diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 1832 |
1 files changed, 990 insertions, 842 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d0166cae1d..7fa31c59b4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,8 +1,8 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 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 Efraim Flashner <efraim@flashner.co.il> +;;; 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> @@ -12,8 +12,11 @@ ;;; Copyright © 2017 Alex Kost <alezost@gmail.com> ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com> ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com> +;;; Copyright © 2021 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,6 +70,7 @@ #: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 pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -74,6 +78,7 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) + #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages tcl) @@ -105,23 +110,23 @@ "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan")))) (build-system gnu-build-system) (inputs - `(("cairo" ,cairo) - ("gettext" ,gettext-minimal) - ("gsl" ,gsl) - ("libxml2" ,libxml2) - ("pango" ,pango) - ("readline" ,readline) - ("gtk" ,gtk+) - ("gtksourceview" ,gtksourceview-3) - ("spread-sheet-widget" ,spread-sheet-widget) - ("zlib" ,zlib))) + (list cairo + gettext-minimal + gsl + libxml2 + pango + readline + gtk+ + gtksourceview-3 + spread-sheet-widget + zlib)) (native-inputs - `(("autoconf" ,autoconf) ;for tests - ("glib" ,glib "bin") ;for glib-genmarshal - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python-2) ;for tests - ("texinfo" ,texinfo))) + (list autoconf ;for tests + `(,glib "bin") ;for glib-genmarshal + perl + pkg-config + python-2 ;for tests + texinfo)) (home-page "https://www.gnu.org/software/pspp/") (synopsis "Statistical analysis") (description @@ -148,8 +153,7 @@ be output in text, PostScript, PDF or HTML.") (build-system gnu-build-system) (home-page "http://mcmc-jags.sourceforge.net/") (native-inputs - `(("gfortran" ,gfortran) - ("lapack" ,lapack))) + (list gfortran lapack)) (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) @@ -190,7 +194,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.1.1") + (version "4.1.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -198,7 +202,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0r6kpnxjbvb7gdfg4m1z8zc6xd225vw81wrnf05ps9ajawk06pji")))) + "1brqmc7mmb0z94kcs4crgl6v9a6sxhm9fm3y177d81vjkxg24di0")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -215,18 +219,15 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") ;; This ensures that Guix can detect embedded store references; ;; see bug #28157 for details. (substitute* "src/library/base/makebasedb.R" - (("compress = TRUE") "compress = FALSE")) - #t)) + (("compress = TRUE") "compress = FALSE")))) (add-before 'configure 'patch-coreutils-paths (lambda* (#:key inputs #:allow-other-keys) - (let* ((coreutils (assoc-ref inputs "coreutils")) - (uname-bin (string-append coreutils "/bin/uname")) - (rm-bin (string-append coreutils "/bin/rm"))) + (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 ")))) - #t)) + (("rm -Rf ") (string-append rm-bin " -Rf ")))))) (add-after 'unpack 'build-reproducibly (lambda _ ;; The documentation contains time stamps to demonstrate @@ -285,17 +286,17 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ;; that is suspected to be the culprit. (substitute* "src/library/methods/DESCRIPTION.in" (("\\(2008\\)\n") "(2008) ") - ((" ``Software") "``Software")) - #t)) + ((" ``Software") "``Software") + (("Data Analysis:.") "Data Analysis:\n") + (("Programming with R") " Programming with R")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") - (setenv "LC_ALL" "C") - #t)) + (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") #t)) + (lambda _ (setenv "PAGER" "cat"))) (add-before 'check 'set-timezone ;; Some tests require the timezone to be set. However, the ;; timezone may not just be "UTC", or else a brittle regression @@ -303,9 +304,8 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (lambda* (#:key inputs #:allow-other-keys) (setenv "TZ" "UTC+1") (setenv "TZDIR" - (string-append (assoc-ref inputs "tzdata") - "/share/zoneinfo")) - #t)) + (search-input-directory inputs + "share/zoneinfo")))) (add-after 'build 'make-info (lambda _ (invoke "make" "info"))) (add-after 'build 'install-info @@ -345,18 +345,19 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ("perl" ,perl) ("pkg-config" ,pkg-config) ("texinfo" ,texinfo) ; for building HTML manuals - ("texlive" ,(texlive-union (list texlive-ae + ("texlive" ,(texlive-updmap.cfg (list texlive-ae texlive-inconsolata texlive-fonts-ec - texlive-amsfonts/patched + texlive-grfext + texlive-amsfonts texlive-latex-base texlive-latex-fancyvrb texlive-latex-graphics - texlive-latex-hyperref - texlive-latex-oberdiek + texlive-hyperref + texlive-oberdiek texlive-latex-tools texlive-latex-upquote - texlive-latex-url + texlive-url texlive-latex-xkeyval))) ("tzdata" ,tzdata-for-tests) ("xz" ,xz))) @@ -403,12 +404,49 @@ available, greatly increasing its breadth and scope.") (arguments `(#:tests? #f ,@(substitute-keyword-arguments (package-arguments r-with-tests) + ((#: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))))))) + `(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) + (let ((out (assoc-ref outputs "out"))) + (substitute* (string-append out "/lib/R/etc/Makeconf") + (("^# configure.*") + "# Removed to avoid extraneous references\n")) + (substitute* (string-append out "/lib/R/bin/libtool") + (((string-append + "(-L)?