;;; ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2017, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
;;; Copyright © 2017–2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2021, 2022, 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
;;; Copyright © 2023 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
;;; Copyright © 2024 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
;;; Copyright © 2025 Jonas Freimuth <jonas.freimuth@posteo.de>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages statistics)
#:use-module (guix 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)
#:use-module (guix build-system gnu)
#:use-module (guix build-system r)
#:use-module (guix build-system pyproject)
#: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)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages ocaml)
#: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)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#: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)
#:use-module (gnu packages tcl)
#:use-module (gnu packages terminals)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages base)
#:use-module (gnu packages uglifyjs)
#:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match))
(define-public pspp
(package
(name "pspp")
(version "2.0.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/pspp/pspp-"
version ".tar.gz"))
(sha256
(base32
"002c08rxym056mn7a73jwjmcazqd4gh5j1cyml603y4ckvqb1nwf"))))
(build-system gnu-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-test-suite
(lambda _
(substitute* "tests/output/tex.at"
(("AT_CHECK\\(\\[LC_ALL=C.UTF-8 pspp")
"AT_CHECK([LC_ALL=en_US.UTF-8 pspp"))))
(add-before 'check 'prepare-tests
;; Prevent irrelevant errors that cause test output mismatches:
;; ‘Fontconfig error: No writable cache directories’
(lambda _
(setenv "XDG_CACHE_HOME" (getcwd)))))))
(inputs
(list cairo
gettext-minimal
gsl
libxml2
pango
readline
gtk+
gtksourceview-3
spread-sheet-widget
zlib))
(native-inputs
(list autoconf ;for tests
`(,glib "bin") ;for glib-genmarshal
perl
pkg-config
python-3 ;for tests
texinfo))
(home-page "https://www.gnu.org/software/pspp/")
(synopsis "Statistical analysis")
(description
"GNU PSPP is a statistical analysis program. It can perform
descriptive statistics, T-tests, linear regression and non-parametric tests.
It features both a graphical interface as well as command-line input. PSPP
is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
can be imported from spreadsheets, text files and database sources and it can
be output in text, PostScript, PDF or HTML.")
(license license:gpl3+)))
(define-public jags
(package
(name "jags")
(version "4.3.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
(version-major version) ".x/Source/"
"JAGS-" version ".tar.gz"))
(sha256
(base32
"0aa2w4g5057vn1qjp954s2kwxfmy1h7p5yn56fyi7sz9nmaq69gr"))))
(build-system gnu-build-system)
(arguments
(list #:configure-flags
#~(list "--with-lapack=-lopenblas"
"--with-blas=-lopenblas")))
(home-page "https://mcmc-jags.sourceforge.net/")
(native-inputs
(list gfortran openblas))
(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)
simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
@enumerate
@item To have a cross-platform engine for the BUGS language;
@item To be extensible, allowing users to write their own functions,
distributions and samplers;
@item To be a platform for experimentation with ideas in Bayesian modelling.
@end enumerate\n")
(license license:gpl2)))
(define-public libxls
(package
(name "libxls")
(version "1.6.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/libxls/libxls/releases/download/"
"v" version "/libxls-" version ".tar.gz"))
(sha256
(base32 "0wg3ymr43aa1j3scyl9x83b2xgg7wilzpil0dj91a8dzji6w7b2x"))))
(build-system gnu-build-system)
(home-page "https://github.com/libxls/libxls")
(synopsis "Read binary (.xls) Excel spreadsheet files")
(description
"libxls is a C library to read .xls spreadsheet files in the binary OLE
BIFF8 format as created by Excel 97 and later versions. It cannot write them.
This package also provides @command{xls2csv} to export Excel files to CSV.")
(license license:bsd-2)))
;; Update this package together with the set of recommended packages: r-boot,
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
(define r-with-tests
(package
(name "r-with-tests")
(version "4.4.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
(version-major version) "/R-"
version ".tar.gz"))
(sha256
(base32
"1v0pp3zdyyyz7krhr9mng48fhsf5k6zxhj9yfic6p1ld7rhcsy0m"))))
(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"
(("dateCreated = Sys.time\\(\\)")
"dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
;; Ensure that gzipped files are reproducible.
(substitute* '("src/library/grDevices/Makefile.in"
"doc/manual/Makefile.in")
(("R_GZIPCMD\\)" line)
(string-append line " -n")))
;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
;; queries the mtime of a given file and records it in an object.
;; This is acceptable at runtime to detect stale source files,
;; but it destroys reproducibility at build time.
;; Similarly, the "srcfilecopy" procedure records the current
;; time. We change both of them to respect SOURCE_DATE_EPOCH.
(substitute* "src/library/base/R/srcfile.R"
(("timestamp <- (timestamp.*|file.mtime.*)" _ time)
(string-append "timestamp <- \
as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
} else { " time "}, origin=\"1970-01-01\")\n")))
;; This library is installed using "install_package_description",
;; so we need to pass the "builtStamp" argument.
