mirror of
https://https.git.savannah.gnu.org/git/guix.git/
synced 2025-07-10 16:50:43 +02:00
97d2a336d8
* gnu/packages/statistics.scm (emacs-ess): Update to Fix install path. Packages must be installed under "site-packages/name-version/". Change-Id: Ifdfbd2ad0d006f9f1cef83230876b9a5656949e3 Signed-off-by: Christopher Baines <mail@cbaines.net>
3414 lines
129 KiB
Scheme
3414 lines
129 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015-2025 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, 2021 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 © 2017–2020, 2022 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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;;; Copyright © 2021, 2022, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
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;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
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;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
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;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
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;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
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;;; Copyright © 2023 Felix Gruber <felgru@posteo.net>
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||
;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
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||
;;; Copyright © 2024 Vinicius Monego <monego@posteo.net>
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;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
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;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
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;;; Copyright © 2025 Jonas Freimuth <jonas.freimuth@posteo.de>
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;;;
|
||
;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||
;;; under the terms of the GNU General Public License as published by
|
||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||
;;; your option) any later version.
|
||
;;;
|
||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
;;; GNU General Public License for more details.
|
||
;;;
|
||
;;; You should have received a copy of the GNU General Public License
|
||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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||
(define-module (gnu packages statistics)
|
||
#:use-module (guix gexp)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix packages)
|
||
#: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 cmake)
|
||
#:use-module (guix build-system emacs)
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||
#:use-module (guix build-system gnu)
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||
#:use-module (guix build-system r)
|
||
#:use-module (guix build-system pyproject)
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||
#:use-module (guix build-system python)
|
||
#:use-module (guix build-system trivial)
|
||
#:use-module (guix build-system ruby)
|
||
#:use-module (gnu packages)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages autotools)
|
||
#:use-module (gnu packages bash)
|
||
#:use-module (gnu packages bison)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages cmake)
|
||
#: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 flex)
|
||
#: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)
|
||
#:use-module (gnu packages java)
|
||
#:use-module (gnu packages javascript)
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||
#:use-module (gnu packages libffi)
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||
#:use-module (gnu packages linux)
|
||
#:use-module (gnu packages machine-learning)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages multiprecision)
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||
#:use-module (gnu packages ncurses)
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||
#:use-module (gnu packages ocaml)
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||
#:use-module (gnu packages pcre)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-build)
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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)
|
||
#:use-module (gnu packages ruby)
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||
#:use-module (gnu packages shells)
|
||
#:use-module (gnu packages sphinx)
|
||
#:use-module (gnu packages ssh)
|
||
#:use-module (gnu packages swig)
|
||
#:use-module (gnu packages tbb)
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||
#:use-module (gnu packages tcl)
|
||
#:use-module (gnu packages terminals)
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||
#:use-module (gnu packages tex)
|
||
#:use-module (gnu packages texinfo)
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||
#:use-module (gnu packages time)
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||
#:use-module (gnu packages tls)
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||
#:use-module (gnu packages base)
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||
#:use-module (gnu packages uglifyjs)
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||
#:use-module (gnu packages version-control)
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||
#: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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||
#:use-module (ice-9 match))
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||
|
||
(define-public pspp
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||
(package
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||
(name "pspp")
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||
(version "2.0.1")
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(source
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||
(origin
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||
(method url-fetch)
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(uri (string-append "mirror://gnu/pspp/pspp-" version ".tar.gz"))
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||
(sha256
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||
(base32
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||
"002c08rxym056mn7a73jwjmcazqd4gh5j1cyml603y4ckvqb1nwf"))))
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||
(build-system gnu-build-system)
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||
(arguments
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||
(list #:phases
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||
#~(modify-phases %standard-phases
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||
(add-after 'unpack 'patch-test-suite
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||
(lambda _
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||
(substitute* "tests/output/tex.at"
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||
(("AT_CHECK\\(\\[LC_ALL=C.UTF-8 pspp")
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||
"AT_CHECK([LC_ALL=en_US.UTF-8 pspp"))))
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||
(add-before 'check 'prepare-tests
|
||
;; Prevent irrelevant errors that cause test output mismatches:
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||
;; ‘Fontconfig error: No writable cache directories’
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||
(lambda _
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||
(setenv "XDG_CACHE_HOME" (getcwd)))))))
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||
(inputs
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||
(list cairo
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||
gettext-minimal
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||
gsl
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||
libxml2
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||
pango
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||
readline
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||
gtk+
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||
gtksourceview-3
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||
spread-sheet-widget
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||
zlib))
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||
(native-inputs
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||
(list autoconf ;for tests
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||
`(,glib "bin") ;for glib-genmarshal
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||
perl
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||
pkg-config
|
||
python-3 ;for tests
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||
texinfo))
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||
(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
|
||
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
|
||
(package
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||
(name "jags")
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||
(version "4.3.1")
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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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||
"0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list #:configure-flags
|
||
#~(list "--with-lapack=-lopenblas"
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||
"--with-blas=-lopenblas")))
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||
(home-page "https://mcmc-jags.sourceforge.net/")
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||
(native-inputs
|
||
(list gfortran openblas))
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||
(synopsis "Gibbs sampler")
|
||
(description "JAGS is Just Another Gibbs Sampler. It is a program for
|
||
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:
|
||
|
||
@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,
|
||
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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||
|
||
(define-public libxls
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||
(package
|
||
(name "libxls")
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||
(version "1.6.2")
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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"))
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||
(sha256
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||
(base32 "0wg3ymr43aa1j3scyl9x83b2xgg7wilzpil0dj91a8dzji6w7b2x"))))
|
||
(build-system gnu-build-system)
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||
(home-page "https://github.com/libxls/libxls")
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||
(synopsis "Read binary (.xls) Excel spreadsheet files")
|
||
(description
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||
"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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||
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This package also provides @command{xls2csv} to export Excel files to CSV.")
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||
(license license:bsd-2)))
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||
;; Update this package together with the set of recommended packages: r-boot,
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||
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
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||
;; 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 "4.5.0")
|
||
(source (origin
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||
(method url-fetch)
|
||
(uri (string-append "mirror://cran/src/base/R-"
|
||
(version-major version) "/R-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1q9wdj225v4sxwfgpaz4crpkiiy2rr4mjkc7jfbxq78d7q8ylcrv"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(list
|
||
#:disallowed-references `(,tzdata-for-tests)
|
||
#:make-flags
|
||
#~(list (string-append "LDFLAGS=-Wl,-rpath=" #$output "/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 _
|
||
;; This ensures that Guix can detect embedded store references;
|
||
;; see bug #28157 for details.
|
||
(substitute* "src/library/base/makebasedb.R"
|
||
(("compress = TRUE") "compress = FALSE"))
|
||
(substitute* '("src/library/tools/Makefile.in"
|
||
"share/make/basepkg.mk"
|
||
"share/make/lazycomp.mk")
|
||
(("makeLazyLoading\\(")
|
||
"makeLazyLoading(compress=FALSE,"))))
|
||
(add-before 'configure 'patch-coreutils-paths
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((uname-bin (search-input-file inputs "/bin/uname"))
|
||
(rm-bin (search-input-file inputs "/bin/rm")))
|
||
(substitute* "src/scripts/R.sh.in"
|
||
(("uname") uname-bin))
|
||
(substitute* "src/unix/sys-std.c"
|
||
(("rm -Rf ") (string-append rm-bin " -Rf ")))
|
||
(substitute* "src/library/parallel/R/detectCores.R"
|
||
(("'grep")
|
||
(string-append "'"
|
||
(search-input-file inputs "/bin/grep")))
|
||
(("\\| wc -l")
|
||
(string-append "| "
|
||
(search-input-file inputs "/bin/wc")
|
||
" -l"))))))
|
||
(add-after 'unpack 'patch-tests
|
||
(lambda _
|
||
;; This is needed because R is run during the check phase and
|
||
;; /bin/sh doesn't exist in the build container.
|
||
(substitute* "src/unix/sys-unix.c"
|
||
(("\"/bin/sh\"")
|
||
(string-append "\"" (which "sh") "\"")))
|
||
;; This test fails because line numbers are off by two.
|
||
(substitute* "tests/reg-packages.R"
|
||
(("8 <= print" m) (string-append "## " m)))))
|
||
(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"
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||
(("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,
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||
;; 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\"))\
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||
} 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"))))
|
||
|
||
;; The "References" section of this file when converted to
|
||
;; package.rds is sometimes stored with a newline, sometimes with
|
||
;; a space. We avoid this problem by removing the line break
|
||
;; that is suspected to be the culprit.
|
||
(substitute* "src/library/methods/DESCRIPTION.in"
|
||
(("\\(2008\\)\n") "(2008) ")
|
||
((" ``Software") "``Software")
|
||
(("Data Analysis:.") "Data Analysis:\n")
|
||
(("Programming with R") " Programming with R"))
|
||
(substitute* "src/library/tools/DESCRIPTION.in"
|
||
(("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr")
|
||
"codetools, methods, xml2, curl, commonmark,
|
||
knitr, xfun, mathjaxr"))))
|
||
(add-before 'build 'set-locales
|
||
(lambda _
|
||
(setlocale LC_ALL "C")
|
||
(setenv "LC_ALL" "C")))
|
||
(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")))
|
||
(add-before 'configure '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.
|
||
;; We also need TZ during the configure step.
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "TZ" "UTC+1")
|
||
(setenv "TZDIR"
|
||
(search-input-directory inputs
|
||
"share/zoneinfo"))))
|
||
(add-before 'check 'set-home
|
||
;; Some tests require that HOME be set.
|
||
(lambda _ (setenv "HOME" "/tmp")))
|
||
(add-before 'build 'use-writable-texmfvar
|
||
;; Use writable TEXMFVAR to generate fonts.
|
||
(lambda _ (setenv "TEXMFVAR" "/tmp")))
|
||
(add-after 'build 'make-info
|
||
(lambda _ (invoke "make" "info")))
|
||
(add-after 'build 'install-info
|
||
(lambda _ (invoke "make" "install-info"))))
|
||
#:configure-flags
|
||
#~(list
|
||
;; 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="
|
||
#$(this-package-input "tcl")
|
||
"/lib/tclConfig.sh")
|
||
(string-append "--with-tk-config="
|
||
#$(this-package-input "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
|
||
(list bzip2
|
||
perl
|
||
pkg-config
|
||
texinfo ; for building HTML manuals
|
||
(texlive-local-tree
|
||
(list texlive-etoolbox
|
||
texlive-fancyvrb
|
||
texlive-inconsolata
|
||
texlive-upquote
|
||
texlive-xkeyval))
|
||
tzdata-for-tests
|
||
xz))
|
||
(inputs
|
||
(list coreutils
|
||
curl
|
||
openblas
|
||
gfortran
|
||
grep
|
||
icu4c
|
||
libdeflate
|
||
libjpeg-turbo
|
||
libpng
|
||
libtiff
|
||
libxt
|
||
;; We need not only cairo here, but pango to ensure that tests for the
|
||
;; "cairo" bitmapType plotting backend succeed.
|
||
pango
|
||
pcre2
|
||
readline
|
||
tcl
|
||
tk
|
||
which
|
||
zlib
|
||
;; This avoids a reference to the ungraftable static bash. R uses the
|
||
;; detected shell for the "system" procedure.
|
||
bash-minimal))
|
||
(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
|
||
(substitute-keyword-arguments (package-arguments r-with-tests)
|
||
((#:tests? #f #f) #f)
|
||
((#:disallowed-references refs '())
|
||
(cons perl refs))
|
||
((#: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))
|
||
((#:phases phases '%standard-phases)
|
||
#~(modify-phases #$phases
|
||
(add-after 'install 'remove-extraneous-references
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(substitute* (string-append #$output "/lib/R/etc/Makeconf")
|
||
(("^# configure.*")
|
||
"# Removed to avoid extraneous references\n"))
|
||
(substitute* (string-append #$output "/lib/R/bin/libtool")
|
||
(((string-append
|
||
"(-L)?("
|
||
(format #false
|
||
"~a/[^-]+-(~{~a~^|~})-[^/]+"
|
||
(%store-directory)
|
||
'("bzip2"
|
||
"file"
|
||
"glibc-utf8-locales"
|
||
"graphite2"
|
||
"libselinux"
|
||
"libsepol"
|
||
"perl"
|
||
"texinfo"
|
||
"texlive-bin"
|
||
"util-macros"
|
||
"xz"))
|
||
"|"
|
||
(format #false "~a/[^-]+-glibc-[^-]+-static"
|
||
(%store-directory))
|
||
")/lib")) ""))))))))))
|
||
|
||
(define-public rmath-standalone
|
||
(package (inherit r-minimal)
|
||
(name "rmath-standalone")
|
||
(arguments
|
||
'(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'set-timezone
|
||
;; We need TZ during the configure step.
