi" ,r-dbi)
|
|
("r-digest" ,r-digest)
|
|
("r-rsqlite" ,r-rsqlite)
|
|
("r-sendmailr" ,r-sendmailr)
|
|
("r-stringi" ,r-stringi)))
|
|
(home-page "https://github.com/tudo-r/BatchJobs")
|
|
(synopsis "Batch computing with R")
|
|
(description
|
|
"This package provides @code{Map}, @code{Reduce} and @code{Filter}
|
|
variants to generate jobs on batch computing systems like PBS/Torque, LSF,
|
|
SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public r-brew
|
|
(package
|
|
(name "r-brew")
|
|
(version "1.0-6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "brew" version))
|
|
(sha256
|
|
(base32
|
|
"1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/brew")
|
|
(synopsis "Templating framework for report generation")
|
|
(description
|
|
"The brew package implements a templating framework for mixing text and R
|
|
code for report generation. The template syntax is similar to PHP, Ruby's erb
|
|
module, Java Server Pages, and Python's psp module.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-desc
|
|
(package
|
|
(name "r-desc")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "desc" version))
|
|
(sha256
|
|
(base32
|
|
"1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-crayon" ,r-crayon)
|
|
("r-r6" ,r-r6)
|
|
("r-rprojroot" ,r-rprojroot)))
|
|
(home-page "https://github.com/r-pkgs/desc")
|
|
(synopsis "Manipulate DESCRIPTION Files")
|
|
(description
|
|
"This package provides tools to read, write, create, and manipulate
|
|
DESCRIPTION files. It is intended for packages that create or manipulate
|
|
other packages.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-commonmark
|
|
(package
|
|
(name "r-commonmark")
|
|
(version "1.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "commonmark" version))
|
|
(sha256
|
|
(base32
|
|
"024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/commonmark")
|
|
(synopsis "CommonMark and Github Markdown Rendering in R")
|
|
(description
|
|
"The CommonMark specification defines a rationalized version of markdown
|
|
syntax. This package uses the @code{cmark} reference implementation for
|
|
converting markdown text into various formats including HTML, LaTeX and groff
|
|
man. In addition, it exposes the markdown parse tree in XML format. The latest
|
|
version of this package also adds support for Github extensions including
|
|
tables, autolinks and strikethrough text.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public r-roxygen2
|
|
(package
|
|
(name "r-roxygen2")
|
|
(version "7.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "roxygen2" version))
|
|
(sha256
|
|
(base32
|
|
"00s1wzx5960k8pzgpz4kikjf4k061hyhnd278y65q6n0wzv3d6vy"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-brew" ,r-brew)
|
|
("r-commonmark" ,r-commonmark)
|
|
("r-desc" ,r-desc)
|
|
("r-digest" ,r-digest)
|
|
("r-knitr" ,r-knitr)
|
|
("r-pkgload" ,r-pkgload)
|
|
("r-purrr" ,r-purrr)
|
|
("r-r6" ,r-r6)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)
|
|
("r-stringi" ,r-stringi)
|
|
("r-stringr" ,r-stringr)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://github.com/klutometis/roxygen")
|
|
(synopsis "In-source documentation system for R")
|
|
(description
|
|
"Roxygen2 is a Doxygen-like in-source documentation system for Rd,
|
|
collation, and NAMESPACE files.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-openssl
|
|
(package
|
|
(name "r-openssl")
|
|
(version "1.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "openssl" version))
|
|
(sha256
|
|
(base32
|
|
"1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libressl" ,libressl)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(propagated-inputs
|
|
`(("r-askpass" ,r-askpass)))
|
|
(home-page "https://github.com/jeroenooms/openssl")
|
|
(synopsis "Toolkit for encryption, signatures and certificates")
|
|
(description
|
|
"This package provides R bindings to OpenSSL libssl and libcrypto, plus
|
|
custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
|
|
and P-521. Cryptographic signatures can either be created and verified
|
|
manually or via x509 certificates. AES block cipher is used in CBC mode for
|
|
symmetric encryption; RSA for asymmetric (public key) encryption. High-level
|
|
envelope functions combine RSA and AES for encrypting arbitrary sized data.
|
|
Other utilities include key generators, hash functions (md5, sha1, sha256,
|
|
etc), base64 encoder, a secure random number generator, and @code{bignum} math
|
|
methods for manually performing crypto calculations on large multibyte
|
|
integers.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-httr
|
|
(package
|
|
(name "r-httr")
|
|
(version "1.4.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "httr" version))
|
|
(sha256
|
|
(base32
|
|
"0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-openssl" ,r-openssl)
|
|
("r-mime" ,r-mime)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://github.com/hadley/httr")
|
|
(synopsis "Tools for working with URLs and HTTP")
|
|
(description
|
|
"The aim of httr is to provide a wrapper for RCurl customised to the
|
|
demands of modern web APIs. It provides useful tools for working with HTTP
|
|
organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
|
|
functions make it easy to control additional request components.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-git2r
|
|
(package
|
|
(name "r-git2r")
|
|
(version "0.27.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "git2r" version))
|
|
(sha256
|
|
(base32
|
|
"1h1vfzym6hi1fqs9p5z5v0f4xldggr425frw8k6dsidah3qhg4h9"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libgit2" ,libgit2)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://github.com/ropensci/git2r")
|
|
(synopsis "Access Git repositories with R")
|
|
(description
|
|
"This package provides an R interface to the libgit2 library, which is a
|
|
pure C implementation of the Git core methods.")
|
|
;; GPLv2 only with linking exception.