(substitute* "src/library/tools/Makefile.in"
(("(install_package_description\\(.*\"')\\)\"" line prefix)
(string-append prefix ", builtStamp='1970-01-01')\"")))
(substitute* "src/library/Recommended/Makefile.in"
(("INSTALL_OPTS =" m)
(string-append m " --built-timestamp=1970-01-01" m)))
;; R bundles an older version of help2man, which does not respect
;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
;; because that breaks a test.
(with-fluids ((%default-port-encoding "ISO-8859-1"))
(substitute* "tools/help2man.pl"
(("my \\$date = strftime \"%B %Y\", localtime" line)
(string-append line " 1"))))
;; 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-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-updmap.cfg
(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-boot
(package
(name "r-boot")
(version "1.3-31")
(source
(origin
(method url-fetch)
(uri (cran-uri "boot" version))
(sha256
(base32
"1ln8079g7l6yxdh7bmcn2acjlln0hvrhhjbp5r0wl0xms662wm6q"))))
(build-system r-build-system)
(native-inputs (list r-survival))
(home-page "https://cran.r-project.org/web/packages/boot")
(synopsis "Bootstrap functions for R")
(description
"This package provides functions and datasets for bootstrapping from the
book \"Bootstrap Methods and Their Application\" by A.C. Davison and
D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
;; Unlimited distribution
(license (license:non-copyleft "file://R/bootfuns.q"))))
(define-public r-mass
(package
(name "r-mass")
(version "7.3-61")
(source
(origin
(method url-fetch)
(uri (cran-uri "MASS" version))
(sha256
(base32
"140ah1719zad8gd0glvy9qlkxxakgz12i5r5gk2bgmwxayzwhi1i"))))
(properties `((upstream-name . "MASS")))
(build-system r-build-system)
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Support functions and datasets for Venables and Ripley's MASS")
(description
"This package provides functions and datasets for the book \"Modern
Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
;; Either version may be picked.
(license (list license:gpl2 license:gpl3))))
(define-public r-class
(package
(name "r-class")
(version "7.3-22")
(source
(origin
(method url-fetch)
(uri (cran-uri "class" version))
(sha256
(base32
"0p6i10jk8mb85bkx4lvixw85lsmgnk4cizcdw33zqhrqx5j436dn"))))
(build-system r-build-system)
(propagated-inputs
(list r-mass))
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "R functions for classification")
(description
"This package provides various functions for classification, including
k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
;; Either of the two versions can be picked.
(license (list license:gpl2 license:gpl3))))
(define-public r-cluster
(package
(name "r-cluster")
(version "2.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "cluster" version))
(sha256
(base32
"0r1i243mjbsx00ccg3f46c5iwnfmjxmhhdjvrj3m799mzpx0xifi"))))
(build-system r-build-system)
;; Tests insist on loading Matrix not from the locations specified with
;; R_LIBS_SITE.
(arguments (list #:tests? #false))
(native-inputs
(list gfortran r-matrix))
(home-page "https://cran.r-project.org/web/packages/cluster")
(synopsis "Methods for cluster analysis")
(description
"This package provides methods for cluster analysis. It is a much
extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
(license license:gpl2+)))
(define-public r-codetools
(package
(name "r-codetools")
(version "0.2-20")
(source
(origin
(method url-fetch)
(uri (cran-uri "codetools" version))
(sha256
(base32
"0qx8zrlickl45wzzbydsbx5f1vmzhn71x7amzpfj71qpxisz7riv"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/codetools")
(synopsis "Code analysis tools for R")
(description "This package provides code analysis tools for R to check R
code for possible problems.")
;; Any version of the GPL.
(license (list license:gpl2+ license:gpl3+))))
(define-public r-foreign
(package
(name "r-foreign")
(version "0.8-87")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
"0mi8vf3bsvrn2nh9kxjlgsmvxrc8icw51scr0mscqyp8r3saq90s"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
(description
"This package provides functions for reading and writing data stored by
some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
for reading and writing some dBase files.")
(license license:gpl2+)))
(define-public r-kernsmooth
(package
(name "r-kernsmooth")
(version "2.23-24")
(source
(origin
(method url-fetch)
(uri (cran-uri "KernSmooth" version))
(sha256
(base32
"0pxc53sw9f4hhxnl3zkalkkk0fvzcfxw7c4ibrb95zbzahwyrcyh"))))
(properties `((upstream-name . "KernSmooth")))
(build-system r-build-system)
(native-inputs
(list gfortran))
(home-page "https://cran.r-project.org/web/packages/KernSmooth")
(synopsis "Functions for kernel smoothing")
(description
"This package provides functions for kernel smoothing (and density
estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
\"Kernel Smoothing\".")
;; Unlimited use and distribution
(license (license:non-copyleft "file://LICENCE.note"))))
(define-public r-lattice
(package
(name "r-lattice")
(version "0.22-6")
(source (origin
(method url-fetch)
(uri (cran-uri "lattice" version))
(sha256
(base32
"1xq09lfjlca6c7mn412hjjav0q66p7wmjrwx5f3ygv3jwh8p4dsb"))))
(build-system r-build-system)
(native-inputs (list r-mass))
(home-page "https://lattice.r-forge.r-project.org/")
(synopsis "High-level data visualization system")
(description
"The lattice package provides a powerful and elegant high-level data
visualization system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs, and is
also flexible enough to handle most nonstandard requirements.")