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "TZ" "UTC+1")
|
||
(setenv "TZDIR"
|
||
(search-input-directory inputs "share/zoneinfo"))))
|
||
(add-after 'configure 'chdir
|
||
(lambda _ (chdir "src/nmath/standalone/"))))))
|
||
(synopsis "Standalone R math library")
|
||
(description
|
||
"This package provides the R math library as an independent package.")))
|
||
|
||
(define-public r
|
||
(package (inherit r-minimal)
|
||
(name "r")
|
||
(source #f)
|
||
(build-system trivial-build-system)
|
||
(arguments '(#:builder (begin (mkdir %output) #t)))
|
||
(propagated-inputs
|
||
(list r-minimal
|
||
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-public r-testthat
|
||
(package
|
||
(name "r-testthat")
|
||
(version "3.2.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "testthat" version))
|
||
(sha256
|
||
(base32
|
||
"1by17pjy05xjc0clbp8kam2lrzy5w00fd0nqqp76l0dwbd57j2qq"))))
|
||
(properties
|
||
'((updater-ignored-native-inputs . ("r-testthat"))))
|
||
(build-system r-build-system)
|
||
;; Some tests require r-xml2, which uses r-testthat.
|
||
(arguments (list #:tests? #false))
|
||
(propagated-inputs
|
||
(list r-brio
|
||
r-callr
|
||
r-cli
|
||
r-desc
|
||
r-digest
|
||
r-evaluate
|
||
r-jsonlite
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-pkgload
|
||
r-praise
|
||
r-processx
|
||
r-ps
|
||
r-r6
|
||
r-rlang
|
||
r-waldo
|
||
r-withr))
|
||
(native-inputs (list r-knitr))
|
||
(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 "2.6.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R6" version))
|
||
(sha256
|
||
(base32
|
||
"1d3k40gnms6458aprrjy899yhjv06lr0arag21zfn4mrn6lfpijr"))))
|
||
(properties
|
||
;; We can't have r-testthat among the inputs here to avoid a dependency
|
||
;; cycle.
|
||
'((updater-ignored-native-inputs . ("r-testthat"))))
|
||
(build-system r-build-system)
|
||
;; Tests require r-testthat, which indirectly depends on this package.
|
||
(arguments (list #:tests? #false))
|
||
(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 "1.1.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rlang" version))
|
||
(sha256
|
||
(base32
|
||
"0c7kaw5lvk4vym67ki0511zbqbx5ca1k1k6y9rayq62fdy3lqm0q"))))
|
||
(properties
|
||
;; We can't have r-testthat among the inputs here to avoid a dependency
|
||
;; cycle.
|
||
'((updater-ignored-native-inputs . ("r-testthat"))))
|
||
(build-system r-build-system)
|
||
;; Tests require r-testthat, which indirectly depends on this package.
|
||
(arguments (list #:tests? #false))
|
||
(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 "3.2.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tibble" version))
|
||
(sha256
|
||
(base32
|
||
"0c916wl19wbhncv05hjzs2vmvvbcxlswjl6i232ygmkzal62v9v5"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-fansi
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-pillar
|
||
r-pkgconfig
|
||
r-rlang
|
||
r-vctrs))
|
||
(native-inputs
|
||
(list r-knitr r-testthat))
|
||
(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 python-vega-datasets
|
||
(package
|
||
(name "python-vega-datasets")
|
||
(version "0.9.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "vega_datasets" version))
|
||
(sha256
|
||
(base32 "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx"))
|
||
(modules '((guix build utils)))
|
||
(patches
|
||
(search-patches "python-vega-datasets-remove-la-riots-code.patch"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-la-riots-dataset
|
||
;; Remove dataset with unclear license.
|
||
(lambda _
|
||
(delete-file "vega_datasets/_data/la-riots.csv"))))))
|
||
(native-inputs (list python-pytest python-setuptools python-wheel))
|
||
(propagated-inputs (list python-pandas))
|
||
(home-page "https://github.com/altair-viz/vega_datasets")
|
||
(synopsis "Example datasets used by Vega-related projects")
|
||
(description "This package provides a collection of datasets used in Vega
|
||
and Vega-Lite examples.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-altair
|
||
(package
|
||
(name "python-altair")
|
||
(version "5.3.0")
|
||
(source (origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/altair-viz/altair")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1lx3pkphi36pljns6jjxhyn9fbrana8f1y6gcg4yca48nvwlfssl"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:test-flags
|
||
;; XXX: This test file requires hard to package python-anywidgets.
|
||
#~(list "--ignore=tests/test_jupyter_chart.py"
|
||
"-k" (string-join
|
||
(list
|
||
;; these tests open an external connection.
|
||
"not test_from_and_to_json_roundtrip"
|
||
"test_render_examples_to_chart"
|
||
;; introduces a circular dependency on altair-viewer.
|
||
"not test_save_html"
|
||
;; these tests require the vl-convert vega compiler
|
||
"test_vegalite_compiler"
|
||
"test_to_dict_with_format_vega"
|
||
"test_to_json_with_format_vega"
|
||
"test_to_url"
|
||
"test_renderer_with_none_embed_options"
|
||
"test_jupyter_renderer_mimetype")
|
||
" and not "))))
|
||
(propagated-inputs (list python-jinja2
|
||
python-jsonschema
|
||
python-numpy
|
||
python-pandas
|
||
python-setuptools
|
||
python-toolz
|
||
python-typing-extensions))
|
||
(native-inputs (list python-black
|
||
python-hatchling
|
||
python-ipython
|
||
python-pytest
|
||
python-vega-datasets))
|
||
(home-page "https://altair-viz.github.io/")
|
||
(synopsis "Declarative statistical visualization library for Python")
|
||
(description
|
||
"Vega-Altair is a declarative statistical visualization library for Python.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-george
|
||
(package
|
||
(name "python-george")
|
||
(version "0.4.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "george" version))
|
||
(sha256
|
||
(base32 "1zvbdq50ds820aj06lr2nrzwg121bkd9bg0aq83gvk7lf8yqgp4v"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs
|
||
(list cmake-minimal
|
||
pybind11
|
||
python-pytest
|
||
python-scikit-build-core
|
||
python-setuptools-scm))
|
||
(propagated-inputs
|
||
(list python-numpy
|
||
python-scipy))
|
||
(home-page "https://george.readthedocs.io")
|
||
(synopsis "Fast Gaussian Processes for regression")
|
||
(description
|
||
"George is a fast and flexible Python library for Gaussian Process (GP)
|
||
Regression, focused on efficiently evaluating the marginalized likelihood of a
|
||
dataset under a GP prior, even as this dataset gets Big.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-getdist
|
||
(package
|
||
(name "python-getdist")
|
||
(version "1.5.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "getdist" version))
|
||
(sha256
|
||
(base32 "01s1p53pqpxbi8sy2030jpjn7gsy67zb7y6p0gf57lgxvp4zx74q"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs
|
||
(list python-pytest
|
||
python-setuptools
|
||
python-wheel))
|
||
(propagated-inputs
|
||
(list python-matplotlib
|
||
python-numpy
|
||
python-packaging
|
||
python-pyyaml
|
||
python-scipy))
|
||
(home-page "https://github.com/cmbant/getdist")
|
||
(synopsis "GetDist Monte Carlo sample analysis, plotting and GUI")
|
||
(description
|
||
"GetDist is a Python package for analysing Monte Carlo samples, including
|
||
correlated samples from Markov Chain Monte Carlo (MCMC).")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public python-hdmedians
|
||
(package
|
||
(name "python-hdmedians")
|
||
(version "0.14.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "hdmedians" version))
|
||
(sha256
|
||
(base32
|
||
"1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-before 'check 'build-extensions
|
||
(lambda _
|
||
;; Cython extensions have to be built before running the tests.
|
||
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
||
(propagated-inputs (list python-cython python-numpy python-setuptools
|
||
python-wheel))
|
||
(native-inputs (list python-nose))
|
||
(home-page "http://github.com/daleroberts/hdmedians")
|
||
(synopsis "High-dimensional medians")
|
||
(description "Various definitions for a high-dimensional median exist and
|
||
this Python package provides a number of fast implementations of these
|
||
definitions. Medians are extremely useful due to their high breakdown
|
||
point (up to 50% contamination) and have a number of nice applications in
|
||
machine learning, computer vision, and high-dimensional statistics.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-nestle
|
||
(package
|
||
(name "python-nestle")
|
||
(version "0.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "nestle" version))
|
||
(sha256
|
||
(base32 "0v94qcqwl519vqhd4wb1zhx4x4q9xhbck8g2h0v2n4mwxgz9irsx"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:tests? #f)) ; no tests in PyPI or Git
|
||
(native-inputs
|
||
(list python-setuptools
|
||
python-wheel))
|
||
(propagated-inputs
|
||
(list python-numpy))
|
||
(home-page "https://github.com/kbarbary/nestle")
|
||
(synopsis "Nested sampling algorithms for evaluating Bayesian evidence")
|
||
(description
|
||
"This package provides an implementation of
|
||
@url{https://en.wikipedia.org/wiki/Nested_sampling_algorithm, Nested Sampling}
|
||
algorithms for evaluating Bayesian evidence.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-arviz
|
||
(package
|
||
(name "python-arviz")
|
||
(version "0.21.0")
|
||
(source (origin
|
||
(method git-fetch) ; PyPI misses some test files
|
||
(uri (git-reference
|
||
(url "https://github.com/arviz-devs/arviz")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"02bqpl61gzn65vhwspi6gx9ln2wlwh8xm418i8vhmls44rvszcxf"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
;; FIXME: matplotlib tests fail because of the "--save" test flag.
|
||
(list #:test-flags #~'("--ignore"
|
||
"arviz/tests/base_tests/test_plots_matplotlib.py")
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'unpack 'remove-radon
|
||
(lambda _
|
||
(delete-file
|
||
;; This dataset is loaded remotely, it's not supposed to
|
||
;; be copied locally.
|
||
"arviz/data/example_data/code/radon/radon.json")))
|
||
(add-before 'check 'write-permission
|
||
(lambda _
|
||
;; 3 tests require write permission.
|
||
(setenv "HOME" "/tmp"))))))
|
||
(native-inputs (list python-cloudpickle python-pytest))
|
||
(propagated-inputs (list python-dm-tree
|
||
python-h5netcdf
|
||
python-matplotlib
|
||
python-numpy
|
||
python-packaging
|
||
python-pandas
|
||
python-scipy
|
||
python-typing-extensions
|
||
python-xarray
|
||
python-xarray-einstats
|
||
python-setuptools
|
||
python-wheel))
|
||
(home-page "https://github.com/arviz-devs/arviz")
|
||
(synopsis "Exploratory analysis of Bayesian models")
|
||
(description
|
||
"ArviZ is a Python package for exploratory analysis of Bayesian models.
|
||
It includes functions for posterior analysis, data storage, model checking,
|
||
comparison and diagnostics.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-pymc
|
||
(package
|
||
(name "python-pymc")
|
||
(version "5.21.0")
|
||
(source (origin
|
||
(method git-fetch) ; no tests in PyPI
|
||
(uri (git-reference
|
||
(url "https://github.com/pymc-devs/pymc")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0azkbl0mpanza35ibdqdm21bf45n3xi26wy01lnxzxqblcjcny9l"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list #:tests? #f ; tests are too computationally intensive
|
||
#:phases #~(modify-phases %standard-phases
|
||
(add-after 'unpack 'versioneer
|
||
(lambda _
|
||
(invoke "versioneer" "install")
|
||
(substitute* "setup.py"
|
||
(("version=versioneer.get_version\\(),")
|
||
(format #f "version=~s," #$version)))))
|
||
;; To create the compiledir for tests.
|
||
(add-before 'check 'write-permissions
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(setenv "HOME" "/tmp")))))))
|
||
(native-inputs (list python-pytest-cov python-versioneer))
|
||
(propagated-inputs (list python-arviz
|
||
python-cachetools
|
||
python-cloudpickle
|
||
python-fastprogress
|
||
python-numpy
|
||
python-pandas
|
||
python-pytensor
|
||
python-scipy
|
||
python-typing-extensions))
|
||
(home-page "https://github.com/pymc-devs/pymc")
|
||
(synopsis "Library for probabilistic programming in Python")
|
||
(description
|
||
"PyMC (formerly PyMC3) is a Python package for Bayesian statistical
|
||
modeling focusing on advanced Markov chain Monte Carlo (MCMC) and variational
|
||
inference (VI) algorithms.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public python-chaospy
|
||
(package
|
||
(name "python-chaospy")
|
||
(version "4.3.13")
|
||
(source (origin ;; PyPI misses Pytest fixtures.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/jonathf/chaospy")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
;; The deprecation warnings break the tests.