(" + (assoc-ref inputs "bzip2") + "|" + (assoc-ref inputs "perl") + "|" + (assoc-ref inputs "texlive") + "|" + (assoc-ref inputs "texlive-bin") + "|" + (assoc-ref inputs "texinfo") + "|" + (assoc-ref inputs "xz") + "|" + (format #false + "/gnu/store/[^-]+-(~{~a~^|~})-[^/]+" + '("glibc-utf8-locales" + "libselinux" + "libsepol" + "file" + "texlive-bin" + "util-macros" + "graphite2")) + "|" + "/gnu/store/[^-]+-glibc-[^-]+-static" + ")/lib")) "")))))))))))) (define-public rmath-standalone (package (inherit r-minimal) @@ -446,14 +484,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-54") + (version "7.3-55") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "08g8ashbcas3ac98kxvchbwc8da9dq9anpngb4arnw62npawq05q")))) + "191i1iylvh2w2hi99fnm06731lma7z5snpjknfff1m9ziyy9qab5")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -467,17 +505,17 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") (define-public r-class (package (name "r-class") - (version "7.3-19") + (version "7.3-20") (source (origin (method url-fetch) (uri (cran-uri "class" version)) (sha256 (base32 - "0dxyxk59fs90713qisanlvk4p0d3l8n8n7zdd4d5c290naaaw83q")))) + "10slys2jny4k2j8l8k97hwrwd6ryzajfnzywqpq2yc9bqxmh8nz6")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "R functions for classification") (description @@ -499,7 +537,7 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") "168l653ygkg21fwrqrf7lsqi5p6jzhgmcvhrwv7lznkdzdhag2jw")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cluster") (synopsis "Methods for cluster analysis") (description @@ -530,14 +568,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-81") + (version "0.8-82") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "0b4rca1bl8xxna05057hchbwfmgjgx0n140szabpc0raizqzks0s")))) + "1yw07yqzfm4w1h92ijyamrmf7rmkqxgamqfd74x7zv4vsn20dvgq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -561,7 +599,7 @@ for reading and writing some dBase files.") (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/KernSmooth") (synopsis "Functions for kernel smoothing") (description @@ -594,18 +632,18 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.3-4") + (version "1.4-0") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0fbcbysp3vaivmp1yasmp8mdsldhr826vfs4vyxrjpjl8jfifhmb")))) + "1xh62bwcly1blpvnagbhjym1qgw87yir3c72ylhvcla05rq67d62")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "http://Matrix.R-forge.R-project.org/") (synopsis "Sparse and dense matrix classes and methods") (description @@ -616,18 +654,18 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-153") + (version "3.1-155") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "1qw0sq64iybyidj0s8m76z4i1gxb1fn27s29i63fw5hvvy7aj9rx")))) + (base32 "0kzzpl63l298yy18x62ypgbhdw61fgm30lc4nlhjjhjj5220yfcz")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nlme") (synopsis "Linear and nonlinear mixed effects models") (description @@ -638,17 +676,16 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-37") + (version "1.8-38") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "14gw714xcyvgrbajijmyd4v8zs84i701g7gyld6z8p7677dgc8w8")))) + (base32 "1fyx8b0xjyx75mp90v314gayzydkca5y90p76jnwxzfnhxbys4nd")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme))) + (list r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/mgcv") (synopsis "Mixed generalised additive model computation") (description @@ -661,14 +698,14 @@ distributions beyond the exponential family.") (define-public r-nnet (package (name "r-nnet") - (version "7.3-16") + (version "7.3-17") (source (origin (method url-fetch) (uri (cran-uri "nnet" version)) (sha256 (base32 - "0smmyx4vhlz99vy4w238y913gq74845v0l1p0g1kgydsp9lijlcr")))) + "0rws3rkd7dz1maz2mkld29jfrixjgacay8rqz7nmi82a2sw0nxgf")))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Feed-forward neural networks and multinomial log-linear models") @@ -699,14 +736,14 @@ classification, regression and survival trees.") (define-public r-spatial (package (name "r-spatial") - (version "7.3-14") + (version "7.3-15") (source (origin (method url-fetch) (uri (cran-uri "spatial" version)) (sha256 (base32 - "0dlafq744mahxpb13llmsrg54fzww8ld1nbxmr7m851gff11kk2j")))) + "1vwc7ingskdj1k4nq418x9yl3cw699pckb9xh5a1yp3g9plknqg5")))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Functions for kriging and point pattern analysis") @@ -729,7 +766,7 @@ analysis.") "0zrikancm9shixvgng89f1610sphlwljczi0fnjbdqn4l85rrarz")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://github.com/therneau/survival") (synopsis "Survival analysis") (description @@ -745,22 +782,22 @@ curves, Cox models, and parametric accelerated failure time models.") (build-system trivial-build-system) (arguments '(#:builder (begin (mkdir %output) #t))) (propagated-inputs - `(("r-minimal" ,r-minimal) - ("r-boot" ,r-boot) - ("r-class" ,r-class) - ("r-cluster" ,r-cluster) - ("r-codetools" ,r-codetools) - ("r-foreign" ,r-foreign) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-nlme" ,r-nlme) - ("r-nnet" ,r-nnet) - ("r-rpart" ,r-rpart) - ("r-spatial" ,r-spatial) - ("r-survival" ,r-survival))))) + (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 @@ -775,7 +812,7 @@ curves, Cox models, and parametric accelerated failure time models.") "0s7isadibxp2wr62r5cpbyh9z31sczzfz4j3rm7gxgjfpqgq8174")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://ff.r-forge.r-project.org") (synopsis "Class for vectors of 1-bit booleans") (description @@ -798,7 +835,7 @@ binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5")))) (build-system