(license license:gpl2+)))
(define-public r-matrix
(package
(name "r-matrix")
(version "1.7-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "Matrix" version))
(sha256
(base32
"189q5dlghkj0i8v526d9adv4z3mm1c9iya041aysyb2f9vqbpjm2"))))
(properties `((upstream-name . "Matrix")))
(build-system r-build-system)
(propagated-inputs
(list r-lattice))
(native-inputs (list r-mass))
(home-page "https://Matrix.R-forge.R-project.org/")
(synopsis "Sparse and dense matrix classes and methods")
(description
"This package provides classes and methods for dense and sparse matrices
and operations on them using LAPACK and SuiteSparse.")
(license license:gpl2+)))
(define-public r-nlme
(package
(name "r-nlme")
(version "3.1-166")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
(base32 "0qlpj3hjnlvd7x3ayjhvvpxlc2z4bfwk9qpglw8mnxbqipp18yi3"))))
(build-system r-build-system)
(propagated-inputs
(list r-lattice))
(native-inputs
(list gfortran))
(home-page "https://cran.r-project.org/web/packages/nlme")
(synopsis "Linear and nonlinear mixed effects models")
(description
"This package provides tools to fit and compare Gaussian linear and
nonlinear mixed-effects models.")
(license license:gpl2+)))
(define-public r-mgcv
(package
(name "r-mgcv")
(version "1.9-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "mgcv" version))
(sha256
(base32 "0cnvbdda243as2bxfsgnnk7xjmp1msgr9i4vbd84jfnxpqvvq3vh"))))
(build-system r-build-system)
(propagated-inputs
(list r-matrix r-nlme))
(home-page "https://cran.r-project.org/web/packages/mgcv")
(synopsis "Mixed generalised additive model computation")
(description
"GAMs, GAMMs and other generalized ridge regression with multiple smoothing
parameter estimation by GCV, REML or UBRE/AIC. The library includes a
@code{gam()} function, a wide variety of smoothers, JAGS support and
distributions beyond the exponential family.")
(license license:gpl2+)))
(define-public r-nnet
(package
(name "r-nnet")
(version "7.3-19")
(source
(origin
(method url-fetch)
(uri (cran-uri "nnet" version))
(sha256
(base32
"1rrc70shnrnn7gyq5fhnmw841a06d8y0vp5pp8xv1lvhj931y959"))))
(build-system r-build-system)
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Feed-forward neural networks and multinomial log-linear models")
(description
"This package provides functions for feed-forward neural networks with a
single hidden layer, and for multinomial log-linear models.")
(license (list license:gpl2+ license:gpl3+))))
(define-public r-rpart
(package
(name "r-rpart")
(version "4.1.23")
(source
(origin
(method url-fetch)
(uri (cran-uri "rpart" version))
(sha256
(base32
"1bxbvbv3jwz1j6yhgswbr6qy574n9rbp3cnwl9badkm6dbnrmf7r"))))
(build-system r-build-system)
(native-inputs (list r-survival))
(home-page "https://cran.r-project.org/web/packages/rpart")
(synopsis "Recursive partitioning and regression trees")
(description
"This package provides recursive partitioning functions for
classification, regression and survival trees.")
(license (list license:gpl2+ license:gpl3+))))
(define-public r-spatial
(package
(name "r-spatial")
(version "7.3-17")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatial" version))
(sha256
(base32
"1msxbxz50qmzjxgix2vcq0f50b4cdvj8nz3qlilp397jrzc3w07i"))))
(build-system r-build-system)
(home-page "https://www.stats.ox.ac.uk/pub/MASS4/")
(synopsis "Functions for kriging and point pattern analysis")
(description
"This package provides functions for kriging and point pattern
analysis.")
;; Either version may be picked.
(license (list license:gpl2 license:gpl3))))
(define-public r-survival
(package
(name "r-survival")
(version "3.7-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "survival" version))
(sha256
(base32
"1vzy8kg159yqnvg733air11la2qrirwcqhn9d67h5c18r67b15nd"))))
(build-system r-build-system)
(propagated-inputs
(list r-matrix))
(home-page "https://github.com/therneau/survival")
(synopsis "Survival analysis")
(description
"This package contains the core survival analysis routines, including
definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
curves, Cox models, and parametric accelerated failure time models.")