|
||
(add-after 'unpack 'dont-treat-deprecation-warnings-as-error
|
||
(lambda _
|
||
(substitute* "pyproject.toml"
|
||
(("\"error::DeprecationWarning\",") "")))))))
|
||
(propagated-inputs (list python-importlib-metadata python-numpoly
|
||
python-numpy python-scipy))
|
||
(native-inputs (list python-pytest python-scikit-learn python-setuptools
|
||
python-wheel))
|
||
(home-page "https://chaospy.readthedocs.io/en/master/")
|
||
(synopsis "Numerical tool for performing uncertainty quantification")
|
||
(description "Chaospy is a numerical toolbox for performing uncertainty
|
||
quantification using polynomial chaos expansions, advanced Monte Carlo
|
||
methods implemented in Python. It also include a full suite of tools for
|
||
doing low-discrepancy sampling, quadrature creation, polynomial manipulations,
|
||
and a lot more.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-patsy
|
||
(package
|
||
(name "python-patsy")
|
||
(version "1.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "patsy" version))
|
||
(sha256
|
||
(base32
|
||
"1i60b6s8zj0w2ks63ip4mr8z14p6pixp76rm9q2qr0gc3qwsk1p7"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs
|
||
(list python-numpy python-scipy))
|
||
(native-inputs
|
||
(list python-pytest python-pytest-cov python-setuptools python-wheel))
|
||
(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 python-kalepy
|
||
(package
|
||
(name "python-kalepy")
|
||
(version "1.4.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "kalepy" version))
|
||
(sha256
|
||
(base32 "1a1d98vjkjs8zwx4hdss3gv67jyf25mmsrdc5qi8hpxminkizb6w"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs
|
||
(list python-pytest
|
||
python-setuptools
|
||
python-wheel))
|
||
(propagated-inputs
|
||
(list python-matplotlib
|
||
python-numba
|
||
python-numpy
|
||
python-scipy
|
||
python-six))
|
||
(home-page "https://github.com/lzkelley/kalepy")
|
||
(synopsis "Kernel Density Estimation (KDE) and sampling")
|
||
(description
|
||
"This package performs KDE operations on multidimensional data to
|
||
calculate estimated PDFs (probability distribution functions), and resample
|
||
new data from those PDFs.")
|
||
;; MIT - setup.py
|
||
;; GPL3+ - LICENSE
|
||
(license (list license:gpl3+ license:expat))))
|
||
|
||
(define-public python-lifelines
|
||
(package
|
||
(name "python-lifelines")
|
||
(version "0.30.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "lifelines" version))
|
||
(sha256
|
||
(base32 "065yajlfydi7x7b1sjxp9h3rqgwrd3w9ivxiyph7y5nbbwkzdxpp"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
;; NOTE: Tests take 15-25min to complete on 16 threads and much longer
|
||
;; in single one, consider to try enabling --numprocesses option.
|
||
#~(list ;; "--numprocesses" (number->string (parallel-job-count))
|
||
;; This accuracy test fails because 0.012 is not < 0.01.
|
||
"-k" "not test_weibull_with_delayed_entries")))
|
||
(native-inputs
|
||
(list python-dill
|
||
python-flaky
|
||
python-joblib
|
||
python-pytest
|
||
;; python-pytest-xdist
|
||
python-setuptools
|
||
python-wheel))
|
||
(propagated-inputs
|
||
(list python-autograd
|
||
python-autograd-gamma
|
||
python-formulaic
|
||
python-matplotlib
|
||
python-numpy
|
||
python-pandas
|
||
python-scipy))
|
||
(home-page "https://github.com/CamDavidsonPilon/lifelines")
|
||
(synopsis
|
||
"Survival analysis including Kaplan Meier, Nelson Aalen and regression")
|
||
(description
|
||
"This package enables survival analysis in Python, including Kaplan
|
||
Meier, Nelson Aalen and regression.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-mapie
|
||
(package
|
||
(name "python-mapie")
|
||
(version "0.9.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "MAPIE" version))
|
||
(sha256
|
||
(base32
|
||
"00qhgfrix5aq7ng1xpvz2gk0d2d2maidbbd8ic9psq1vdqs6vp2a"))))
|
||
(build-system pyproject-build-system)
|
||
(native-inputs (list python-pandas python-pytest python-setuptools
|
||
python-wheel))
|
||
(propagated-inputs (list python-numpy python-scikit-learn))
|
||
(home-page "https://github.com/scikit-learn-contrib/MAPIE")
|
||
(synopsis "Module for estimating prediction intervals")
|
||
(description "MAPIE allows you to easily estimate prediction intervals
|
||
(or prediction sets) using your favourite scikit-learn-compatible model for
|
||
single-output regression or multi-class classification settings.
|
||
|
||
Prediction intervals output by MAPIE encompass both aleatoric and epistemic
|
||
uncertainties and are backed by strong theoretical guarantees thanks to
|
||
conformal prediction methods intervals.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-emcee
|
||
(package
|
||
(name "python-emcee")
|
||
(version "3.1.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "emcee" version))
|
||
(sha256
|
||
(base32 "0zb3ihja3hyj6zjbhkpxhyyppnv58q2jjg0yd1lwmydqdaplvbqi"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy))
|
||
(native-inputs (list python-coverage
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-setuptools
|
||
python-setuptools-scm
|
||
python-wheel))
|
||
(home-page "https://emcee.readthedocs.io/en/stable/")
|
||
(synopsis "Ensemble sampling toolkit for MCMC")
|
||
(description
|
||
"@code{emcee} is a Python implementation of the affine-invariant ensemble
|
||
sampler for Markov chain Monte Carlo (MCMC).")
|
||
(license license:expat)))
|
||
|
||
(define-public python-statsmodels
|
||
(package
|
||
(name "python-statsmodels")
|
||
(version "0.14.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "statsmodels" version))
|
||
(sha256
|
||
(base32 "1927ysv7m46m1x3wz05i0s3r5x0nasmidf2yy54djrp9i7bcfxb8"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(for-each delete-file (find-files "." "\\.c$")))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
;; 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))))))))
|
||
(propagated-inputs
|
||
(list python-numpy python-packaging python-pandas python-patsy
|
||
python-scipy))
|
||
(native-inputs
|
||
(list python-colorama
|
||
python-cython
|
||
python-flake8
|
||
python-isort
|
||
python-joblib
|
||
python-matplotlib
|
||
python-pytest
|
||
python-pytest-randomly
|
||
python-pytest-xdist
|
||
python-setuptools-scm
|
||
python-setuptools
|
||
python-wheel))
|
||
(home-page
|
||
(string-append "https://www.statsmodels.org/v" version "/"))
|
||
(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 python-openturns
|
||
(package
|
||
(name "python-openturns")
|
||
(version "1.24")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/openturns/openturns")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1k7vgmlg5dybrbn61nzlsyx2142byi9jv357zv7mzf6b4y133k7k"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(delete 'check)
|
||
;; This is a Python package which is fully managed by CMake. In
|
||
;; cmake-build-system the check phase runs before install, but the
|
||
;; Python modules required for testing are only installed in the
|
||
;; install phase. Move check to after the install phase.
|
||
(add-after 'install 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "ctest" "--exclude-regex"
|
||
;; XXX: Cpp tests fail in 'No such file or directory',
|
||
;; skip for now and only run the Python tests.
|
||
;; TODO: To pass the Python tests below, Ipopt must be
|
||
;; built with MUMPS support, but simply adding mumps
|
||
;; to the inputs doesn't work for it to be found,
|
||
;; possibly because MUMPS doesn't generate a .pc file.
|
||
(string-join
|
||
(list "^cpp"
|
||
"pyinstallcheck_Bonmin_std"
|
||
"pyinstallcheck_Bonmin_4dsoo"
|
||
"pyinstallcheck_Bonmin_MIT15"
|
||
"pyinstallcheck_Bonmin_swiler2014"
|
||
"pyinstallcheck_Ipopt_std"
|
||
"pyinstallcheck_example_plot_optimization_bonmin"
|
||
"pyinstallcheck_coupling_tools"
|
||
;; Subprocess aborted for these tests.
|
||
"pyinstallcheck_Study_std"
|
||
"pyinstallcheck_OptimizationAlgorithm_std"
|
||
"pyinstallcheck_docstring_missing")
|
||
"|"))))))))
|
||
(native-inputs
|
||
(list bison
|
||
dvisvgm
|
||
flex
|
||
python-numpydoc
|
||
python-sphinx
|
||
;; python-sphinx-gallery ;; Currently broken
|
||
swig))
|
||
(inputs
|
||
(list openblas ; the only required dependency
|
||
;; The dependecies below are all optional.
|
||
bonmin
|
||
boost
|
||
cbc ;; Maybe this should be propagated by Bonmin?
|
||
ceres
|
||
cminpack
|
||
dlib
|
||
hdf5
|
||
hmat
|
||
ipopt
|
||
libxml2
|
||
mpc
|
||
mpfr
|
||
nlopt
|
||
pagmo
|
||
primesieve
|
||
python-wrapper
|
||
spectra
|
||
tbb))
|
||
(propagated-inputs
|
||
(list python-chaospy
|
||
python-dill
|
||
python-matplotlib
|
||
python-numpy
|
||
python-pandas
|
||
python-scipy))
|
||
(home-page "https://openturns.github.io/www/")
|
||
(synopsis "Uncertainty treatment library")
|
||
(description
|
||
"OpenTURNS is a scientific C++ and Python library including an internal
|
||
data model and algorithms dedicated to the treatment of uncertainties. The
|
||
main goal of this library is giving to specific applications all the
|
||
functionalities needed to treat uncertainties in studies.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public python-resample
|
||
(package
|
||
(name "python-resample")
|
||
(version "1.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "resample" version))
|
||
(sha256
|
||
(base32 "0p8valf472y5nx45ddk7w5nsmph1725zb0k3a2zs6zyacqczrpb2"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-numpy python-scipy))
|
||
(native-inputs (list python-pytest python-setuptools python-wheel))
|
||
(home-page "https://github.com/scikit-hep/resample")
|
||
(synopsis "Resampling-based inference in Python")
|
||
(description "This package provides a resampling-based inference based on
|
||
data resampling and permutation.
|
||
|
||
Features:
|
||
|
||
@itemize
|
||
@item Bootstrap resampling: ordinary or balanced with optional stratification
|
||
@item Extended bootstrap resampling: also varies sample size
|
||
@item Parametric resampling: Gaussian, Poisson, gamma, etc.)
|
||
@item Jackknife estimates of bias and variance of any estimator
|
||
@item Compute bootstrap confidence intervals (percentile or BCa) for any
|
||
estimator
|
||
@item Permutation-based variants of traditional statistical tests (USP test of
|
||
independence and others)
|
||
@item Tools for working with empirical distributions (CDF, quantile, etc.)
|
||
@end itemize")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-rversions
|
||
(package
|
||
(name "r-rversions")
|
||
(version "2.1.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rversions" version))
|
||
(sha256
|
||
(base32
|
||
"0q5ip3rkhcxz7472fbqddrw3a2wm31b18w7ax0pi6wc27qiihn6y"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-curl r-xml2))
|
||
(native-inputs (list r-testthat))
|
||
(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-roxygen2
|
||
(package
|
||
(name "r-roxygen2")
|
||
(version "7.3.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "roxygen2" version))
|
||
(sha256
|
||
(base32
|
||
"0701v8dglv0mdsjs1mijpylpciiijb2schplavkf5drjj6gqg25p"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-brew
|
||
r-cli
|
||
r-commonmark
|
||
r-cpp11
|
||
r-desc
|
||
r-knitr
|
||
r-pkgload
|
||
r-purrr
|
||
r-r6
|
||
r-rlang
|
||
r-stringi
|
||
r-stringr
|
||
r-withr
|
||
r-xml2))
|
||
(native-inputs
|
||
(list r-knitr r-testthat))
|
||
(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-rstudioapi
|
||
(package
|
||
(name "r-rstudioapi")
|
||
(version "0.17.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rstudioapi" version))
|
||
(sha256
|
||
(base32
|
||
"029rbfdw9b57mcnx8yblgrwd79v47ky068mr3w9p61lnr21zjzk1"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
(list r-knitr r-testthat))
|
||
(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-readr
|
||
(package
|
||
(name "r-readr")
|
||
(version "2.1.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "readr" version))
|
||
(sha256
|
||
(base32
|
||
"02p1jjal73j39r49ba4jlvbx8bdqmm96nsdp47igyv54w1gmm9hg"))))
|
||
(build-system r-build-system)
|
||
(properties
|
||
'((updater-extra-native-inputs . ("r-stringi"))))
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-before 'check 'set-timezone
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; Two tests would fail without this.