r-build-system) (propagated-inputs - `(("r-bit" ,r-bit))) + (list r-bit)) (home-page "http://ff.r-forge.r-project.org/") (synopsis "S3 class for vectors of 64 bit integers") (description @@ -811,6 +848,58 @@ 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") @@ -832,13 +921,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.28") + (version "0.6.29") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "006vqwfrry84xn51lxlfalzn9yqr1k81s39r0zy251azx5sqqcja")))) + (base32 "1ncwc5fwsylwlcp9vhkhszw8m5sifg74apig2m2pf168lha1yb3r")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -910,7 +999,7 @@ algorithms.") (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/magrittr/index.html") - (synopsis "A forward-pipe operator for R") + (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 @@ -931,7 +1020,7 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh")))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace))) + (list r-colorspace)) (home-page "https://cran.r-project.org/web/packages/munsell") (synopsis "Munsell colour system") (description @@ -973,7 +1062,7 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (sha256 (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "http://had.co.nz/plyr") (synopsis "Tools for Splitting, Applying and Combining Data") (description @@ -1035,7 +1124,7 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org") (properties `((upstream-name . "sendmailR"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc))) + (list r-base64enc)) (home-page "https://cran.r-project.org/web/packages/sendmailR") (synopsis "Send email using R") @@ -1047,17 +1136,17 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.7.4") + (version "1.7.6") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1mda4612sc573zabsvygnla3vpnf3mql58fc9j450540h6hlwfv2")))) + "1v0rj5svgvn1mlf69yzm6jm00fxmrsxazs9xymzrf0apxjpxb8qf")))) (build-system r-build-system) - (inputs `(("icu4c" ,icu4c))) - (native-inputs `(("pkg-config" ,pkg-config))) + (inputs (list icu4c)) + (native-inputs (list pkg-config)) (home-page "http://stringi.rexamine.com/") (synopsis "Character string processing facilities") (description @@ -1082,9 +1171,7 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47")))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-stringi" ,r-stringi))) + (list r-glue r-magrittr r-stringi)) (home-page "https://github.com/hadley/stringr") (synopsis "Simple, consistent wrappers for common string operations") (description @@ -1107,9 +1194,7 @@ the input of another.") (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq")))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr))) + (list r-plyr r-rcpp r-stringr)) (home-page "https://github.com/hadley/reshape") (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package") (description @@ -1129,21 +1214,21 @@ using just two functions: melt and dcast (or acast).") (base32 "1si46bf9p09qzs208hqffwcb40305p361whmwhc1pwrsmx7jjxdh")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-glue" ,r-glue) - ("r-gtable" ,r-gtable) - ("r-isoband" ,r-isoband) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-tibble" ,r-tibble) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-svglite" ,r-svglite) ; Needed for 'ggsave' - ("r-withr" ,r-withr))) + (list r-digest + r-glue + r-gtable + r-isoband + r-mass + r-mgcv + r-tibble + r-rlang + r-scales + r-svglite ; Needed for 'ggsave' + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://ggplot2.tidyverse.org") - (synopsis "An implementation of the grammar of graphics") + (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 @@ -1165,10 +1250,9 @@ aesthetic attributes.") "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-mass" ,r-mass))) + (list r-ggplot2 r-mass)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/andrie/ggdendro") (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2") (description "This is a set of tools for dendrograms and tree plots using @@ -1193,14 +1277,11 @@ agnes cluster diagrams.") "1p3ip0qwpg8f63jfx0b8vbac6l20ddid8xvxzkfi6i858pybnawp")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("cairo" ,cairo) - ("freetype2" ,freetype) - ("zlib" ,zlib))) + (list cairo freetype zlib)) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-systemfonts" ,r-systemfonts))) + (list r-rcpp r-systemfonts)) (home-page "https://cran.r-project.org/web/packages/gdtools") (synopsis "Utilities for graphical rendering") (description @@ -1221,13 +1302,11 @@ and to generate base64 encoded string from raster matrix.") "19ggknw5322yw7r1bzhw0bqggcrpn0qxddk7kblpqnra2zz2brkn")))) (build-system r-build-system) (inputs - `(("libpng" ,libpng) - ("zlib" ,zlib))) + (list libpng zlib)) (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-systemfonts" ,r-systemfonts))) + (list r-cpp11 r-systemfonts)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/svglite") (synopsis "SVG graphics device") (description @@ -1278,16 +1357,16 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "0i0kfyg43nryyka2bjlgz4x75w965224qp36wz1hl7a2lswb6ajp")))) + "0n2gf5flmcrkad7p0pzsnsgwjl5006yi7lyz9lisqxhw8xykgv2n")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") (description @@ -1300,13 +1379,13 @@ R/DBMS implementations.") (define-public r-bh (package (name "r-bh") - (version "1.75.0-0") + (version "1.78.0-0") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "0nkgvl5qjs2a7jv0ncsrl4fqaw2pdaj7a1pncdv6kp874sci0k5f")))) + "1cwc1q8w9d6i81nclgi7lycsnpj0dcbxlv9rdb0f04r0d03rv7iv")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") @@ -1347,7 +1426,7 @@ adapted for other output formats, such as HTML or LaTeX.") "0353aj975mj0yjc91z76bbfy86y7d5cvlqqyfr93cdng14nnd0dx")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://yihui.org/formatr/") (synopsis "Format R code automatically") (description @@ -1369,7 +1448,7 @@ There is also a Shiny app as a user interface in this package.") "0kgdv2vf1lz3b5kbal9s83gg6812nw7fvrq0rkyr0v4k1lwi3zxy")))) (build-system r-build-system) (propagated-inputs - `(("r-xfun" ,r-xfun))) + (list r-xfun)) ;; We cannot add knitr to the inputs, because highr depends on xfun, which ;; is an input to knitr. #; @@ -1386,13 +1465,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.11") + (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "1h7fz0rqnp970r9q0d95qcxpxm9mb98rqhcdncx0w2qdkyj2fm11")))) + "0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") @@ -1418,8 +1497,7 @@ data derived from /etc/mime.types in UNIX-type systems.") ;; package. (arguments `(#:tests? #f)) (propagated-inputs - `(("r-mime" ,r-mime) - ("r-xfun" ,r-xfun))) + (list r-mime r-xfun)) (home-page "https://github.com/rstudio/markdown") (synopsis "Markdown rendering for R") (description @@ -1449,20 +1527,16 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.34") + (version "1.37") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "0p6jdicyqknrqilcjm2h4r6vza5lpzccnsdirj92jb3ljg10b0by")))) + "0qyp78v3hz4qimlc3w4hj5dzp44n2w085ay0l1zvxsxs9142mk9r")))) (build-system r-build-system) (propagated-inputs - `(("r-evaluate" ,r-evaluate) - ("r-highr" ,r-highr) - ("r-stringr" ,r-stringr) - ("r-xfun" ,r-xfun) - ("r-yaml" ,r-yaml))) + (list r-evaluate r-highr r-stringr r-xfun r-yaml)) (home-page "https://yihui.org/knitr/") (synopsis "General-purpose package for dynamic report generation in R") (description @@ -1487,9 +1561,7 @@ generation in R using Literate Programming techniques.") (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-markdown" ,r-markdown))) + (list r-knitr r-rmarkdown r-markdown)) (home-page "https://github.com/jimhester/knitrBootstrap") (synopsis "Knitr bootstrap framework") (description @@ -1500,13 +1572,13 @@ from knitr Rmarkdown.") (define-public r-microbenchmark (package (name "r-microbenchmark") - (version "1.4-7") + (version "1.4.9") (source (origin (method url-fetch) (uri (cran-uri "microbenchmark" version)) (sha256 (base32 - "1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6")))) + "1lpzpffnjiwnxxl0jhrvyj88fvxqksnpccbpq953xwqf6ypjqga4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/microbenchmark/") (synopsis "Accurate timing functions for R") @@ -1527,10 +1599,7 @@ the execution time of R expressions.") "02vp1y7zhv22id43j5c0gdcgn9171dyypqp8rqrlc3w5a7n565kv")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-lobstr" ,r-lobstr) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr))) + (list r-codetools r-lobstr r-rcpp r-stringr)) (home-page "https://github.com/hadley/pryr") (synopsis "Tools for computing on the R language") (description @@ -1541,17 +1610,16 @@ understand the language at a deeper level.") (define-public r-memoise (package (name "r-memoise") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "memoise" version)) (sha256 (base32 - "1bzcv7pmls3bx2w5ccv1pm20wycbfqba1v76k0fjgmjsm6hy76pz")))) + "1srdzv2bp0splislrabmf1sfbqfi3hn189nq7kxhgjn8k3p38l7q")))) (build-system r-build-system) (propagated-inputs - `(("r-cachem" ,r-cachem) - ("r-rlang" ,r-rlang))) + (list r-cachem r-rlang)) (home-page "https://github.com/hadley/memoise") (synopsis "Memoise functions for R") (description @@ -1562,13 +1630,13 @@ you call it again with the same arguments it returns the pre-computed value.") (define-public r-crayon (package (name "r-crayon") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "crayon" version)) (sha256 (base32 - "1ir963s6zk9l32fw257y54p7898cd7z7yazkn9h6j2cdfhpf9dh8")))) + "0mxq87qsvz5znfncrb6yjchzv6iwpn9lr386i02y6xiycizkjd7f")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/crayon") (synopsis "Colored terminal output for R") @@ -1602,36 +1670,36 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.0.4") + (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "0iqizv2gpv9fg766qv8hbkmc6c5i9xcfrmq9k5m2550p28zff2w3")))) + "0ndnmv3gbhlsyqya382wqfkkhlrgpdjmh7mymsv6ja52ihbachgd")))) (build-system r-build-system) (propagated-inputs - `(("r-brio" ,r-brio) - ("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-ellipsis" ,r-ellipsis) - ("r-evaluate" ,r-evaluate) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-pkgload" ,r-pkgload) - ("r-praise" ,r-praise) - ("r-processx" ,r-processx) - ("r-ps" ,r-ps) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-waldo" ,r-waldo) - ("r-withr" ,r-withr))) + (list r-brio + r-callr + r-cli + r-crayon + r-desc + r-digest + r-ellipsis + 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 - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/testthat") (synopsis "Unit testing for R") (description @@ -1664,13 +1732,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.4.11") + (version "0.4.12") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "1pfm24jjkxzdb5qcbc05dcjxyk69zpfr5jv4xakqh1xh41mr43kl")))) + "05cr08smr8dlk10m810rw4qi1yhgnny83rwkxib0l4my71br29ia")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1682,26 +1750,26 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.1.4") + (version "3.1.6") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "0zqpg2haph0qi1x5r6wr083xckab9gw21jbr9spcr8xdf43hx1vk")))) + "14l2i6ri3v5y0h8g0ahc4kz0pdqsp5yabxk2w8wavss6y44xjcsv")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-fansi" ,r-fansi) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-pkgconfig" ,r-pkgconfig) - ("r-pillar" ,r-pillar) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs))) + (list r-ellipsis + r-fansi + r-lifecycle + r-magrittr + r-pkgconfig + r-pillar + r-rlang + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") (description @@ -1721,23 +1789,23 @@ and printing capabilities than traditional data frames.") "0g8jsxclj9cgm7a2lyazy78sj62rbzw812lsw3fdsbz0pknkmznj")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-pillar" ,r-pillar) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-ellipsis + r-generics + r-glue + r-lifecycle + r-magrittr + r-pillar + r-r6 + r-rlang + r-tibble + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/dplyr") (synopsis "Tools for working with data frames in R") (description - "dplyr is the next iteration of plyr. It is focussed on tools for + "dplyr is the next iteration of plyr. It is focused on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key @@ -1759,23 +1827,23 @@ database.") "025wqpmxdhzblb0pf58m3qh5h6bf5x8qvkf47vyl1cjsp13wz95b")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-blob" ,r-blob) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) + (list r-assertthat + r-blob + r-dbi + r-dplyr + r-ellipsis + r-glue + r-lifecycle + r-magrittr + r-purrr + r-r6 + r-rlang + r-tibble + r-tidyselect + r-vctrs + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/dbplyr") (synopsis "Dplyr back end for databases") (description @@ -1798,7 +1866,7 @@ features require SQL translation to be provided by the package author.") "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2")))) (build-system r-build-system) (inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/acepack") (synopsis "Functions for regression transformations") (description @@ -1841,7 +1909,7 @@ side.") "1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/locfit") (synopsis "Local regression, likelihood and density estimation") (description @@ -1870,19 +1938,18 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0kgbvap5v2spnkz3dwfm4jh4qcpvbzdn9s8bzfnhzabz9qjdxw8k")))) + "0arx5wna0sh0vf5q8rjhh8nqdmnvg2pdpbhljl9l0x4kwm8vjhgp")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") (description @@ -1905,7 +1972,7 @@ and fast file reading.") "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "http://xtable.r-forge.r-project.org/") (synopsis "Export R tables to LaTeX or HTML") (description @@ -1915,25 +1982,24 @@ and fast file reading.") (define-public python-patsy (package (name "python-patsy") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (pypi-uri "patsy" version)) (sha256 (base32 - "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi")))) + "17dn72519gvwifw3i8mzwlslxmxkl8ihzfrxg1iblsk70iwdwlsh")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (invoke "nosetests" "-v")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? (invoke "pytest" "-vv"))))))) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-six" ,python-six))) + (list python-numpy python-scipy python-six)) (native-inputs - `(("python-nose" ,python-nose))) + (list python-pytest)) (home-page "https://github.com/pydata/patsy") (synopsis "Describe statistical models and build design matrices") (description @@ -1950,14 +2016,17 @@ building design matrices.") (define-public python-statsmodels (package (name "python-statsmodels") - (version "0.11.1") + (version "0.13.1") (source (origin (method url-fetch) (uri (pypi-uri "statsmodels" version)) (sha256 - (base32 - "1w6mf8b86vizi2895j11szqryr2v1ckjig3wp9fv94aslfh3zpjv")))) + (base32 "0sbsyxgpzhys5padhkhrj71z4i1q41sm938pz0x8ff6jjvcchvh0")) + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file (find-files "." "\\.c$")))))) (build-system python-build-system) (arguments `(;; The test suite is very large and rather brittle. Tests often fail @@ -1978,15 +2047,10 @@ building design matrices.") line))) #t))))) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-pandas" ,python-pandas) - ("python-patsy" ,python-patsy) - ("python-matplotlib" ,python-matplotlib))) + (list python-numpy python-scipy python-pandas python-patsy + python-matplotlib)) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx))) + (list python-cython python-nose python-sphinx)) (home-page "http://statsmodels.sourceforge.net/") (synopsis "Statistical modeling and econometrics in Python") (description @@ -1998,6 +2062,16 @@ inference for statistical models.") (define-public python2-statsmodels (let ((stats (package-with-python2 python-statsmodels))) (package/inherit stats + ;; Version 0.11.1 and later does not work with Python 2. It may build + ;; fine but loading modules fails. + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "statsmodels" version)) + (sha256 + (base32 + "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4")))) (propagated-inputs `(("python2-pytz" ,python2-pytz) ("python2-numpy" ,python2-numpy) @@ -2018,7 +2092,7 @@ inference for statistical models.") "13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/coda") (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") (description "This package provides functions for summarizing and plotting @@ -2040,9 +2114,7 @@ chain.") "09f5kh2mwygqpnvf53k0r54k0cvaafxm9x4nm819gwv05k2g9dpc")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-pixmap" ,r-pixmap) - ("r-sp" ,r-sp))) + (list r-mass r-pixmap r-sp)) (home-page "http://pbil.univ-lyon1.fr/ADE-4") (synopsis "Multivariate data analysis and graphical display") (description @@ -2053,21 +2125,19 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz")))) + "138w7hb487al9cbahmnk5rhi23k8a9g7nk7s5dyxd3k1646rqknb")))) (build-system r-build-system) (inputs - `(("libxml2" ,libxml2) - ("zlib" ,zlib))) + (list libxml2 zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/hadley/xml2") (synopsis "Parse XML with R") (description @@ -2088,7 +2158,7 @@ files in R. It is built on top of the libxml2 C library.") "1gm3wr8xqpqiby7q1dr3zxim77v0bvvrqi0hlazf5g3gnkrp2zc3")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://github.com/wesleyburr/multitaper/") (synopsis "Multitaper spectral analysis tools") (description @@ -2113,8 +2183,7 @@ jackknifed confidence intervals are available for most estimates.") "1cbwwbz8lqx2n33xr4q904whvld22s63rpyy1nn93395l7ssrakr")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-xml2" ,r-xml2))) + (list r-curl r-xml2)) (home-page "https://github.com/metacran/rversions") (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") (description @@ -2144,14 +2213,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.2.1") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "1mf2nz78l97lbxyagv55bcxrny51ds8g28h307cfa1g3ayylp0x2")))) + "0x144hij0rzhrxdq3k5ph8fk7pdgl1avjca25j4mlpmhzdckqp44")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") @@ -2177,7 +2246,7 @@ R version.") "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports))) + (list r-backports)) (home-page "https://github.com/mllg/checkmate") (synopsis "Fast and versatile argument checks") (description @@ -2200,7 +2269,7 @@ worries about execution time overhead.") (properties `((upstream-name . "BBmisc"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate))) + (list r-checkmate)) (home-page "https://github.com/berndbischl/BBmisc") (synopsis "Miscellaneous functions for R package development") (description @@ -2221,8 +2290,7 @@ of R packages.") "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d")))) (build-system r-build-system) (propagated-inputs - `(("r-bbmisc" ,r-bbmisc) - ("r-checkmate" ,r-checkmate))) + (list r-bbmisc r-checkmate)) (home-page "https://github.com/mllg/fail") (synopsis "File abstraction interface layer (FAIL)") (description @@ -2244,16 +2312,16 @@ or source files in a key-value fashion.") (properties `((upstream-name . "BatchJobs"))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-bbmisc" ,r-bbmisc) - ("r-brew" ,r-brew) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-rsqlite" ,r-rsqlite) - ("r-sendmailr" ,r-sendmailr) - ("r-stringi" ,r-stringi))) + (list r-backports + r-bbmisc + r-brew + r-checkmate + r-data-table + r-dbi + r-digest + r-rsqlite + r-sendmailr + r-stringi)) (home-page "https://github.com/tudo-r/BatchJobs") (synopsis "Batch computing with R") (description @@ -2284,19 +2352,17 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "1sw4vya3l971gpccq4gnjywgbl73bgx8la18l0wy617qv94f905y")))) + "0jfnwn1kpiill8v4hmzdk90yz4gk2ha0prr2p0hq36s40v3y8842")))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-r6" ,r-r6) - ("r-rprojroot" ,r-rprojroot))) + (list r-crayon r-r6 r-rprojroot)) (home-page "https://github.com/r-pkgs/desc") (synopsis "Manipulate DESCRIPTION Files") (description @@ -2340,21 +2406,21 @@ tables, autolinks and strikethrough text.") "1zf55wywlpy7mk7zfyi3s9fhhg1m9kvafzj46iqw5cbvnlg3ssdk")))) (build-system r-build-system) (propagated-inputs - `(("r-brew" ,r-brew) - ("r-commonmark" ,r-commonmark) - ("r-cpp11" ,r-cpp11) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-knitr" ,r-knitr) - ("r-pkgload" ,r-pkgload) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-xml2" ,r-xml2))) + (list r-brew + r-commonmark + r-cpp11 + r-desc + r-digest + r-knitr + r-pkgload + r-purrr + r-r6 + r-rlang + r-stringi + r-stringr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description @@ -2365,22 +2431,30 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.4.5") + (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1xy1w0rljzsgvsg91fh9hs6h9rx58mza1vg6rig9ykp9m2ml3hag")))) + "0na3yficxg0hjql9pvz96f66yh4g5k2hfwcricb705z7f2pk5f23")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'do-not-use-versioned-linking + (lambda _ + (substitute* "configure" + (("PKG_LIBS=\"\\$\\{PKG_LIBS_VERSIONED\\}\"") + "PKG_LIBS=\"${PKG_LIBS}\""))))))) (inputs - `(("libressl" ,libressl))) + (list openssl)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (propagated-inputs - `(("r-askpass" ,r-askpass))) + (list r-askpass)) (home-page "https://github.com/jeroenooms/openssl") (synopsis "Toolkit for encryption, signatures and certificates") (description @@ -2408,13 +2482,9 @@ integers.") "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite) - ("r-openssl" ,r-openssl) - ("r-mime" ,r-mime) - ("r-r6" ,r-r6))) + (list r-curl r-jsonlite r-openssl r-mime r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/httr") (synopsis "Tools for working with URLs and HTTP") (description @@ -2427,19 +2497,18 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.28.0") + (version "0.29.