(license license:lgpl2.0+)))
(define-public r
(package (inherit r-minimal)
(name "r")
(source #f)
(build-system trivial-build-system)
(arguments '(#:builder (begin (mkdir %output) #t)))
(propagated-inputs
(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-bit
(package
(name "r-bit")
(version "4.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bit" version))
(sha256
(base32
"1vfbwy2kl5rykmh1r9lw4s9yw7dnia18h0ks266p2q9dikiwbpc9"))))
(build-system r-build-system)
(native-inputs
(list r-knitr r-rmarkdown r-testthat))
(home-page "https://ff.r-forge.r-project.org")
(synopsis "Class for vectors of 1-bit booleans")
(description
"This package provides bitmapped vectors of booleans (no @code{NA}s),
coercion from and to logicals, integers and integer subscripts, fast boolean
operators and fast summary statistics. With @code{bit} class vectors of true
binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
(license license:gpl2)))
(define-public r-bit64
(package
(name "r-bit64")
(version "4.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bit64" version))
(sha256
(base32
"0bn7d9dlmr7arbj2090hhkxs9kc0wni5aw39a6nh0243v0zmc8d3"))))
(build-system r-build-system)
(propagated-inputs
(list r-bit))
(home-page "https://ff.r-forge.r-project.org/")
(synopsis "S3 class for vectors of 64 bit integers")
(description
"The bit64 package provides serializable S3 atomic 64 bit (signed)
integers that can be used in vectors, matrices, arrays and @code{data.frames}.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as @code{match} and @code{order} support
interactive data exploration and manipulation and optionally leverage
caching.")
(license license:gpl2)))
(define-public r-chorddiag
(package
(name "r-chorddiag")
(version "0.1.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mattflor/chorddiag")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1bpy9q861l1hyyiqbx2f7qzp7j7im8bkcfdwgxzk5fm0250p359a"))
;; Delete minified JavaScript file
(snippet
'(delete-file "inst/htmlwidgets/lib/d3/d3.min.js"))))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/htmlwidgets/lib/d3"
(let ((source (assoc-ref inputs "d3.v4.js"))
(target "d3.min.js"))
(format #true "Processing ~a --> ~a~%"
source target)
(invoke "esbuild" source "--minify"
(string-append "--outfile=" target)))))))))
(propagated-inputs
(list r-htmlwidgets r-rcolorbrewer))
(native-inputs
`(("esbuild" ,esbuild)
("r-knitr" ,r-knitr)
("d3.v4.js"
,(origin
(method url-fetch)
(uri "https://d3js.org/d3.v4.js")
(sha256
(base32
"0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
(home-page "https://github.com/mattflor/chorddiag")
(synopsis "Create D3 chord diagram")
(description
"This package provides tools to create interactive chords diagrams via
the D3 Javascript library. Chord diagrams show directed relationships among a
group of entities. This package is based on
@url{http://bl.ocks.org/mbostock/4062006} with some modifications (fading) and
additions (tooltips, bipartite diagram type).")
(license license:gpl3+)))
(define-public r-dichromat
(package
(name "r-dichromat")
(version "2.0-0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dichromat" version))
(sha256
(base32 "10b0avdar3d1y8x2ya3x5kqxqg0z0mq872hdzvc1nn4amplph1d1"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/dichromat")
(synopsis "Color schemes for dichromats")
(description
"Dichromat collapses red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.")
(license license:gpl2+)))
(define-public r-digest
(package
(name "r-digest")
(version "0.6.37")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
(base32 "0883iyjbd50f0gwz6hgdmcsrk0i0fkjaix9hz6d4m2jbk54x3i42"))))
(build-system r-build-system)
;; Vignettes require r-knitr, which requires r-digest, so we have to
;; disable them and the tests.
(arguments
`(#:tests? #f
#:configure-flags (list "--no-build-vignettes")))
(native-inputs (list r-simplermarkdown))
(home-page "https://dirk.eddelbuettel.com/code/digest.html")
(synopsis "Create cryptographic hash digests of R objects")
(description
"This package contains an implementation of a function @code{digest()} for
the creation of hash digests of arbitrary R objects (using the md5, sha-1,
sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
of R language objects, as well as a function @code{hmac()} to create hash-based
message authentication code.
Please note that this package is not meant to be deployed for cryptographic
purposes for which more comprehensive (and widely tested) libraries such as
OpenSSL should be used.")
(license license:gpl2+)))
(define-public r-estimability
(package
(name "r-estimability")
(version "1.5.1")
(source (origin
(method url-fetch)
(uri (cran-uri "estimability" version))
(sha256
(base32
"1sa42rczhzfj0dkn8v1pq6b752rh6h7x553gcgl7g27x75mbk9iw"))))
(build-system r-build-system)
(native-inputs (list r-knitr))
(home-page "https://cran.r-project.org/web/packages/estimability")
(synopsis "Tools for assessing estimability of linear predictions")
(description "This package provides tools for determining estimability of
linear functions of regression coefficients, and @code{epredict} methods that
handle non-estimable cases correctly.")
(license license:gpl2+)))
(define-public r-labeling
(package
(name "r-labeling")
(version "0.4.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "labeling" version))
(sha256
(base32 "1wk4wa1s8f17b5lf8vs5hxsmyadp2ccmyg4hamq7sdvlrk14yby6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/labeling")
(synopsis "Axis labeling algorithms")
(description "The labeling package provides a range of axis labeling
algorithms.")
(license license:expat)))
(define-public r-magrittr
(package
(name "r-magrittr")
(version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "magrittr" version))
(sha256
(base32 "1ljmrrm36y31db5z4cl863ap8k3jcaxk0qzy3f0cn6iag4zzigx2"))))
(properties
;; We can't have r-knitr or r-testthat among the inputs here, because
;; that would lead to dependency cycles.