|
||
(setenv "TZ" "UTC+1")
|
||
(setenv "TZDIR"
|
||
(search-input-directory inputs
|
||
"share/zoneinfo")))))))
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-clipr
|
||
r-cpp11
|
||
r-crayon
|
||
r-hms
|
||
r-lifecycle
|
||
r-r6
|
||
r-rlang
|
||
r-tibble
|
||
r-tzdb
|
||
r-vroom))
|
||
(native-inputs
|
||
(list r-knitr r-stringi r-testthat tzdata-for-tests))
|
||
(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-rcpparmadillo
|
||
(package
|
||
(name "r-rcpparmadillo")
|
||
(version "14.4.3-1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RcppArmadillo" version))
|
||
(sha256
|
||
(base32
|
||
"0f54x1nphwd5b0ipjqj3xql6zxgby8m3xri881zh2a9yih2mckqi"))))
|
||
(properties `((upstream-name . "RcppArmadillo")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp))
|
||
(native-inputs (list r-tinytest))
|
||
(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-rprojroot
|
||
(package
|
||
(name "r-rprojroot")
|
||
(version "2.0.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rprojroot" version))
|
||
(sha256
|
||
(base32
|
||
"16bf6ga5fgm83j3m67plw5i54az2vdbvw5m99ixaqkd24pxn7x5m"))))
|
||
(build-system r-build-system)
|
||
;; Tests require r-testthat, which uses this package.
|
||
(arguments (list #:tests? #false))
|
||
(native-inputs
|
||
(list r-knitr))
|
||
(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 "2.29")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rmarkdown" version))
|
||
(sha256
|
||
(base32 "0a0995dc0h4dvdkb0ivd23pnwzyrr9l59fg3ssm9r1kc662sqqk6"))))
|
||
(properties
|
||
`((upstream-name . "rmarkdown")
|
||
(updater-extra-propagated-inputs . ("pandoc"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list pandoc
|
||
r-bslib
|
||
r-evaluate
|
||
r-fontawesome
|
||
r-htmltools
|
||
r-jquerylib
|
||
r-jsonlite
|
||
r-knitr
|
||
r-tinytex
|
||
r-xfun
|
||
r-yaml))
|
||
(native-inputs
|
||
(list esbuild r-knitr r-testthat))
|
||
(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-rsqlite
|
||
(package
|
||
(name "r-rsqlite")
|
||
(version "2.3.11")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RSQLite" version))
|
||
(sha256
|
||
(base32
|
||
"0n87p111wqkwc0hck8z9rcq8194pglrc3cb2s8y0h41bfsdj2siz"))))
|
||
(properties
|
||
'((upstream-name . "RSQLite")
|
||
;; These are not strictly necessary for running tests and adding them
|
||
;; would cause dependency cycles.
|
||
(updater-ignored-native-inputs . ("r-dbitest" "r-ndbi"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
;; Needed for one failing test
|
||
(add-before 'check 'set-locale
|
||
(lambda _ (setenv "LC_ALL" "en_US.UTF-8"))))))
|
||
(propagated-inputs
|
||
(list r-bit64
|
||
r-blob
|
||
r-cpp11
|
||
r-dbi
|
||
r-memoise
|
||
r-pkgconfig
|
||
r-plogr
|
||
r-rlang))
|
||
(native-inputs
|
||
(list r-callr
|
||
r-hms
|
||
r-knitr
|
||
r-magrittr
|
||
r-testthat
|
||
r-withr))
|
||
(home-page "https://github.com/rstats-db/RSQLite")
|
||
(synopsis "SQLite interface for R")
|
||
(description
|
||
"This package embeds the SQLite database engine in R and provides an
|
||
interface compliant with the DBI package. The source for the SQLite
|
||
engine (version 3.8.8.2) is included.")
|
||
(license license:lgpl2.0+)))
|
||
|
||
(define-public r-rcurl
|
||
(package
|
||
(name "r-rcurl")
|
||
(version "1.98-1.17")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RCurl" version))
|
||
(sha256
|
||
(base32
|
||
"0c30pkjhpdihif2y6ymafwhyjqwxnzyj7w0jpwc9w5hnq6k78667"))))
|
||
(properties `((upstream-name . "RCurl")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
;; Tests require internet connection.
|
||
#:tests? #false
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'respect-CURL_CA_BUNDLE
|
||
(lambda _
|
||
(substitute* "R/options.S"
|
||
(("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
|
||
(string-append "\
|
||
certs = Sys.getenv(\"CURL_CA_BUNDLE\")
|
||
if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
|
||
" m))))))))
|
||
(inputs
|
||
(list curl libxml2))
|
||
(propagated-inputs
|
||
(list r-bitops))
|
||
(home-page "https://www.omegahat.net/RCurl")
|
||
(synopsis "General network client interface for R")
|
||
(description
|
||
"The package allows one to compose general HTTP requests and provides
|
||
convenient functions to fetch URIs, GET and POST forms, etc. and process the
|
||
results returned by the Web server. This provides a great deal of control
|
||
over the HTTP/FTP/... connection and the form of the request while providing a
|
||
higher-level interface than is available just using R socket connections.
|
||
Additionally, the underlying implementation is robust and extensive,
|
||
supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
|
||
ldap, and also supports cookies, redirects, authentication, etc.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public r-segmented
|
||
(package
|
||
(name "r-segmented")
|
||
(version "2.1-4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "segmented" version))
|
||
(sha256
|
||
(base32
|
||
"1sziji3cs46admkawvxjl4idc7krnijf9amfk2fzbk8c3b4fglmb"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-mass r-nlme))
|
||
(home-page "https://cran.r-project.org/web/packages/segmented")
|
||
(synopsis "Regression models with breakpoints estimation")
|
||
(description
|
||
"Given a regression model, segmented updates the model by adding one or
|
||
more segmented (i.e., piecewise-linear) relationships. Several variables with
|
||
multiple breakpoints are allowed.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-snow
|
||
(package
|
||
(name "r-snow")
|
||
(version "0.4-4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "snow" version))
|
||
(sha256
|
||
(base32
|
||
"1j8kvf3imxijsqkdjz4i9s7qggfxqrpas46y5wz6za92y937yn44"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/snow")
|
||
(synopsis "Support for simple parallel computing in R")
|
||
(description
|
||
"The snow package provides support for simple parallel computing on a
|
||
network of workstations using R. A master R process calls @code{makeCluster}
|
||
to start a cluster of worker processes; the master process then uses functions
|
||
such as @code{clusterCall} and @code{clusterApply} to execute R code on the
|
||
worker processes and collect and return the results on the master.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-sparsem
|
||
(package
|
||
(name "r-sparsem")
|
||
(version "1.84-2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "SparseM" version))
|
||
(sha256
|
||
(base32
|
||
"0rc6x466jhalb6baxxhffmmcpi03nndvvighp696rrvrhsxzv015"))))
|
||
(properties
|
||
`((upstream-name . "SparseM")))
|
||
(native-inputs
|
||
(list gfortran r-knitr))
|
||
(build-system r-build-system)
|
||
(home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
|
||
(synopsis "Sparse linear algebra")
|
||
(description
|
||
"This package provides some basic linear algebra functionality for sparse
|
||
matrices. It includes Cholesky decomposition and backsolving as well as
|
||
standard R subsetting and Kronecker products.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-registry
|
||
(package
|
||
(name "r-registry")
|
||
(version "0.5-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "registry" version))
|
||
(sha256
|
||
(base32
|
||
"1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/registry")
|
||
(synopsis "Infrastructure for R package registries")
|
||
(description
|
||
"This package provides a generic infrastructure for creating and using R
|
||
package registries.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rngtools
|
||
(package
|
||
(name "r-rngtools")
|
||
(version "1.5.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rngtools" version))
|
||
(sha256
|
||
(base32
|
||
"0kd7x214cqw7hzpmk1iqy1bn7j6x0ady0yz2hsdbclbq9k57d33z"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-digest))
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://renozao.github.io/rngtools")
|
||
(synopsis "Utility functions for working with random number generators")
|
||
(description
|
||
"This package contains a set of functions for working with Random Number
|
||
Generators (RNGs). In particular, it defines a generic S4 framework for
|
||
getting/setting the current RNG, or RNG data that are embedded into objects
|
||
for reproducibility. Notably, convenient default methods greatly facilitate
|
||
the way current RNG settings can be changed.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-rtsne
|
||
(package
|
||
(name "r-rtsne")
|
||
(version "0.17")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "Rtsne" version))
|
||
(sha256
|
||
(base32
|
||
"02srqmfkdj7v9gyhssaqdarg4ljn2ds77w25a5w0dm66sqa6ibis"))))
|
||
(properties
|
||
`((upstream-name . "Rtsne")
|
||
(updater-extra-native-inputs . ("r-irlba"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp))
|
||
(native-inputs (list r-irlba r-testthat))
|
||
(home-page "https://github.com/jkrijthe/Rtsne")
|
||
(synopsis "T-distributed stochastic neighbor embedding")
|
||
(description
|
||
"This package provides an R wrapper around the fast T-distributed
|
||
Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
|
||
;; The declared license for this package is BSD-3, but it also includes
|
||
;; code licensed under BSD-4.
|
||
(license (list license:bsd-3 license:bsd-4))))
|
||
|
||
(define-public r-synchronicity
|
||
(package
|
||
(name "r-synchronicity")
|
||
(version "1.3.10")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "synchronicity" version))
|
||
(sha256
|
||
(base32
|
||
"12svf4xzb9s3m1h2ddqgl6q2v57ifsj2p80j8cg2k0543a43pww2"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-bh r-bigmemory-sri r-rcpp r-uuid))
|
||
(home-page "http://www.bigmemory.org")
|
||
(synopsis "Boost mutex functionality in R")
|
||
(description "This package provides support for synchronization
|
||
via mutexes and may eventually support interprocess communication and
|
||
message passing.")
|
||
;; Users can choose either LGPLv3 or ASL2.0.
|
||
(license (list license:lgpl3 license:asl2.0))))
|
||
|
||
(define-public r-r-methodss3
|
||
(package
|
||
(name "r-r-methodss3")
|
||
(version "1.8.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.methodsS3" version))
|
||
(sha256
|
||
(base32
|
||
"0bkwj9c2cpgb0ibk9znh8qh4k1wzp3bkhaxyhf41xjflv9hmwbc2"))))
|
||
(properties `((upstream-name . "R.methodsS3")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/R.methodsS3")
|
||
(synopsis "S3 methods simplified")
|
||
(description
|
||
"This package provides methods that simplify the setup of S3 generic
|
||
functions and S3 methods. Major effort has been made in making definition of
|
||
methods as simple as possible with a minimum of maintenance for package
|
||
developers. For example, generic functions are created automatically, if
|
||
missing, and naming conflict are automatically solved, if possible. The
|
||
method @code{setMethodS3()} is a good start for those who in the future may
|
||
want to migrate to S4.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-oo
|
||
(package
|
||
(name "r-r-oo")
|
||
(version "1.27.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.oo" version))
|
||
(sha256
|
||
(base32
|
||
"1xbh8bcv6yiyy59pja78zvbcr7g28dmalw0j1swdh9zhq6f5kbsz"))))
|
||
(properties `((upstream-name . "R.oo")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-r-methodss3))
|
||
(home-page "https://github.com/HenrikBengtsson/R.oo")
|
||
(synopsis "R object-oriented programming with or without references")
|
||
(description
|
||
"This package provides methods and classes for object-oriented
|
||
programming in R with or without references. Large effort has been made on
|
||
making definition of methods as simple as possible with a minimum of
|
||
maintenance for package developers.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-utils
|
||
(package
|
||
(name "r-r-utils")
|
||
(version "2.13.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.utils" version))
|
||
(sha256
|
||
(base32
|
||
"09fg7f0z0zdxjndfwmcsyi2z54bp7xxcwdx0hpzji68j9v1l685b"))))
|
||
(properties `((upstream-name . "R.utils")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-references
|
||
(lambda _
|
||
(substitute* '("R/System.R"
|
||
"R/GString-class.R")
|
||
(("/usr/bin/env uname") (which "uname"))
|
||
(("/usr/bin/env whoami") (which "whoami"))))))))
|
||
(propagated-inputs
|
||
(list r-r-methodss3 r-r-oo))
|
||
(native-inputs
|
||
(list r-digest))
|
||
(home-page "https://github.com/HenrikBengtsson/R.utils")
|
||
(synopsis "Various programming utilities")
|
||
(description
|
||
"This package provides utility functions useful when programming and
|
||
developing R packages.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-cache
|
||
(package
|
||
(name "r-r-cache")
|
||
(version "0.17.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.cache" version))
|
||
(sha256
|
||
(base32
|
||
"089dh928a42q2ymf1cvan3rxrh4whal4zk6z5khmplgd28r9arg2"))))
|
||
(properties `((upstream-name . "R.cache")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'set-HOME
|
||
(lambda _ (setenv "HOME" "/tmp"))))))
|
||
(propagated-inputs
|
||
(list r-digest r-r-methodss3 r-r-oo r-r-utils))
|
||
(home-page "https://github.com/HenrikBengtsson/R.cache")
|
||
(synopsis "Light-weight caching of objects and results")
|
||
(description
|
||
"This package provides methods for caching or memoization of objects and
|
||
results. With this package, any R object can be cached in a key-value storage
|
||
where the key can be an arbitrary set of R objects. The cache memory is
|
||
persistent (on the file system).")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-r-rsp
|
||
(package
|
||
(name "r-r-rsp")
|
||
(version "0.46.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "R.rsp" version))
|
||
(sha256
|
||
(base32
|
||
"1frkgjc2mzvjnay8g5nky1bvxv60wvsypmmdj6mbsfjnzq7ni7qs"))))
|
||
(properties `((upstream-name . "R.rsp")))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
;; Vignettes require r-r-devices, which uses r-r-rsp.