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rstudioapi
|
|
(package
|
|
(name "r-rstudioapi")
|
|
(version "0.11")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rstudioapi" version))
|
|
(sha256
|
|
(base32
|
|
"0srh0m4mw4k6s7spwb84l4cx4xnn04cp5cjxi0fwza7bwavpzq0k"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rstudioapi")
|
|
(synopsis "Safely access the RStudio API")
|
|
(description
|
|
"This package provides functions to access the RStudio API and provide
|
|
informative error messages when it's not available.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-devtools
|
|
(package
|
|
(name "r-devtools")
|
|
(version "2.3.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "devtools" version))
|
|
(sha256
|
|
(base32
|
|
"1l6w765q180bg5mmdq5k2ymf6apz7ldhnknzf6ynfp1kf70pbhsg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-cli" ,r-cli)
|
|
("r-covr" ,r-covr)
|
|
("r-crayon" ,r-crayon)
|
|
("r-desc" ,r-desc)
|
|
("r-digest" ,r-digest)
|
|
("r-dt" ,r-dt)
|
|
("r-ellipsis" ,r-ellipsis)
|
|
("r-glue" ,r-glue)
|
|
("r-git2r" ,r-git2r)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-memoise" ,r-memoise)
|
|
("r-pkgbuild" ,r-pkgbuild)
|
|
("r-pkgload" ,r-pkgload)
|
|
("r-rcmdcheck" ,r-rcmdcheck)
|
|
("r-remotes" ,r-remotes)
|
|
("r-rlang" ,r-rlang)
|
|
("r-roxygen2" ,r-roxygen2)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-rversions" ,r-rversions)
|
|
("r-sessioninfo" ,r-sessioninfo)
|
|
("r-testthat" ,r-testthat)
|
|
("r-usethis" ,r-usethis)
|
|
("r-withr" ,r-withr)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/hadley/devtools")
|
|
(synopsis "Tools to make developing R packages easier")
|
|
(description "The devtools package is a collection of package development
|
|
tools to simplify the devolpment of R packages.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-withr
|
|
(package
|
|
(name "r-withr")
|
|
(version "2.2.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "withr" version))
|
|
(sha256
|
|
(base32
|
|
"10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/jimhester/withr")
|
|
(synopsis "Run code with temporarily modified global state")
|
|
(description
|
|
"This package provides a set of functions to run R code in an environment
|
|
in which global state has been temporarily modified. Many of these functions
|
|
were originally a part of the r-devtools package.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-hms
|
|
(package
|
|
(name "r-hms")
|
|
(version "0.5.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hms" version))
|
|
(sha256
|
|
(base32
|
|
"1baki0qw5ijgiflvsdvqj3apg4yanf12vx14kwbqdzk5rz46fasf"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rlang" ,r-rlang)
|
|
("r-pkgconfig" ,r-pkgconfig)
|
|
("r-vctrs" ,r-vctrs)))
|
|
(home-page "https://github.com/rstats-db/hms")
|
|
(synopsis "Pretty time of day")
|
|
(description
|
|
"This package implements an S3 class for storing and formatting
|
|
time-of-day values, based on the @code{difftime} class.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-readr
|
|
(package
|
|
(name "r-readr")
|
|
(version "1.3.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "readr" version))
|
|
(sha256
|
|
(base32
|
|
"1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-clipr" ,r-clipr)
|
|
("r-crayon" ,r-crayon)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-hms" ,r-hms)
|
|
("r-tibble" ,r-tibble)
|
|
("r-r6" ,r-r6)
|
|
("r-bh" ,r-bh)))
|
|
(home-page "https://github.com/hadley/readr")
|
|
(synopsis "Read tabular data")
|
|
(description
|
|
"This package provides functions to read flat or tabular text files from
|
|
disk (or a connection).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-plotrix
|
|
(package
|
|
(name "r-plotrix")
|
|
(version "3.7-8")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plotrix" version))
|
|
(sha256
|
|
(base32
|
|
"104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/plotrix")
|
|
(synopsis "Various plotting functions")
|
|
(description
|
|
"This package provides lots of plotting, various labeling, axis and color
|
|
scaling functions for R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-gridbase
|
|
(package
|
|
(name "r-gridbase")
|
|
(version "0.4-7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gridBase" version))
|
|
(sha256
|
|
(base32
|
|
"09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/gridBase")
|
|
(synopsis "Integration of base and grid graphics")
|
|
(description
|
|
"This package provides an integration of base and grid graphics for R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-latticeextra
|
|
(package
|
|
(name "r-latticeextra")
|
|
(version "0.6-29")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "latticeExtra" version))
|
|
(sha256
|
|
(base32
|
|
"04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
|
|
(properties `((upstream-name . "latticeExtra")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-jpeg" ,r-jpeg)
|
|
("r-lattice" ,r-lattice)
|
|
("r-png" ,r-png)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)))
|
|
(home-page "http://latticeextra.r-forge.r-project.org/")
|
|
(synopsis "Extra graphical utilities based on lattice")
|
|
(description
|
|
"Building on the infrastructure provided by the lattice package, this
|
|
package provides several new high-level graphics functions and methods, as
|
|
well as additional utilities such as panel and axis annotation functions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rcpparmadillo
|
|
(package
|
|
(name "r-rcpparmadillo")
|
|
(version "0.9.900.1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppArmadillo" version))
|
|
(sha256
|
|
(base32
|
|
"1zisw2yrb9qmmrs7q8y83mrm7lh1c2786h70gs8jwc0si16x0lq5"))))
|
|
(properties `((upstream-name . "RcppArmadillo")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/RcppCore/RcppArmadillo")
|
|
(synopsis "Rcpp integration for the Armadillo linear algebra library")
|
|
(description
|
|
"Armadillo is a templated C++ linear algebra library that aims towards a
|
|
good balance between speed and ease of use. Integer, floating point and
|
|
complex numbers are supported, as well as a subset of trigonometric and
|
|
statistics functions. Various matrix decompositions are provided through
|
|
optional integration with LAPACK and ATLAS libraries. This package includes
|
|
the header files from the templated Armadillo library.")