'((updater-ignored-native-inputs . ("r-knitr" "r-testthat"))))
(build-system r-build-system)
;; Tests require r-testthat, which uses this package.
(arguments (list #:tests? #false))
(home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
(synopsis "Forward-pipe operator for R")
(description
"Magrittr provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward a value, or the result
of an expression, into the next function call/expression. There is flexible
support for the type of right-hand side expressions. For more information,
see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
(license license:expat)))
(define-public r-munsell
(package
(name "r-munsell")
(version "0.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "munsell" version))
(sha256
(base32 "19i9jjawlqciw4n4h99a4sm0lbc77la3pqyzjvnwsrh7qjdgv8h3"))))
(build-system r-build-system)
(propagated-inputs
(list r-colorspace))
(native-inputs (list r-testthat))
(home-page "https://cran.r-project.org/web/packages/munsell")
(synopsis "Munsell colour system")
(description
"The Munsell package contains Functions for exploring and using the
Munsell colour system.")
(license license:expat)))
(define-public r-permute
(package
(name "r-permute")
(version "0.9-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "permute" version))
(sha256
(base32
"1h4dyhcsv8p3h3qxsy98pib9v79dddvrnq7qx6abkblsazxqzy7g"))))
(build-system r-build-system)
(native-inputs (list r-knitr r-testthat))
;; Tests do not run correctly, but running them properly would entail a
;; circular dependency with vegan.
(home-page "https://github.com/gavinsimpson/permute")
(synopsis "Functions for Generating Restricted Permutations of Data")
(description
"This package provides a set of restricted permutation designs for freely
exchangeable, line transects (time series), spatial grid designs and permutation
of blocks (groups of samples). @code{permute} also allows split-plot designs,
in which the whole-plots or split-plots or both can be freely exchangeable.")
(license license:gpl2+)))
(define-public r-plyr
(package
(name "r-plyr")
(version "1.8.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "plyr" version))
(sha256
(base32 "00z1mvqisnzbbwcwax1gm9ilahpgp21kk4l7hqdz8fym27vygd8m"))))
(build-system r-build-system)
(propagated-inputs (list r-rcpp))
(native-inputs (list r-testthat))
(home-page "http://had.co.nz/plyr")
(synopsis "Tools for Splitting, Applying and Combining Data")
(description
"Plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each piece and
then put all the pieces back together. For example, you might want to fit a
model to each spatial location or time point in your study, summarise data by
panels or collapse high-dimensional arrays to simpler summary statistics.")
(license license:expat)))
(define-public r-proto
(package
(name "r-proto")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "proto" version))
(sha256
(base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
(build-system r-build-system)
(native-inputs (list r-testthat))
(home-page "https://github.com/hadley/proto")
(synopsis "Prototype object-based programming")
(description
"Proto is an object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.")
(license license:gpl2+)))
(define-public r-rcolorbrewer
(package
(name "r-rcolorbrewer")
(version "1.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "RColorBrewer" version))
(sha256
(base32 "1h0s0f4vvlk40cagp3qwhd0layzkjcnqkiwjyhwqns257i1gahjg"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/RColorBrewer")
(synopsis "ColorBrewer palettes")
(description
"This package provides color schemes for maps (and other graphics)
designed by Cynthia Brewer as described at http://colorbrewer2.org")
;; Includes code licensed under bsd-4
(license license:asl2.0)))
(define-public r-sendmailr
(package
(name "r-sendmailr")
(version "1.4-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "sendmailR" version))
(sha256
(base32
"1balci88r2ci51xdh5zaqm3ss3vnry8pbkx2qngppc7n2gy932sv"))))
(properties `((upstream-name . "sendmailR")))
(build-system r-build-system)
(propagated-inputs
(list r-base64enc))
(native-inputs (list r-knitr))
(home-page "https://cran.r-project.org/web/packages/sendmailR")
(synopsis "Send email using R")
(description
"This package contains a simple SMTP client which provides a portable
solution for sending email, including attachments, from within R.")
(license license:gpl2+)))
(define-public r-stringi
(package
(name "r-stringi")
(version "1.8.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
"1wv9qqxl84l44kpvkx0lmyciinrh9pa5512jm56gsaqs9pvgh6f2"))))
(build-system r-build-system)
(inputs (list icu4c))
(native-inputs (list pkg-config))
(home-page "http://stringi.rexamine.com/")
(synopsis "Character string processing facilities")
(description
"This package allows for fast, correct, consistent, portable, as well as
convenient character string/text processing in every locale and any native
encoding. Owing to the use of the ICU library, the package provides R users
with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
programmers. Among available features there are: pattern searching
(e.g. via regular expressions), random string generation, string collation,
transliteration, concatenation, date-time formatting and parsing, etc.")
(license license:bsd-3)))
(define-public r-stringr
(package
(name "r-stringr")
(version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringr" version))
(sha256
(base32 "1pj5xwg8kq2jllmszgkw96qj37wlb0x0vx4f3m5j211zpd8yrbd4"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs))
(native-inputs (list r-knitr r-testthat))
(home-page "https://github.com/hadley/stringr")
(synopsis "Simple, consistent wrappers for common string operations")
(description
"Stringr is a consistent, simple and easy to use set of wrappers around
the fantastic @code{stringi} package. All function and argument names (and
positions) are consistent, all functions deal with \"NA\"'s and zero length
vectors in the same way, and the output from one function is easy to feed into
the input of another.")