|
||
#:test-types '(list "tests")
|
||
#:phases
|
||
'(modify-phases %standard-phases
|
||
(add-after 'unpack 'set-HOME
|
||
(lambda _ (setenv "HOME" "/tmp")))
|
||
(add-after 'unpack 'delete-broken-test
|
||
(lambda _
|
||
;; The multi,selfcontained.R tests fail because r-r-devices is
|
||
;; missing. It depends on r-r-rsp, so we can't add it.
|
||
(delete-file "tests/multi,selfcontained.R"))))))
|
||
(propagated-inputs
|
||
(list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
|
||
(home-page "https://github.com/HenrikBengtsson/R.rsp")
|
||
(synopsis "Dynamic generation of scientific reports")
|
||
(description
|
||
"The RSP markup language provides a powerful markup for controlling the
|
||
content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
|
||
documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
|
||
to many other literate programming languages, with RSP it is straightforward
|
||
to loop over mixtures of code and text sections, e.g. in month-by-month
|
||
summaries. RSP has also several preprocessing directives for incorporating
|
||
static and dynamic contents of external files (local or online) among other
|
||
things. RSP is ideal for self-contained scientific reports and R package
|
||
vignettes.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public r-tidyselect
|
||
(package
|
||
(name "r-tidyselect")
|
||
(version "1.2.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tidyselect" version))
|
||
(sha256
|
||
(base32
|
||
"0g4h8mfm5ima0izy4h0c65q478473xsj4hskh15dzg5z1fx9g7hn"))))
|
||
(properties
|
||
'((updater-extra-native-inputs . ("r-stringr"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli r-glue r-lifecycle r-rlang r-vctrs r-withr))
|
||
(native-inputs
|
||
(list r-knitr r-stringr r-testthat))
|
||
(home-page "https://cran.r-project.org/web/packages/tidyselect")
|
||
(synopsis "Select from a set of strings")
|
||
(description
|
||
"This package provides a backend for the selecting functions of the
|
||
tidyverse. It makes it easy to implement select-like functions in your own
|
||
packages in a way that is consistent with other tidyverse interfaces for
|
||
selection.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-tidyr
|
||
(package
|
||
(name "r-tidyr")
|
||
(version "1.3.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tidyr" version))
|
||
(sha256
|
||
(base32
|
||
"0pc3ad9k36lk3c5qbgx4blhs8aihqyysfxljyirgahsmrdhw4878"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-cli
|
||
r-cpp11
|
||
r-dplyr
|
||
r-glue
|
||
r-lifecycle
|
||
r-magrittr
|
||
r-purrr
|
||
r-rlang
|
||
r-stringr
|
||
r-tibble
|
||
r-tidyselect
|
||
r-vctrs))
|
||
(native-inputs
|
||
(list r-knitr r-testthat))
|
||
(home-page "https://github.com/hadley/tidyr")
|
||
(synopsis "Tidy data with `spread()` and `gather()` functions")
|
||
(description
|
||
"tidyr is a reframing of the reshape2 package designed to accompany the
|
||
tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
|
||
a solid pipeline for data analysis. It is designed specifically for tidying
|
||
data, not the general reshaping that reshape2 does, or the general aggregation
|
||
that reshape did. In particular, built-in methods only work for data frames,
|
||
and tidyr provides no margins or aggregation.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-rematch
|
||
(package
|
||
(name "r-rematch")
|
||
(version "2.0.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rematch" version))
|
||
(sha256
|
||
(base32
|
||
"09jwg3glp32q4ml4khhzi8j7bzg9zhqqdg1m6r8gibh756zzgnhm"))))
|
||
(build-system r-build-system)
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://github.com/MangoTheCat/rematch")
|
||
(synopsis "Match regular expressions with a nicer API")
|
||
(description
|
||
"This package provides a small wrapper on @code{regexpr} to extract the
|
||
matches and captured groups from the match of a regular expression to a
|
||
character vector.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-spams
|
||
(package
|
||
(name "r-spams")
|
||
(version "2.6.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.inria.fr/thoth/spams-devel")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0qvj87fw4sm54c7dvhxjgmgvnyyrrz9fk6dqp3ak0gwgb42gqh60"))))
|
||
(build-system r-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(add-after 'patch-generated-file-shebangs 'patch-paths
|
||
(lambda _
|
||
(substitute* (cons* "swig/setRelease"
|
||
"swig/R/docmatlab2R"
|
||
"swig/R/mkdist"
|
||
(find-files "." "(^mk|\\.sh$)"))
|
||
(("/bin/pwd") "pwd")
|
||
(("/bin/rm") "rm"))))
|
||
(add-after 'patch-paths 'mkdist
|
||
(lambda _
|
||
(chdir "swig/R")
|
||
(setenv "TEXINPUTS" (string-append (getcwd) "/../../doc:"))
|
||
(substitute* "mkdist"
|
||
(("^SWIG=.*")
|
||
(string-append "SWIG=" (which "swig")))
|
||
(("^../mkdoc") "")) ;requires texlive-aeguill
|
||
(invoke "./mkdist")
|
||
(chdir "dist/spams-R/spams")))
|
||
;; Don't tune for the building machine.
|
||
(add-after 'mkdist 'no-mtune
|
||
(lambda _
|
||
(substitute* "src/Makevars"
|
||
(("-mtune=native") ""))))
|
||
(add-after 'no-mtune 'use-c++11
|
||
(lambda _
|
||
(substitute* "src/Makevars"
|
||
(("-DUSE_BLAS_LIB" m)
|
||
(string-append m " -std=c++11"))))))))
|
||
(native-inputs
|
||
(list hevea
|
||
perl
|
||
swig
|
||
(texlive-local-tree
|
||
(list texlive-aeguill texlive-jknapltx))))
|
||
(propagated-inputs
|
||
(list r-lattice
|
||
r-matrix))
|
||
(home-page "https://gitlab.inria.fr/thoth/spams-devel/")
|
||
(synopsis "Toolbox for solving sparse estimation problems")
|
||
(description "SPAMS (SPArse Modeling Software) is an optimization toolbox
|
||
for solving various sparse estimation problems. It includes tools for the
|
||
following problems:
|
||
|
||
@enumerate
|
||
@item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
|
||
component analysis} (PCA), ...)
|
||
@item Solving sparse decomposition problems with LARS, coordinate descent,
|
||
OMP, SOMP, proximal methods
|
||
@item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
|
||
group lasso, tree-structured regularization, structured sparsity with
|
||
overlapping groups,...).
|
||
@end enumerate\n")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-runit
|
||
(package
|
||
(name "r-runit")
|
||
(version "0.4.33")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RUnit" version))
|
||
(sha256
|
||
(base32
|
||
"0pybwvd57vf71vvlxdrynw5n6s5gnbqnwvq0qpd395ggqypwb95j"))))
|
||
(properties `((upstream-name . "RUnit")))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/RUnit")
|
||
(synopsis "R unit test framework")
|
||
(description
|
||
"This package provides R functions implementing a standard unit testing
|
||
framework, with additional code inspection and report generation tools.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-sfsmisc
|
||
(package
|
||
(name "r-sfsmisc")
|
||
(version "1.1-20")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sfsmisc" version))
|
||
(sha256
|
||
(base32
|
||
"0svpqdcwq62y5d2ywcdrqn1lpq1jvfqx9mxl0dxxa08whahhyqs4"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/sfsmisc")
|
||
(synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
|
||
(description
|
||
"This package provides useful utilities from Seminar fuer Statistik ETH
|
||
Zurich, including many that are related to graphics.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rocr
|
||
(package
|
||
(name "r-rocr")
|
||
(version "1.0-11")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ROCR" version))
|
||
(sha256
|
||
(base32
|
||
"0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
|
||
(properties `((upstream-name . "ROCR")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-gplots))
|
||
(native-inputs
|
||
(list r-knitr r-testthat))
|
||
(home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
|
||
(synopsis "Visualizing the performance of scoring classifiers")
|
||
(description
|
||
"ROCR is a flexible tool for creating cutoff-parameterized 2D performance
|
||
curves by freely combining two from over 25 performance measures (new
|
||
performance measures can be added using a standard interface). Curves from
|
||
different cross-validation or bootstrapping runs can be averaged by different
|
||
methods, and standard deviations, standard errors or box plots can be used to
|
||
visualize the variability across the runs. The parameterization can be
|
||
visualized by printing cutoff values at the corresponding curve positions, or
|
||
by coloring the curve according to cutoff. All components of a performance
|
||
plot can be quickly adjusted using a flexible parameter dispatching
|
||
mechanism.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-sourcetools
|
||
(package
|
||
(name "r-sourcetools")
|
||
(version "0.1.7-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sourcetools" version))
|
||
(sha256
|
||
(base32
|
||
"1l9i9ram12pjks8h2gzmj119wf4ixwyhljsfv289dn8dgbdjp0cn"))))
|
||
(build-system r-build-system)
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://cran.r-project.org/web/packages/sourcetools")
|
||
(synopsis "Tools for reading, tokenizing and parsing R code")
|
||
(description
|
||
"The sourcetools package provides both an R and C++ interface for the
|
||
tokenization of R code, and helpers for interacting with the tokenized
|
||
representation of R code.")
|
||
(license license:expat)))
|
||
|
||
(define-public r-statmod
|
||
(package
|
||
(name "r-statmod")
|
||
(version "1.5.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "statmod" version))
|
||
(sha256
|
||
(base32
|
||
"1jbf07h0mnncn2qp4wcw5bnbvsw3lizpd3cg0cpb8mcxn3wkw76n"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/statmod")
|
||
(native-inputs
|
||
(list gfortran))
|
||
(synopsis "Statistical modeling")
|
||
(description
|
||
"This package provides a collection of algorithms and functions to aid
|
||
statistical modeling. It includes growth curve comparisons, limiting dilution
|
||
analysis (aka ELDA), mixed linear models, heteroscedastic regression,
|
||
inverse-Gaussian probability calculations, Gauss quadrature and a secure
|
||
convergence algorithm for nonlinear models. It also includes advanced
|
||
generalized linear model functions that implement secure convergence,
|
||
dispersion modeling and Tweedie power-law families.")