|
|
;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
|
|
;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
|
|
;; later, as is the rest of 'Rcpp'.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bitops
|
|
(package
|
|
(name "r-bitops")
|
|
(version "1.0-6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bitops" version))
|
|
(sha256
|
|
(base32
|
|
"176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/bitops")
|
|
(synopsis "Bitwise operations")
|
|
(description
|
|
"This package provides functions for bitwise operations on integer
|
|
vectors.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-catools
|
|
(package
|
|
(name "r-catools")
|
|
(version "1.18.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "caTools" version))
|
|
(sha256
|
|
(base32
|
|
"0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
|
|
(properties `((upstream-name . "caTools")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bitops" ,r-bitops)))
|
|
(home-page "https://cran.r-project.org/web/packages/caTools")
|
|
(synopsis "Various tools including functions for moving window statistics")
|
|
(description
|
|
"This package contains several basic utility functions including:
|
|
moving (rolling, running) window statistic functions, read/write for GIF and
|
|
ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
|
|
encoder/decoder, round-off-error-free sum and cumsum, etc.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-rprojroot
|
|
(package
|
|
(name "r-rprojroot")
|
|
(version "1.3-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rprojroot" version))
|
|
(sha256
|
|
(base32
|
|
"12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)))
|
|
(home-page "https://github.com/krlmlr/rprojroot")
|
|
(synopsis "Finding files in project subdirectories")
|
|
(description
|
|
"This package helps accessing files relative to a project root. It
|
|
provides helpers for robust, reliable and flexible paths to files below a
|
|
project root. The root of a project is defined as a directory that matches a
|
|
certain criterion, e.g., it contains a certain regular file.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-rmarkdown
|
|
(package
|
|
(name "r-rmarkdown")
|
|
(version "2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rmarkdown" version))
|
|
(sha256
|
|
(base32 "196r3hq1gcr6iamxllq4k40cb109b16ng24ky0q68bwrll80q1mh"))))
|
|
(properties `((upstream-name . "rmarkdown")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-evaluate" ,r-evaluate)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-knitr" ,r-knitr)
|
|
("r-mime" ,r-mime)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tinytex" ,r-tinytex)
|
|
("r-xfun" ,r-xfun)
|
|
("r-yaml" ,r-yaml)
|
|
("ghc-pandoc" ,ghc-pandoc)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://rmarkdown.rstudio.com")
|
|
(synopsis "Convert R Markdown documents into a variety of formats")
|
|
(description
|
|
"This package provides tools to convert R Markdown documents into a
|
|
variety of formats.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-gtable
|
|
(package
|
|
(name "r-gtable")
|
|
(version "0.3.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gtable" version))
|
|
(sha256
|
|
(base32
|
|
"1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
|
|
(properties `((upstream-name . "gtable")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/gtable")
|
|
(synopsis "R library to arrange grobs in tables")
|
|
(description
|
|
"Gtable is a collection of tools to make it easier to work with
|
|
\"tables\" of grobs.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-gridextra
|
|
(package
|
|
(name "r-gridextra")
|
|
(version "2.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gridExtra" version))
|
|
(sha256
|
|
(base32
|
|
"0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
|
|
(properties `((upstream-name . "gridExtra")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gtable" ,r-gtable)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ;for building vignettes
|
|
(home-page "https://github.com/baptiste/gridextra")
|
|
(synopsis "Miscellaneous functions for \"Grid\" graphics")
|
|
(description
|
|
"This package provides a number of user-level functions to work with
|
|
@code{grid} graphics, notably to arrange multiple grid-based plots on a page,
|
|
and draw tables.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-pkgconfig
|
|
(package
|
|
(name "r-pkgconfig")
|
|
(version "2.0.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgconfig" version))
|
|