(license license:gpl2+)))
(define-public r-reshape2
(package
(name "r-reshape2")
(version "1.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "reshape2" version))
(sha256
(base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
(build-system r-build-system)
(propagated-inputs
(list r-plyr r-rcpp r-stringr))
(native-inputs (list r-testthat))
(home-page "https://github.com/hadley/reshape")
(synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
(description
"Reshape2 is an R library to flexibly restructure and aggregate data
using just two functions: melt and dcast (or acast).")
(license license:expat)))
(define-public r-ggplot2
(package
(name "r-ggplot2")
(version "3.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggplot2" version))
(sha256
(base32 "08a72kizg42mdm35170fnpn8l6r4n3j1yvbgiq1k8dlvz4jb8n3w"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli
r-glue
r-gtable
r-isoband
r-lifecycle
r-mass
r-mgcv
r-rlang
r-scales
r-svglite ; Needed for 'ggsave'
r-tibble
r-vctrs
r-withr))
(native-inputs
(list r-knitr r-testthat))
(home-page "https://ggplot2.tidyverse.org")
(synopsis "Implementation of the grammar of graphics")
(description
"Ggplot2 is an implementation of the grammar of graphics in R. It
combines the advantages of both base and lattice graphics: conditioning and
shared axes are handled automatically, and you can still build up a plot step
by step from multiple data sources. It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map data to
aesthetic attributes.")
(license license:gpl2+)))
(define-public r-ggdendro
(package
(name "r-ggdendro")
(version "0.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "ggdendro" version))
(sha256
(base32
"0sdayyzvhkbli0ha68mc0f7cgp36njv9ign37d63l21hvd6w6h0r"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2 r-mass))
(native-inputs
(list r-knitr r-testthat))
(home-page "https://github.com/andrie/ggdendro")
(synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
(description "This is a set of tools for dendrograms and tree plots using
ggplot2. The ggplot2 philosophy is to clearly separate data from the
presentation. Unfortunately the plot method for dendrograms plots directly
to a plot device with out exposing the data. The ggdendro package resolves
this by making available functions that extract the dendrogram plot data.
The package provides implementations for tree, rpart, as well as diana and
agnes cluster diagrams.")
(license license:gpl2+)))
(define-public r-gdtools
(package
(name "r-gdtools")
(version "0.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "gdtools" version))
(sha256
(base32
"0vv8g0h5fkpna5b3fqrj6dkdxpqr0ws5sdmzgysb17gw4vviq39b"))))
(build-system r-build-system)
(native-inputs
(list pkg-config r-testthat))
(inputs
(list cairo fontconfig freetype zlib))
(propagated-inputs
(list r-fontquiver r-htmltools r-rcpp r-systemfonts))
(home-page "https://cran.r-project.org/web/packages/gdtools")
(synopsis "Utilities for graphical rendering")
(description
"The @code{gdtools} package provides functionalities to get font metrics
and to generate base64 encoded string from raster matrix.")
(license license:gpl3)))
(define-public r-svglite
(package
(name "r-svglite")
(version "2.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "svglite" version))
(sha256
(base32 "0m0axxrkiih4wmrp9qh803p4l92fdgrsbxaww38z89widx75da7h"))))
(properties `((upstream-name . "svglite")))
(build-system r-build-system)
(inputs (list libpng zlib))
(propagated-inputs (list r-cpp11 r-systemfonts))
(native-inputs (list r-fontquiver r-knitr r-testthat r-xml2))
(home-page "https://svglite.r-lib.org")
(synopsis "SVG graphics device")
(description
"@code{svglite} is a graphics device that produces clean
@dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
considerably faster, produces smaller files, and leaves text as is.")
(license license:gpl2+)))
(define-public r-assertthat
(package
(name "r-assertthat")
(version "0.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "assertthat" version))
(sha256
(base32
"17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
(build-system r-build-system)
(native-inputs (list r-testthat))
(home-page "https://github.com/hadley/assertthat")
(synopsis "Easy pre and post assertions")
(description
"Assertthat is an extension to stopifnot() that makes it easy to declare
the pre and post conditions that your code should satisfy, while also
producing friendly error messages so that your users know what they've done
wrong.")
(license license:gpl3+)))
(define-public r-lazyeval
(package
(name "r-lazyeval")
(version "0.2.2")
(source (origin
(method url-fetch)
(uri (cran-uri "lazyeval" version))
(sha256
(base32
"1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
(build-system r-build-system)
(native-inputs (list r-knitr r-testthat))
(home-page "https://github.com/hadley/lazyeval")
(synopsis "Lazy (non-standard) evaluation in R")
(description
"This package provides the tools necessary to do non-standard
evaluation (NSE) in R.")