|
||
;; Statmod is distributed under either license
|
||
(license (list license:gpl2 license:gpl3))))
|
||
|
||
(define-public r-rann
|
||
(package
|
||
(name "r-rann")
|
||
(version "2.6.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RANN" version))
|
||
(sha256
|
||
(base32
|
||
"0wlpkf6vilw871ac2bxy5nr790cfs6sax5k8m0fhasxbansxbxvf"))))
|
||
(properties
|
||
`((upstream-name . "RANN")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://github.com/jefferis/RANN")
|
||
(synopsis "Fast nearest neighbour search")
|
||
(description
|
||
"This package finds the k nearest neighbours for every point in a given
|
||
dataset in O(N log N) time using Arya and Mount's ANN library. Provides
|
||
approximate, exact searches, fixed radius searches, bd and kb trees.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-randomforest
|
||
(package
|
||
(name "r-randomforest")
|
||
(version "4.7-1.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "randomForest" version))
|
||
(sha256
|
||
(base32
|
||
"04aan0wzkfdl2nh4z8fls7qhgz80xl7px7c4282dbfj8nqkk5lxa"))))
|
||
(properties `((upstream-name . "randomForest")))
|
||
(build-system r-build-system)
|
||
(home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
|
||
(native-inputs
|
||
(list gfortran))
|
||
(synopsis "Breiman and Cutler's random forests for classification and regression")
|
||
(description
|
||
"This package provides the Breiman and Cutler's random forests algorithm, based on a
|
||
forest of trees using random inputs, for classification and regression.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-robustbase
|
||
(package
|
||
(name "r-robustbase")
|
||
(version "0.99-4-1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "robustbase" version))
|
||
(sha256
|
||
(base32
|
||
"14gz260amdy60shm3bfsw214471by27yac6r66fs6rjgc7kxw7j8"))))
|
||
(build-system r-build-system)
|
||
;; FIXME: test failure
|
||
;; Error in if (grepl("^Fedora", osVersion) && !is32) identical(i.a4Out, :
|
||
;; missing value where TRUE/FALSE needed
|
||
(arguments (list #:tests? #false))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(propagated-inputs
|
||
(list r-deoptimr))
|
||
(home-page "https://robustbase.r-forge.r-project.org/")
|
||
(synopsis "Basic robust statistics")
|
||
(description
|
||
"This package analyzes data with robust methods such as
|
||
regression methodology including model selections and multivariate statistics.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rrcov
|
||
(package
|
||
(name "r-rrcov")
|
||
(version "1.7-7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "rrcov" version))
|
||
(sha256
|
||
(base32
|
||
"1xbhrpmb3bn4h83kr214jmhr0rx5mgjrf396iz70mnq3g425lbqb"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-lattice r-mvtnorm r-pcapp r-robustbase))
|
||
(native-inputs
|
||
(list gfortran r-mass))
|
||
(home-page "https://cran.r-project.org/web/packages/rrcov")
|
||
(synopsis "Scalable robust estimators with high breakdown Point")
|
||
(description
|
||
"This package provides an implementation of robust location and scatter
|
||
estimation and robust multivariate analysis with high breakdown point.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-robust
|
||
(package
|
||
(name "r-robust")
|
||
(version "0.7-5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "robust" version))
|
||
(sha256
|
||
(base32
|
||
"1k0s5i9r0lyz3qsw76dd514qclggqj9k2axmgj86df81j6f2mh53"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-fit-models r-lattice r-mass r-robustbase r-rrcov))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(home-page "https://cran.r-project.org/web/packages/robust")
|
||
(synopsis "Port of the S+ \"Robust Library\"")
|
||
(description
|
||
"This package is a port of the S+ \"Robust Library\". It provides
|
||
methods for robust statistics, notably for robust regression and robust
|
||
multivariate analysis.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-trimcluster
|
||
(package
|
||
(name "r-trimcluster")
|
||
(version "0.1-5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "trimcluster" version))
|
||
(sha256
|
||
(base32
|
||
"12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/trimcluster")
|
||
(synopsis "Cluster analysis with trimming")
|
||
(description
|
||
"The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
|
||
Matran (1997). This optimizes the k-means criterion under trimming a portion
|
||
of the points.")
|
||
;; Any GPL version
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-rcppeigen
|
||
(package
|
||
(name "r-rcppeigen")
|
||
(version "0.3.4.0.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RcppEigen" version))
|
||
(sha256
|
||
(base32
|
||
"1fs2wmsq2s6nzhkrx59li4x1zvcjhk9mhmc2pdz8pm4z2ai7pbgc"))))
|
||
(properties `((upstream-name . "RcppEigen")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-rcpp))
|
||
(home-page "http://eigen.tuxfamily.org")
|
||
(synopsis "Rcpp integration for the Eigen templated linear algebra library")
|
||
(description
|
||
"This package provides an integration of Eigen in R using a C++ template
|
||
library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
|
||
It supports dense and sparse matrices on integer, floating point and complex numbers,
|
||
decompositions of such matrices, and solutions of linear systems.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-rcppprogress
|
||
(package
|
||
(name "r-rcppprogress")
|
||
(version "0.4.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RcppProgress" version))
|
||
(sha256
|
||
(base32
|
||
"0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi"))))
|
||
(properties `((upstream-name . "RcppProgress")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://github.com/kforner/rcpp_progress")
|
||
(synopsis "Interruptible progress bar for C++ in R packages")
|
||
(description
|
||
"This package displays a progress bar in the R console for long running
|
||
computations taking place in C++ code, and support for interrupting those computations
|
||
even in multithreaded code, typically using OpenMP.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-tmvnsim
|
||
(package
|
||
(name "r-tmvnsim")
|
||
(version "1.0-2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tmvnsim" version))
|
||
(sha256
|
||
(base32
|
||
"03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
|
||
(properties `((upstream-name . "tmvnsim")))
|
||
(build-system r-build-system)
|
||
(native-inputs (list gfortran))
|
||
(home-page "https://www.r-project.org")
|
||
(synopsis "Truncated multivariate normal simulation")
|
||
(description
|
||
"This package implements importance sampling from the truncated
|
||
multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
|
||
simulator. Unlike Gibbs sampling which can get stuck in one truncation
|
||
sub-region depending on initial values, this package allows truncation based
|
||
on disjoint regions that are created by truncation of absolute values. The
|
||
GHK algorithm uses simple Cholesky transformation followed by recursive
|
||
simulation of univariate truncated normals hence there are also no convergence
|
||
issues. Importance sample is returned along with sampling weights, based on
|
||
which, one can calculate integrals over truncated regions for multivariate
|
||
normals.")
|
||
(license license:gpl2)))
|
||
|
||
(define-public r-sn
|
||
(package
|
||
(name "r-sn")
|
||
(version "2.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "sn" version))
|
||
(sha256
|
||
(base32
|
||
"1g92vwbg0kqnqpsgianid2r91334p5shi39hr26v2z6wj5nvbxpr"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-mnormt r-numderiv r-quantreg))
|
||
(native-inputs (list r-r-rsp))
|
||
(home-page "http://azzalini.stat.unipd.it/SN")
|
||
(synopsis "The skew-normal and skew-t distributions")
|
||
(description
|
||
"This package provides functionalities to build and manipulate
|
||
probability distributions of the skew-normal family and some related
|
||
ones, notably the skew-t family, and provides related statistical
|
||
methods for data fitting and diagnostics, in the univariate and the
|
||
multivariate case.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-tclust
|
||
(package
|
||
(name "r-tclust")
|
||
(version "2.1-0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tclust" version))
|
||
(sha256
|
||
(base32
|
||
"1vx9nbm20hclf54js2ip09h6fhqhkn0gq90a08hhn5b1n25gvvxk"))))
|
||
(properties
|
||
'((updater-extra-native-inputs . ("r-cluster" "r-mclust" "r-sn"))))
|
||
(build-system r-build-system)
|
||
;; These are all suggested packages, not build dependencies.
|
||
(propagated-inputs
|
||
(list r-doparallel
|
||
r-foreach
|
||
r-mass
|
||
r-rcpp
|
||
r-rcpparmadillo
|
||
r-rlang))
|
||
(native-inputs (list r-cluster r-mclust r-sn))
|
||
(home-page "https://cran.r-project.org/web/packages/tclust")
|
||
(synopsis "Robust trimmed clustering")
|
||
(description
|
||
"This package implements different robust clustering
|
||
algorithms (@code{tclust}) based on trimming and including some graphical
|
||
diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-ranger
|
||
(package
|
||
(name "r-ranger")
|
||
(version "0.17.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "ranger" version))
|
||
(sha256
|
||
(base32
|
||
"0dlxl1cgxd778gzvnnvnxlwm37q825fw48g2kwyzjyliwi6dz36l"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-matrix r-rcpp r-rcppeigen))
|
||
(native-inputs (list r-survival r-testthat))
|
||
(home-page "https://github.com/imbs-hl/ranger")
|
||
(synopsis "Fast implementation of random forests")
|
||
(description
|
||
"This package provides a fast implementation of Random Forests,
|
||
particularly suited for high dimensional data. Ensembles of classification,
|
||
regression, survival and probability prediction trees are supported. Data from
|
||
genome-wide association studies can be analyzed efficiently.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public r-tsne
|
||
(package
|
||
(name "r-tsne")
|
||
(version "0.1-3.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "tsne" version))
|
||
(sha256
|
||
(base32
|
||
"126q6ha25wx9mdsfngzkyp8j2fj81ri1knjdq1iyvwx3q1dwdaql"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://github.com/jdonaldson/rtsne/")
|
||
(synopsis "t-Distributed Stochastic Neighbor Embedding for R")
|
||
(description
|
||
"This package provides a pure R implementation of the t-SNE algorithm.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-tgconfig
|
||
(let ((commit "15cf199436ae0b2ac0006b2ca7f0aeeb5c9d4445")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-tgconfig")
|
||
(version (git-version "0.1.2" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tanaylab/tgconfig")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "159m8hhbk9ip2fdy6zsa96v0173q1awcrzdz2rr2796awfaxjgx1"))))
|
||
(properties `((upstream-name . "tgconfig")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-yaml))
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://github.com/tanaylab/tgconfig")
|
||
(synopsis "Infrastructure for managing package parameters")
|
||
(description
|
||
"This is a package to provide infrastructure for managing package parameters.
|
||
Parameters are easy to get in relevant functions within a package,
|
||
and rrror is thrown if a parameter is missing. Developers are able
|
||
to register parameters and set their default value in a config file
|
||
that is part of the package in YAML format, and users are able to
|
||
override parameters using their own YAML. Users get an exception
|
||
when trying to override a parameter that was not registered, and
|
||
can load multiple parameters to the current environment.")
|
||
(license license:gpl3+))))
|
||
|
||
(define-public r-tgutil
|
||
(let ((commit "db4ff8b98082f8e4dbdeacb452641d215fd3c7ff")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-tgutil")
|
||
(version (git-version "0.1.15" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tanaylab/tgutil")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "00rsqs7f896piywh84jr8fkphbbx4jb7radf6znhhj6fip63yn91"))))
|
||
(properties `((upstream-name . "tgutil")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-broom
|
||
r-cowplot
|
||
r-data-table
|
||
r-dplyr
|
||
r-ggplot2
|
||
r-glue
|
||
r-magrittr
|
||
r-matrix
|
||
r-matrixstats
|
||
r-qlcmatrix
|
||
r-readr
|
||
r-rlang
|
||
r-scales
|
||
r-tibble
|
||
r-tidyr))
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://github.com/tanaylab/tgutil")
|
||
(synopsis "Simple utility functions for Tanay lab code")
|
||
(description
|
||
"This package provides simple utility functions that are shared
|
||
across several packages maintained by the Tanay lab.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-catterplots
|
||
(let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
|
||
(revision "3"))
|
||
(package
|
||
(name "r-catterplots")
|
||
(version (git-version "0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Gibbsdavidl/CatterPlots")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-png))
|
||
(home-page "https://github.com/Gibbsdavidl/CatterPlots")
|
||
(synopsis "Scatter plots with cat shaped points")
|
||
(description "Did you ever wish you could make scatter plots with cat
|
||
shaped points? Now you can!")
|
||
(license license:asl2.0))))
|
||
|
||
(define-public r-nnlm
|
||
(let ((commit "4574bca9456fe2285b668b4c22a908cffbad10a0")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-nnlm")
|
||
(version (git-version "0.4.4" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/linxihui/NNLM")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1qzvav4ch0j1k7jcqzk9cvl8dx79fapmvdzmzzyl8smscybhfgba"))))
|
||
(properties `((upstream-name . "NNLM")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppprogress))
|
||
(native-inputs (list r-knitr r-testthat))
|
||
(home-page "https://github.com/linxihui/NNLM")
|
||
(synopsis "Fast and versatile non-negative matrix factorization")
|
||
(description
|
||
"This is a package for @dfn{Non-Negative Linear Models} (NNLM). It
|
||
implements fast sequential coordinate descent algorithms for non-negative
|
||
linear regression and @dfn{non-negative matrix factorization} (NMF). It
|
||
supports mean square error and Kullback-Leibler divergence loss. Many other
|
||
features are also implemented, including missing value imputation, domain
|
||
knowledge integration, designable W and H matrices and multiple forms of
|
||
regularizations.")
|
||
(license license:bsd-2))))
|
||
|
||
(define-public r-swne
|
||
(let ((commit "05fc3ee4e09b2c34d99c69d3b97cece4c1c34143")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-swne")
|
||
(version (git-version "0.6.20" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/yanwu2014/swne")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0crlpg9kclbv4v8250p3086a3lk6f2hcq79psqkdylc1qnrx3kfx"))))
|
||
(properties `((upstream-name . "swne")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-fnn
|
||
r-ggplot2
|
||
r-ggrepel
|
||
r-hash
|
||
r-ica
|
||
r-igraph
|
||
r-irlba
|
||
r-jsonlite
|
||
r-liger
|
||
r-mass
|
||
r-matrix
|
||
r-mgcv
|
||
r-nnlm ;not listed but required at install time
|
||
r-plyr
|
||
r-proxy
|
||
r-rcolorbrewer
|
||
r-rcpp
|
||
r-rcpparmadillo
|
||
r-rcppeigen
|
||
r-reshape
|
||
r-reshape2
|
||
r-snow
|
||
r-umap
|
||
r-usedist))
|
||
(home-page "https://github.com/yanwu2014/swne")
|
||
(synopsis "Visualize high dimensional datasets")
|
||
(description
|
||
"@dfn{Similarity Weighted Nonnegative Embedding} (SWNE) is a method for
|
||
visualizing high dimensional datasets. SWNE uses Nonnegative Matrix
|
||
Factorization to decompose datasets into latent factors, projects those
|
||
factors onto 2 dimensions, and embeds samples and key features in 2 dimensions
|
||
relative to the factors. SWNE can capture both the local and global dataset
|
||
structure, and allows relevant features to be embedded directly onto the
|
||
visualization, facilitating interpretation of the data.")