(license license:gpl3+)))
(define-public r-dbi
(package
(name "r-dbi")
(version "1.2.3")
(source (origin
(method url-fetch)
(uri (cran-uri "DBI" version))
(sha256
(base32
"1gid1mfzq1j3n5fsnpzdb50p2m73z92s6njp0sgr503aaskhhryg"))))
(build-system r-build-system)
(native-inputs
(list r-knitr r-testthat))
(home-page "https://github.com/rstats-db/DBI")
(synopsis "R database interface")
(description
"The DBI package provides a database interface (DBI) definition for
communication between R and relational database management systems. All
classes in this package are virtual and need to be extended by the various
R/DBMS implementations.")
(license license:lgpl2.0+)))
(define-public r-bh
(package
(name "r-bh")
(version "1.84.0-0")
(source (origin
(method url-fetch)
(uri (cran-uri "BH" version))
(sha256
(base32
"1b7igvvy9f13l969a26j2bdzib2laq3m4w1x0xsxjb2pbxsn1dkg"))))
(build-system r-build-system)
(home-page "https://github.com/eddelbuettel/bh")
(synopsis "R package providing subset of Boost headers")
(description
"This package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages.")
(license license:boost1.0)))
(define-public r-evaluate
(package
(name "r-evaluate")
(version "1.0.1")
(source (origin
(method url-fetch)
(uri (cran-uri "evaluate" version))
(sha256
(base32
"1qki65w0qr8wndpsydy7frhdddbm122284zkn8ccdqskbgjw6v23"))))
(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)
(home-page "https://github.com/hadley/evaluate")
(synopsis "Parsing and evaluation tools for R")
(description
"This package provides tools that allow you to recreate the parsing,
evaluation and display of R code, with enough information that you can
accurately recreate what happens at the command line. The tools can easily be
adapted for other output formats, such as HTML or LaTeX.")
(license license:gpl3+)))
(define-public r-formatr
(package
(name "r-formatr")
(version "1.14")
(source (origin
(method url-fetch)
(uri (cran-uri "formatR" version))
(sha256
(base32
"0k271w4bhlj7r9igkiyfw7d7bg30s2mn4sr4alb8f9w57wnapfjf"))))
(build-system r-build-system)
(native-inputs
(list r-knitr r-testit))
(home-page "https://yihui.org/formatr/")
(synopsis "Format R code automatically")
(description
"This package provides a function to format R source code. Spaces and
indent will be added to the code automatically, and comments will be preserved
under certain conditions, so that R code will be more human-readable and tidy.
There is also a Shiny app as a user interface in this package.")
(license license:gpl3+)))
(define-public r-highr
(package
(name "r-highr")
(version "0.11")
(source (origin
(method url-fetch)
(uri (cran-uri "highr" version))
(sha256
(base32
"19z0gwdy46z6gb46b3fs2ljxa2cn0bpvx7aam0jk75h180l183g9"))))
(properties
;; We can't have r-knitr among the inputs here, because r-highr depends
;; on r-xfun, which is an input to r-knitr.
'((updater-ignored-native-inputs . ("r-knitr"))))
(build-system r-build-system)
;; Do not build vignettes as they need r-knitr.
(arguments (list #:test-types '(list "tests")))
(propagated-inputs (list r-xfun))
(native-inputs (list r-testit))
(home-page "https://github.com/yihui/highr")
(synopsis "Syntax highlighting for R source code")
(description
"This package provides syntax highlighting for R source code. Currently
it supports LaTeX and HTML output. Source code of other languages is
supported via Andre Simon's highlight package.")
(license license:gpl3+)))
(define-public r-httpgd
(let ((commit "3f5f55822c4dce930155b91cedcfd4d483e3294e")
(revision "1"))
(package
(name "r-httpgd")
(version (git-version "2.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nx10/httpgd")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "14i7mhbv1vcz2886w9lii9zhgr4zhhc844349syb989nhhzg552n"))))
(properties `((upstream-name . "httpgd")))
(build-system r-build-system)
;; XXX On the build farm the tests fail with "Too many open files". It
;; works fine on my laptop.
(arguments (list #:tests? #false))
(propagated-inputs (list r-asioheaders r-cpp11 r-unigd))
(native-inputs (list r-knitr r-testthat))
(home-page "https://github.com/nx10/httpgd")
(synopsis "HTTP server graphics device")
(description
"This package provides a graphics device for R that is accessible via
network protocols. This package was created to make it easier to embed live R
graphics in integrated development environments and other applications. The
included HTML/@code{JavaScript} client (plot viewer) aims to provide a better
overall user experience when dealing with R graphics. The device
asynchronously serves graphics via HTTP and @code{WebSockets}'.")
(license license:gpl2+))))
(define-public r-mime
(package
(name "r-mime")
(version "0.12")
(source (origin
(method url-fetch)
(uri (cran-uri "mime" version))
(sha256
(base32
"0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059"))))
(build-system r-build-system)
(home-page "https://github.com/yihui/mime")
(synopsis "R package to map filenames to MIME types")
(description
"This package guesses the MIME type from a filename extension using the
data derived from /etc/mime.types in UNIX-type systems.")
(license license:gpl2)))
(define-public r-markdown
(package
(name "r-markdown")
(version "1.13")
(source (origin
(method url-fetch)
(uri (cran-uri "markdown" version))
(sha256
(base32
"1nfgngskgb4r34r3cnkm0gn7p1axpcb7rpyi0jxg4nygfk322m1q"))))
(build-system r-build-system)
;; Skip check phase because the tests require the r-knitr package to be
;; installed. This prevents installation failures. Knitr normally
;; shouldn't be available since r-markdown is a dependency of the r-knitr
;; package.
(arguments `(#:tests? #f))
(propagated-inputs
(list r-commonmark r-xfun))
(home-page "https://github.com/rstudio/markdown")
(synopsis "Markdown rendering for R")
(description
"This package provides R bindings to the Sundown Markdown rendering
library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
syntax that can be converted to XHTML or other formats.")
(license license:gpl2)))
(define-public r-yaml
(package
(name "r-yaml")
(version "2.3.10")
(source (origin
(method url-fetch)
(uri (cran-uri "yaml" version))
(sha256
(base32
"0v9al1fh82vpjhml91j73sim7gfyc0154kxaam41sdkf6qnx8dp2"))))
(build-system r-build-system)
(native-inputs (list r-runit))
(home-page "https://cran.r-project.org/web/packages/yaml/")
(synopsis "Methods to convert R data to YAML and back")
(description
"This package implements the libyaml YAML 1.1 parser and
emitter (http://pyyaml.org/wiki/LibYAML) for R.")
(license license:bsd-3)))
(define-public r-knitr
(package
(name "r-knitr")
(version "1.49")
(source (origin
(method url-fetch)
(uri (cran-uri "knitr" version))
(sha256
(base32
"1lx2k2gg14pmpbh8i884mdaqx0zaf0x07x1001z3hja6cmwwali9"))))
(properties
;; We can't have r-litedown among the inputs here to avoid a dependency
;; cycle.
'((updater-ignored-native-inputs . ("r-litedown"))))
(build-system r-build-system)
;; Tests need r-tibble, which needs r-knitr.
(arguments (list #:tests? #false))
(propagated-inputs
(list r-evaluate r-highr r-xfun r-yaml))
(home-page "https://yihui.org/knitr/")
(synopsis "General-purpose package for dynamic report generation in R")
(description
"This package provides a general-purpose tool for dynamic report
generation in R using Literate Programming tech/download/stklos-"
version ".tar.gz"))
(sha256
(base32
"0hd05r5pr3yhgq44n5sqdmvkpgnhf5fybmis2g3gwj10z52h7gvd"))))
(build-system gnu-build-system)
(native-inputs (list pkg-config))
(inputs (list gmp libgc pcre2 libffi readline))
(arguments
(list
#:modules `((ice-9 ftw)
,@%default-gnu-modules)
#:configure-flags
#~(list (string-append "LDFLAGS=-L"
#$(this-package-input "readline")
"/lib -lreadline"))
#:phases
#~(modify-phases %standard-phases
(add-before 'configure 'patch-sh-references
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash (which "bash")))
(substitute* "configure"
(("/bin/sh") bash)))))
(add-after 'configure 'patch-rm-references
(lambda _
(let ((rm (which "rm")))
(substitute* (find-files "." "^Makefile$")
(("/bin/rm") rm))))))))
(properties
'((release-monitoring-url . "https://stklos.net/download.html")))
(home-page "https://stklos.net")
(synopsis "R7RS Scheme with CLOS-like object system")
(description
"STklos is a free Scheme system mostly compliant with the languages
features defined in R7RS small. The aim of this implementation is to be fast
as well as light. The implementation is based on an ad-hoc Virtual
Machine. STklos can also be compiled as a library and embedded in an
application.")
(license gpl2+)))
(define-public r7rs-small-texinfo
(let ((commit "38a703976ea6353e32b52a5187dbdaf77fb2f050")
(revision "3"))
(package
(name "r7rs-small-texinfo")
(version (git-version "0.1.0" revision commit))
(home-page "https://codeberg.org/Zipheir/r7rs-small-texinfo/")
(source
(origin
(uri (git-reference
(url home-page)
(commit commit)))
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32 "1fr02fyhiwd364jkfy1n5w31pq3kx1rl5w634421g05702yb47x3"))))
(native-inputs (list bash texinfo))
(inputs '())
(build-system copy-build-system)
(arguments
(list
#:install-plan #~'(("r7rs-small.info" "share/info/"))
#:phases #~(modify-phases %standard-phases
(add-after 'unpack 'compile-the-files
(lambda _
(let* ((source-directory-path (string-append (getcwd)
"/doc/r7rs-small"))
(build-script-path (string-append
source-directory-path
"/build.sh"))
(info-directory-path (string-append #$output
"/share/info")))
(chdir source-directory-path)
(system* "bash" build-script-path "info")
(mkdir-p info-directory-path)
(copy-file (string-append source-directory-path
"/r7rs-small.info")
(string-append info-directory-path
"/r7rs-small.info"))))))))
(synopsis
"R7RS Small standard of the Scheme programming language in Info format")
(description
"Revised^7 Report of the Algorithmic Language Scheme adapted to Texinfo format.")
(license (non-copyleft "file://COPYING")))))