|
||
(license license:gpl2))))
|
||
|
||
(define-public r-languageserver
|
||
(let ((commit "004da9388f9b19990f031c8dc9b527fb406378ba")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-languageserver")
|
||
(version (git-version "0.3.12" revision commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/REditorSupport/languageserver")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "05f22bjpc87fngzq4jsk2q2yb2i3ha03b377r0wx15d0b8xaa1ix"))))
|
||
(properties `((upstream-name . "languageserver")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-callr
|
||
r-collections
|
||
r-fs
|
||
r-jsonlite
|
||
r-lintr
|
||
r-r6
|
||
r-roxygen2
|
||
r-stringi
|
||
r-styler
|
||
r-xml2
|
||
r-xmlparsedata))
|
||
(native-inputs (list r-mockery r-testthat))
|
||
(home-page "https://github.com/REditorSupport/languageserver")
|
||
(synopsis "Language Server for R")
|
||
(description
|
||
"This package provides an implementation of the Language Server
|
||
Protocol for R. The
|
||
@url{https://microsoft.github.io/language-server-protocol/,Language Server
|
||
protocol} is used by an editor client to integrate features like auto
|
||
completion.")
|
||
(license license:expat))))
|
||
|
||
(define-public python-rpy2
|
||
(package
|
||
(name "python-rpy2")
|
||
(version "3.5.17")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "rpy2" version))
|
||
(sha256
|
||
(base32
|
||
"10nmydlbmi0vyim7sx71isx3z2mnnfjmhf3248cicy9x1z1hizyv"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs
|
||
(list python-cffi
|
||
python-six
|
||
python-jinja2
|
||
python-numpy
|
||
python-pandas
|
||
python-pytz
|
||
python-ipython
|
||
python-tzlocal))
|
||
(inputs
|
||
(list icu4c
|
||
libdeflate
|
||
pcre
|
||
python-numpy
|
||
readline
|
||
r-minimal
|
||
r-survival
|
||
r-ggplot2
|
||
r-rsqlite
|
||
r-dplyr
|
||
r-dbplyr
|
||
zlib))
|
||
(native-inputs
|
||
(list python-coverage
|
||
python-ipython
|
||
python-numpy
|
||
python-pandas
|
||
python-pytest
|
||
python-pytest-cov
|
||
python-setuptools
|
||
python-wheel))
|
||
(home-page "https://rpy2.github.io")
|
||
(synopsis "Python interface to the R language")
|
||
(description "rpy2 is a redesign and rewrite of rpy. It is providing a
|
||
low-level interface to R from Python, a proposed high-level interface,
|
||
including wrappers to graphical libraries, as well as R-like structures and
|
||
functions.")
|
||
;; Any of these licenses can be picked for the R interface. The whole
|
||
;; project is released under GPLv2+ according to the license declaration
|
||
;; in "setup.py".
|
||
(license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
|
||
|
||
(define-public python-rchitect
|
||
(package
|
||
(name "python-rchitect")
|
||
(version "0.4.7")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/randy3k/rchitect")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1ijbb0v77ir7j64r4r4kznv03wyc57rcqa9jnsc46476il79dcrk"))))
|
||
(build-system pyproject-build-system)
|
||
(propagated-inputs (list python-cffi python-packaging python-six))
|
||
(native-inputs (list python-pytest
|
||
python-pytest-cov
|
||
python-pytest-mock
|
||
python-setuptools
|
||
python-wheel
|
||
;; R dependencies needed only for testing.
|
||
r-minimal
|
||
r-reticulate))
|
||
(home-page "https://github.com/randy3k/rchitect")
|
||
(synopsis "Mapping R API to Python")
|
||
(description
|
||
"rchitect provides access to R functionality from Python. Its
|
||
main use is as the driver for radian, the R console.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-radian
|
||
(package
|
||
(name "python-radian")
|
||
(version "0.6.13")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/randy3k/radian")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0nnwgvifhsxdac7rr9d2zspc97xx0vyzxn1v9g4bnm9061rragc3"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:phases #~(modify-phases %standard-phases
|
||
(add-before 'check 'set-home
|
||
(lambda _
|
||
;; During tests radian wants to write history files to
|
||
;; $HOME which causes tests to fail when that does not
|
||
;; exist. Test fails then look like
|
||
;; "Exception: value is " with the value being empty.
|
||
(setenv "HOME" "/tmp"))))))
|
||
(propagated-inputs (list python-prompt-toolkit python-pygments
|
||
python-rchitect))
|
||
(native-inputs (list python-coverage
|
||
python-pexpect
|
||
python-ptyprocess
|
||
python-pyte
|
||
python-pytest
|
||
python-setuptools
|
||
python-wheel
|
||
;; Needed afaict only for
|
||
;; `tests/test_reticulate.py::test_completion`.
|
||
python-jedi
|
||
;; R dependencies needed only for testing.
|
||
r-askpass
|
||
r-minimal
|
||
r-reticulate
|
||
;; Needed for sh tests.
|
||
git-minimal))
|
||
(home-page "https://github.com/randy3k/radian")
|
||
(synopsis "R console")
|
||
(description
|
||
"Radian is an alternative console for the R program with multiline
|
||
editing and rich syntax highlight. One would consider Radian as a IPython
|
||
clone for R, though its design is more aligned to Julia.")
|
||
(license license:expat)))
|
||
|
||
(define-public java-jdistlib
|
||
(package
|
||
(name "java-jdistlib")
|
||
(version "0.4.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
|
||
version "-src.jar"))
|
||
(sha256
|
||
(base32
|
||
"1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
|
||
(build-system ant-build-system)
|
||
(arguments
|
||
`(#:jar-name "jdistlib.jar"
|
||
#:jdk ,icedtea-8
|
||
#:tests? #f ; no dedicated test directory
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'fix-broken-encoding
|
||
(lambda _
|
||
(with-fluids ((%default-port-encoding "ISO-8859-1"))
|
||
(substitute* "src/jdistlib/Beta.java"
|
||
(("Scheff.+-Tukey") "Scheffe-Tukey")))
|
||
#t)))))
|
||
(propagated-inputs
|
||
(list java-jtransforms))
|
||
(native-inputs
|
||
(list java-junit))
|
||
(home-page "https://jdistlib.sourceforge.net/")
|
||
(synopsis "Java library of statistical distributions")
|
||
(description "JDistlib is the Java Statistical Distribution Library, a
|
||
Java package that provides routines for various statistical distributions.")
|
||
;; The files that were translated from R code are under GPLv2+; some files
|
||
;; are under the GPLv3, which is a mistake. The author confirmed in an
|
||
;; email that this whole project should be under GPLv2+.
|
||
(license license:gpl2+)))
|
||
|
||
(define-public emacs-ess
|
||
(package
|
||
(name "emacs-ess")
|
||
(version "25.01.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/emacs-ess/ESS")
|
||
(commit (string-append "v" version))))
|
||
(sha256
|
||
(base32 "0v56b47qidpyxvyk0q487qxhj9si0jkm852frl832iraks02l5h5"))
|
||
(file-name (git-file-name name version))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
#~(begin
|
||
;; Stop ESS from trying to bundle an external julia-mode.el.
|
||
(substitute* "lisp/Makefile"
|
||
((" \\$\\(JULIAS)") "")
|
||
(("\ttest.*julia-mode.*\\.el") ""))
|
||
;; Only build docs in info format.
|
||
(substitute* "doc/Makefile"
|
||
(("all : info text")
|
||
"all : info")
|
||
(("install: install-info install-other-docs")
|
||
"install: install-info"))
|
||
;; Stop install-info from trying to update the info directory.
|
||
(substitute* "doc/Makefile"
|
||
((".*/dir.*") ""))
|
||
;; Avoid generating ess-autoloads.el twice.
|
||
(substitute* "Makefile"
|
||
(("all: lisp doc etc autoloads")
|
||
"all: lisp doc etc"))
|
||
;; Install to correct directories.
|
||
(substitute* "Makefile"
|
||
(("mkdir -p \\$\\(ESSDESTDIR)")
|
||
"$(MAKE) -C lisp install; $(MAKE) -C doc install")
|
||
(("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/")
|
||
"$(MAKE) -C etc install"))))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(let ((base-directory (string-append "/share/emacs/site-lisp/"
|
||
"ess-" version)))
|
||
(list
|
||
#:modules '((guix build gnu-build-system)
|
||
(guix build utils)
|
||
(guix build emacs-utils))
|
||
#:imported-modules `(,@%default-gnu-imported-modules
|
||
(guix build emacs-build-system)
|
||
(guix build emacs-utils))
|
||
#:make-flags
|
||
#~(list (string-append "PREFIX=" #$output)
|
||
(string-append "ETCDIR=" #$output #$base-directory "/etc")
|
||
(string-append "LISPDIR=" #$output #$base-directory)
|
||
(string-append "INFODIR=" #$output "/share/info"))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(add-before 'check 'skip-failing-tests
|
||
(lambda _
|
||
(let-syntax
|
||
((disable-tests
|
||
(syntax-rules ()
|
||
((_ ())
|
||
(syntax-error "test names list must not be empty"))
|
||
((_ (test-name ...))
|
||
(substitute* (find-files "test" "\\.el$")
|
||
(((string-append "^\\(ert-deftest " test-name ".*")
|
||
all)
|
||
(string-append all "(skip-unless nil)\n"))
|
||
...))))
|
||
(disable-etests ;different test syntax
|
||
(syntax-rules ()
|
||
((_ ())
|
||
(syntax-error "test names list must not be empty"))
|
||
((_ (test-name ...))
|
||
(for-each
|
||
(lambda (file)
|
||
(emacs-batch-edit-file file
|
||
'(progn
|
||
(dolist (test (list test-name ...))
|
||
(goto-char (point-min))
|
||
(let ((s (format "etest-deftest %s "
|
||
test)))
|
||
(when (search-forward s nil t)
|
||
(beginning-of-line)
|
||
(kill-sexp))))
|
||
(basic-save-buffer))))
|
||
(find-files "test" "\\.el$"))))))
|
||
(disable-tests ("ess--derive-connection-path"
|
||
"ess-eval-line-test"
|
||
"ess-eval-region-test"
|
||
"ess-mock-remote-process"
|
||
"ess-r-load-ESSR-github-fetch-no"
|
||
"ess-r-load-ESSR-github-fetch-yes"
|
||
"ess-set-working-directory-test"
|
||
"ess-test-r-startup-directory"))
|
||
(disable-etests ("ess-r-eval-ns-env-roxy-tracebug-test"
|
||
"ess-r-eval-sink-freeze-test"
|
||
;; Looks like an off-by-one error.
|
||
"ess--command-browser-unscoped-essr")))))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests? (invoke "make" "test"))))))))
|
||
(native-inputs (list perl r-roxygen2 texinfo))
|
||
(inputs (list emacs-minimal r-minimal))
|
||
(propagated-inputs (list emacs-julia-mode))
|
||
(home-page "https://ess.r-project.org/")
|
||
(synopsis "Emacs mode for statistical analysis programs")
|
||
(description
|
||
"Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It
|
||
is designed to support editing of scripts and interaction with various
|
||
statistical analysis programs such as R, Julia, and JAGS.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public emacs-poly-r
|
||
(package
|
||
(name "emacs-poly-r")
|
||
(version "0.2.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/polymode/poly-R")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0a4wx73jkngw5nbq1fa4jfhba6bsmyn6vnsf887x3xhb5v3ykhsg"))))
|
||
(build-system emacs-build-system)
|
||
(propagated-inputs
|
||
(list emacs-ess emacs-poly-noweb emacs-polymode-markdown
|
||
emacs-polymode))
|
||
(properties '((upstream-name . "poly-R")))
|
||
(home-page "https://github.com/polymode/poly-markdown")
|
||
(synopsis "Polymodes for the R language")
|
||
(description
|
||
"This package provides a number of polymodes for working with mixed R
|
||
files, including Rmarkdown files.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public readstat
|
||
(package
|
||
(name "readstat")
|
||
(version "1.1.9")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/WizardMac/ReadStat")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0aqalr86d7h9sp9zjkydw3ap4s54qgq2ml6p8gd0gnn1jf0ljm72"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list autoconf automake gnu-gettext libtool))
|
||
(inputs
|
||
(list zlib))
|
||
(home-page "https://github.com/WizardMac/ReadStat")
|
||
(synopsis "Convert SAS, Stata, and SPSS files")
|
||
(description "Command-line tool and C library for reading files from
|
||
popular stats packages like SAS, Stata and SPSS.")
|
||
(license license:expat)))
|
||
|
||
(define-public python-pyreadstat
|
||
(package
|
||
(name "python-pyreadstat")
|
||
(version "1.2.4")
|
||
;; No tests in the PyPI tarball.
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Roche/pyreadstat")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0zysrzixvqw2lwwykxqg5yj8a0zyv5s2bmk22x30f4rj2hgvq1pv"))
|
||
(patches (search-patches "python-pyreadstat-link-libiconv.patch"))))
|
||
(arguments
|
||
'(#:phases (modify-phases %standard-phases
|
||
(add-before 'check 'change-home-dir
|
||
(lambda _
|
||
;; test_sav_expand and test_sav_write_basic_expanduser need a
|
||
;; home directory with write permissions.
|
||
(setenv "HOME" "/tmp")))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
;; The source also contains tests/test_version.py
|
||
;; which checks the version in __init__.py against the
|
||
;; one in setup.py. Since this requires texlive
|
||
;; dependencies to run and is also not mentioned in
|
||
;; how_to_test.md, this test is skipped.
|
||
(invoke "python" "tests/test_basic.py")))))))
|
||
(build-system python-build-system)
|
||
(propagated-inputs (list python-pandas))
|
||
(inputs (list libiconv zlib))
|
||
(native-inputs (list python-cython-3))
|
||
(home-page "https://github.com/Roche/pyreadstat")
|
||
(synopsis
|
||
"Read and write SAS, SPSS and Stata files into/from Pandas DataFrames")
|
||
(description
|
||
"This Python package can be used to read and write SAS, SPSS and Stata
|
||
files into/from Pandas DataFrames. It is a wrapper around the C library
|
||
@code{readstat}.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public xlispstat
|
||
(let ((commit "f1bea6053df658ee48612bf1f63c35de99e2c649")
|
||
(revision "0"))
|
||
(package
|
||
(name "xlispstat")
|
||
(version (git-version "3.52.23" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/jhbadger/xlispstat.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1p0cmgy19kbkxia139cb5w9dnkp2cdqp5n3baag6cq3prn3n71mf"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:parallel-build? #f ; Parallel builds are not supported
|
||
#:configure-flags (list "--with-gcc")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(with-output-to-file "exit.lsp"
|
||
(lambda () (display "(exit)")))
|
||
(invoke "./xlisp" "tests/test" "exit")))))))
|
||
(inputs (list tcsh
|
||
libx11
|
||
libxmu
|
||
libxext
|
||
libxpm
|
||
libxaw
|
||
ncurses
|
||
gnuplot))
|
||
(native-inputs (list pkg-config))
|
||
(synopsis "Statistical analysis environment with interactive graphics")
|
||
(description "XLISP-STAT is a statistical environment based on a Lisp
|
||
dialect called XLISP. To facilitate statistical computations, standard
|
||
functions for addition, logarithms, etc., have been modified to operate on
|
||
lists and arrays of numbers, and a number of basic statistical functions have
|
||
been added. Many of these functions have been written in Lisp, and additional
|
||
functions can be added easily by a user. Several basic forms of plots,
|
||
including histograms, scatterplots, rotatable plots and scatterplot matrices
|
||
are provided. These plots support various forms of interactive highlighting
|
||
operations and can be linked so points highlighted in one plot will be
|
||
highlighted in all linked plots. Interactions with the plots are controlled
|
||
by the mouse, menus and dialog boxes. An object-oriented programming system
|
||
is used to allow menus, dialogs, and the response to mouse actions to be
|
||
customized.")
|
||
(home-page "https://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/")
|
||
(license license:expat))))
|
||
|
||
(define-public r-rlrsim
|
||
(package
|
||
(name "r-rlrsim")
|
||
(version "3.1-8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "RLRsim" version))
|
||
(sha256
|
||
(base32 "06i4slc7fj8xifq20i1vqfadfw2p81b0kfzga60139hnryz1zpva"))))
|
||
(properties `((upstream-name . "RLRsim")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-lme4 r-mgcv r-nlme r-rcpp))
|
||
(home-page "https://github.com/fabian-s/RLRsim")
|
||
(synopsis
|
||
"Exact (Restricted) Likelihood Ratio Tests for Mixed and Additive Models")
|
||
(description
|
||
"Rapid, simulation-based exact (restricted) likelihood ratio tests for testing
|
||
the presence of variance components/nonparametric terms for models fit with
|
||
@code{nlme::lme()}, @code{lme4::lmer()}, @code{lmeTest::lmer()},
|
||
@code{gamm4::gamm4()}, @code{mgcv::gamm()} and @code{SemiPar::spm()}.")
|
||
(license (list license:gpl2+ license:gpl3+))))
|
||
|
||
(define-public r-simr
|
||
(package
|
||
(name "r-simr")
|
||
(version "1.0.7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "simr" version))
|
||
(sha256
|
||
(base32 "1rfnhyqvdazvar7r1ml71lskh1hdk3yfzv5jlcz18wzffscgkgmb"))))
|
||
(properties `((upstream-name . "simr")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-binom
|
||
r-car
|
||
r-iterators
|
||
r-lme4
|
||
r-lmertest
|
||
r-pbkrtest
|
||
r-plotrix
|
||
r-plyr
|
||
r-rlrsim
|
||
r-stringr))
|
||
(native-inputs (list r-knitr r-testthat))
|
||
(home-page "https://github.com/pitakakariki/simr")
|
||
(synopsis
|
||
"Power analysis for generalized linear mixed models by simulation")
|
||
(description
|
||
"This package lets you calculate power for generalized linear mixed
|
||
models, using simulation. It was designed to work with models fit using the
|
||
@code{lme4} package. The package is described in
|
||
@url{doi:10.1111/2041-210X.12504, Green and MacLeod (2016)}.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public r-mixedpower
|
||
;; This commit contains fixes for R>=4.2 and contains new features. A
|
||
;; newer release does not exist.
|
||
(let ((commit "b2b87068546327d8f592d141e5482e0478c1b2ee")
|
||
(revision "2"))
|
||
(package
|
||
(name "r-mixedpower")
|
||
(version (git-version "2.0" revision commit))
|
||
(source
|
||
(origin
|
||
;; Not available on CRAN.
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/DejanDraschkow/mixedpower")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0pys66a6c1k2fp5qk9grhzg1q1d3q51rggcilmdssimkmcsm234z"))))
|
||
(properties `((upstream-name . "mixedpower")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs
|
||
(list r-doparallel r-foreach r-ggplot2 r-lme4 r-reshape2))
|
||
(home-page "https://github.com/DejanDraschkow/mixedpower")
|
||
(synopsis
|
||
"Pilotdata based simulations for estimating power in linear mixed models")
|
||
(description
|
||
"Mixedpower uses pilotdata and a linear mixed model fitted with lme4 to
|
||
simulate new data sets. Power is computed separate for every effect in the
|
||
model output as the relation of significant simulations to all simulations.
|
||
More conservative simulations as a protection against a bias in the pilotdata
|
||
are available as well as methods for plotting the results.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-colorway
|
||
(let ((commit "8ba8f0026aba37752c6770de45bf53b1b0f48afc")
|
||
(revision "1"))
|
||
(package
|
||
(name "r-colorway")
|
||
(version (git-version "0.2.0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/hypercompetent/colorway")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0r6yhnzx3ll1z12pp6y8fqbrx7v18rcff2j2179bqy9ca2d2d94l"))))
|
||
(properties `((upstream-name . "colorway")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-dplyr r-ggplot2 r-rlang))
|
||
(home-page "https://github.com/hypercompetent/colorway")
|
||
(synopsis "Functions for colors in R")
|
||
(description
|
||
"This package provides a collection of (mostly simple) functions for
|
||
generating and manipulating colors in R.")
|
||
(license license:gpl3))))
|
||
|
||
(define-public r-reghelper
|
||
(package
|
||
(name "r-reghelper")
|
||
(version "1.1.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "reghelper" version))
|
||
(sha256
|
||
(base32
|
||
"1vd8kd719kyjp65zym6zx3vax1q2kbhpl6la71d5aa59s54ylri3"))))
|
||
(properties `((upstream-name . "reghelper")))
|
||
(build-system r-build-system)
|
||
(propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme r-rlang))
|
||
(native-inputs (list r-testthat))
|
||
(home-page "https://github.com/jeff-hughes/reghelper")
|
||
(synopsis "Helper Functions for Regression Analysis")
|
||
(description
|
||
"This package provides a set of functions used to automate commonly used methods
|
||
in regression analysis. This includes plotting interactions, and calculating
|
||
simple slopes, standardized coefficients, regions of significance (Johnson &
|
||
Neyman, 1936; cf. Spiller et al., 2012), etc.")
|
||
(license license:gpl3)))
|
||
|
||
(define-public ruby-enumerable-statistics
|
||
(package
|
||
(name "ruby-enumerable-statistics")
|
||
(version "2.0.7")
|
||
;; Source at RubyGems.org doesn't have tests.
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/mrkn/enumerable-statistics.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1a8k2dvm1v0g6hcrbnzy0f7d63hdmpmldfdkl8wr32nbl05xnifa"))
|
||
(modules '((guix build utils)))
|
||
(snippet `(begin
|
||
(substitute* "enumerable-statistics.gemspec"
|
||
;; benchmark-driver gem is used for
|
||
;; performance benchmarking, and isn't
|
||
;; needed for tests.
|
||
(("spec.add_development_dependency \"benchmark-driver\"\n")
|
||
""))))))
|
||
(build-system ruby-build-system)
|
||
(native-inputs (list bundler
|
||
ruby-rake
|
||
ruby-rake-compiler
|
||
ruby-rspec
|
||
ruby-test-unit
|
||
ruby-fuubar
|
||
ruby-yard))
|
||
(synopsis "Library which provides statistics features for Enumerable")
|
||
(description
|
||
"@code{Enumerable::Statistics} provides some methods to calculate
|
||
statistical summary in arrays and enumerables.")
|
||
(home-page "https://github.com/mrkn/enumerable-statistics")
|
||
(license license:expat)))
|
||
|
||
(define-public python-pgmpy
|
||
(package
|
||
(name "python-pgmpy")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch) ;pypi package does not include test data
|
||
(uri (git-reference
|
||
(url "https://github.com/pgmpy/pgmpy")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1hg6wrg3jcac71zn4gknni1wrn38wa86ka3sgp2bndz59mx6sr2s"))))
|
||
(build-system pyproject-build-system)
|
||
(arguments
|
||
(list
|
||
#:test-flags
|
||
#~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
|
||
"-k" (string-join
|
||
;; AssertionError: False is not true
|
||
(list "not test_query_evidence"
|
||
;; ValueError: Experimental support for categorical
|
||
;; data is not implemented for current tree method
|
||
;; yet.
|
||
"test_pillai"
|
||
"test_estimate_with_cache_no_llm_calls"
|
||
"test_estimate_with_orientations"
|
||
;; _flapack.error: (liwork>=max(1,10*n)||liwork==-1)
|
||
;; failed for 10th keyword liwork: dsyevr:liwork=1
|
||
"test_estimate"
|
||
"test_score_bnlearn"
|
||
"test_score_manual")
|
||
" and not "))))
|
||
(propagated-inputs (list python-daft
|
||
python-joblib
|
||
python-networkx
|
||
python-numpy
|
||
python-opt-einsum
|
||
python-pandas
|
||
python-pyparsing
|
||
python-pytorch
|
||
python-scikit-learn
|
||
python-scipy
|
||
python-statsmodels
|
||
python-tqdm))
|
||
(native-inputs (list python-mock
|
||
python-pyro-ppl
|
||
python-pytest
|
||
python-pytest-xdist
|
||
python-setuptools
|
||
python-wheel
|
||
python-xgboost))
|
||
(home-page "https://github.com/pgmpy/pgmpy")
|
||
(synopsis "Probabilistic Graphical Models library")
|
||
(description
|
||
"This package provides a library for Probabilistic Graphical Models. It
|
||
can be used for learning (Structure and Parameter), inference (Probabilistic
|
||
and Causal), and simulations in Bayesian Networks.")
|
||
(license license:expat)))
|