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "1wjmbs9cmm16pm3g0rmqp7cxxyh95m5lgx4fx5bpgj6j466i8vff")))) + "13nlrhma6kavvhranb43w3003vadfkyrn2f4l3r63iqavj0s3xzq")))) (build-system r-build-system) (inputs - `(("libgit2" ,libgit2) - ("zlib" ,zlib))) + (list libgit2 zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/ropensci/git2r") (synopsis "Access Git repositories with R") (description @@ -2460,7 +2529,7 @@ pure C implementation of the Git core methods.") "12vdfzzjc6mv4h105l8cp108j3hjk0mqmg23m6mqr3jarfymphxa")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") (description @@ -2471,37 +2540,37 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "01cg2ykg0av6z7bgl41njcxcii8vjj8ipch26xazp4yjai8abw3i")))) + "0kvbw218jp8pd2lgdjyn94v2iji75s385hkn1qbikcm0pjlmj8g4")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-desc" ,r-desc) - ("r-ellipsis" ,r-ellipsis) - ("r-fs" ,r-fs) - ("r-httr" ,r-httr) - ("r-lifecycle" ,r-lifecycle) - ("r-memoise" ,r-memoise) - ("r-pkgbuild" ,r-pkgbuild) - ("r-pkgload" ,r-pkgload) - ("r-rcmdcheck" ,r-rcmdcheck) - ("r-remotes" ,r-remotes) - ("r-rlang" ,r-rlang) - ("r-roxygen2" ,r-roxygen2) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rversions" ,r-rversions) - ("r-sessioninfo" ,r-sessioninfo) - ("r-testthat" ,r-testthat) - ("r-usethis" ,r-usethis) - ("r-withr" ,r-withr))) + (list r-callr + r-cli + r-desc + r-ellipsis + r-fs + r-httr + r-lifecycle + r-memoise + r-pkgbuild + r-pkgload + r-rcmdcheck + r-remotes + r-rlang + r-roxygen2 + r-rstudioapi + r-rversions + r-sessioninfo + r-testthat + r-usethis + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/devtools") (synopsis "Tools to make developing R packages easier") (description "The devtools package is a collection of package development @@ -2511,16 +2580,16 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "1j5srffi748yxphwli56lkbh4cga0kmz38dyzganzkw0nx66mya8")))) + "0k4x2bd9wb24n3dyg7rdjicdjs5ay2kk5lfgkrcjsv6cki2wgnlv")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") (description @@ -2542,11 +2611,7 @@ were originally a part of the r-devtools package.") "0qlh4s1g9rbm6c3s906dhw3xsz28m8fg6cyynlkhvis533dk0pvb")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-lifecycle" ,r-lifecycle) - ("r-pkgconfig" ,r-pkgconfig) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs))) + (list r-ellipsis r-lifecycle r-pkgconfig r-rlang r-vctrs)) (home-page "https://github.com/rstats-db/hms") (synopsis "Pretty time of day") (description @@ -2557,28 +2622,28 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "2.0.1") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "0cj5k3ykkhixgdsqm1gnmpc0d8z04l3fhvm2dr5xp7cpmhgsrpfr")))) + "115w3hgp1w6hr0h2nz840i6mm1pnqzwfbxcmf9ca3qs7llc7k4q3")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-clipr" ,r-clipr) - ("r-cpp11" ,r-cpp11) - ("r-crayon" ,r-crayon) - ("r-hms" ,r-hms) - ("r-lifecycle" ,r-lifecycle) - ("r-tibble" ,r-tibble) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-tzdb" ,r-tzdb) - ("r-vroom" ,r-vroom))) + (list r-cli + r-clipr + r-cpp11 + r-crayon + r-hms + r-lifecycle + r-tibble + r-r6 + r-rlang + r-tzdb + r-vroom)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/readr") (synopsis "Read tabular data") (description @@ -2635,10 +2700,7 @@ scaling functions for R.") (properties `((upstream-name . "latticeExtra"))) (build-system r-build-system) (propagated-inputs - `(("r-jpeg" ,r-jpeg) - ("r-lattice" ,r-lattice) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-jpeg r-lattice r-png r-rcolorbrewer)) (home-page "http://latticeextra.r-forge.r-project.org/") (synopsis "Extra graphical utilities based on lattice") (description @@ -2650,17 +2712,17 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.6.0.0") + (version "0.10.7.5.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v")))) + "0516j6n657kxm8sdbxf3jd9z40px9mv7zza4fz8nih63f5iiw1kw")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/RcppCore/RcppArmadillo") (synopsis "Rcpp integration for the Armadillo linear algebra library") (description @@ -2706,7 +2768,7 @@ vectors.") (properties `((upstream-name . "caTools"))) (build-system r-build-system) (propagated-inputs - `(("r-bitops" ,r-bitops))) + (list r-bitops)) (home-page "https://cran.r-project.org/web/packages/caTools") (synopsis "Various tools including functions for moving window statistics") (description @@ -2729,7 +2791,7 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") "07wy07yhms8zln9qb0iwx69dq08h4lrdi8kavjcplfxcskq638az")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/krlmlr/rprojroot") (synopsis "Finding files in project subdirectories") (description @@ -2752,19 +2814,18 @@ certain criterion, e.g., it contains a certain regular file.") (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs - `(("r-evaluate" ,r-evaluate) - ("r-htmltools" ,r-htmltools) - ("r-jquerylib" ,r-jquerylib) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-stringr" ,r-stringr) - ("r-tinytex" ,r-tinytex) - ("r-xfun" ,r-xfun) - ("r-yaml" ,r-yaml) - ("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc))) + (list r-evaluate + r-htmltools + r-jquerylib + r-jsonlite + r-knitr + r-stringr + r-tinytex + r-xfun + r-yaml + pandoc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rmarkdown.rstudio.com") (synopsis "Convert R Markdown documents into a variety of formats") (description @@ -2804,9 +2865,9 @@ variety of formats.") (properties `((upstream-name . "gridExtra"))) (build-system r-build-system) (propagated-inputs - `(("r-gtable" ,r-gtable))) + (list r-gtable)) (native-inputs - `(("r-knitr" ,r-knitr))) ;for building vignettes + (list r-knitr)) ;for building vignettes (home-page "https://github.com/baptiste/gridextra") (synopsis "Miscellaneous functions for \"Grid\" graphics") (description @@ -2845,8 +2906,7 @@ that package, other packages are unaffected.") "1yn7f13icaix0apxp4drnciwdn8bx8xmbd129jd7ck4rcly0axj9")))) (build-system r-build-system) (propagated-inputs - `(("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs))) + (list r-rlang r-vctrs)) (home-page "https://github.com/hadley/blob") (synopsis "Simple S3 Class for representing vectors of binary data") (description "Raw vectors in R are useful for storing a single binary @@ -2858,25 +2918,25 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.8") + (version "2.2.9") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "1hscgi11px9hq0sx78c2lkfzq121rlvmhxmqf305xg6lgqdxr2hv")))) + "075vsnbkcwpwnn87b06mhbg2fflqhjvbylhbkg0d3v3rl7zg28s4")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs - `(("r-dbi" ,r-dbi) - ("r-memoise" ,r-memoise) - ("r-plogr" ,r-plogr) - ("r-rcpp" ,r-rcpp) - ("r-bit64" ,r-bit64) - ("r-blob" ,r-blob) - ("r-pkgconfig" ,r-pkgconfig))) + (list r-dbi + r-memoise + r-plogr + r-rcpp + r-bit64 + r-blob + r-pkgconfig)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description @@ -2914,7 +2974,7 @@ if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) } (inputs `(("libcurl" ,curl))) (propagated-inputs - `(("r-bitops" ,r-bitops))) + (list r-bitops)) (home-page "http://www.omegahat.net/RCurl") (synopsis "General network client interface for R") (description @@ -2942,10 +3002,9 @@ ldap, and also supports cookies, redirects, authentication, etc.") `((upstream-name . "XML"))) (build-system r-build-system) (inputs - `(("libxml2" ,libxml2) - ("zlib" ,zlib))) + (list libxml2 zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.omegahat.net/RSXML") (synopsis "Tools for parsing and generating XML within R") (description @@ -2995,7 +3054,7 @@ plotted and compared with the asymptotic curve.") (properties `((upstream-name . "lambda.r"))) (build-system r-build-system) (propagated-inputs - `(("r-formatr" ,r-formatr))) + (list r-formatr)) (home-page "https://cran.r-project.org/web/packages/lambda.r") (synopsis "Functional programming extension for R") (description @@ -3040,8 +3099,7 @@ options defined in other packages.") (properties `((upstream-name . "futile.logger"))) (build-system r-build-system) (propagated-inputs - `(("r-futile-options" ,r-futile-options) - ("r-lambda-r" ,r-lambda-r))) + (list r-futile-options r-lambda-r)) (home-page "https://cran.r-project.org/web/packages/futile.logger") (synopsis "Logging utility for R") (description @@ -3074,13 +3132,13 @@ multiple breakpoints are allowed.") (define-public r-snow (package (name "r-snow") - (version "0.4-3") + (version "0.4-4") (source (origin (method url-fetch) (uri (cran-uri "snow" version)) (sha256 (base32 - "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5")))) + "1j8kvf3imxijsqkdjz4i9s7qggfxqrpas46y5wz6za92y937yn44")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/snow") (synopsis "Support for simple parallel computing in R") @@ -3105,7 +3163,7 @@ worker processes and collect and return the results on the master.") (properties `((upstream-name . "SparseM"))) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (build-system r-build-system) (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html") (synopsis "Sparse linear algebra") @@ -3148,10 +3206,9 @@ data.") "1qb83b1jvpmk8d6kfibkm5q2hiki0x5gipy758mwa62n56gdcnpv")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-iterators" ,r-iterators))) + (list r-codetools r-iterators)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/foreach") (synopsis "Foreach looping construct for R") (description @@ -3179,8 +3236,7 @@ parallel.") (properties `((upstream-name . "doParallel"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators))) + (list r-foreach r-iterators)) (home-page "https://cran.r-project.org/web/packages/doParallel") (synopsis "Foreach parallel adaptor for the 'parallel' package") (description @@ -3202,8 +3258,7 @@ using the parallel package.") (properties `((upstream-name . "doMC"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators))) + (list r-foreach r-iterators)) (home-page "https://cran.r-project.org/web/packages/doMC") (synopsis "Foreach parallel adaptor for the 'parallel' package") (description @@ -3231,7 +3286,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/1.10.20/js/dataTables.semanticui.js" "1477f49xyxs4phias789mbspv23w8alxchhl5b5iy0aw6vd35c43" "datatables") - + ("https://cdn.datatables.net/autofill/2.3.4/js/dataTables.autoFill.js" "04i6n7r3512gzfihl5wnhrvm0klnjp41g1z6cny3j803hvmnp8zk" "datatables-extensions/AutoFill") @@ -3310,7 +3365,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/colreorder/1.5.2/js/colReorder.jqueryui.js" "1rd8hijz3prg2y36fvqczrpdzixibjy2dxgs2fmgr8wrm8k01rrm" "datatables-extensions/ColReorder") - + ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/dataTables.fixedColumns.js" "0vsqk2fv59n351bdfcbvhmvpq38qwf41j1cn810xz1l1i07cg4hg" "datatables-extensions/FixedColumns") @@ -3329,7 +3384,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/fixedColumns.semanticui.js" "1kqsap9y0d25a7m5zjakipifl5qi2qr72kfj4ap3zxavd8md2wyn" "datatables-extensions/FixedColumns") - + ("https://cdn.datatables.net/fixedheader/3.1.6/js/dataTables.fixedHeader.js" "1ml5ilnm8nirr6rsgmzn75l1k0hcjz3sqk6h1y1gy8cpwpklvqri" "datatables-extensions/FixedHeader") @@ -3348,7 +3403,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/fixedheader/3.1.6/js/fixedHeader.semanticui.js" "1v0i6dc68h8l8673fb5970igzkl7as36riv504iyg82glfi7n877" "datatables-extensions/FixedHeader") - + ("https://cdn.datatables.net/keytable/2.5.1/js/dataTables.keyTable.js" "16iib2icxsjh93x5hd42gpsl7bzpcsqb7zjgj0m1s02ls45bdlv5" "datatables-extensions/KeyTable") @@ -3386,7 +3441,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/responsive/2.2.3/js/responsive.bootstrap4.js" "1zjh15p7n1038sggaxv1xvcwbkhw2nk1ndx745s6cxiqb69y3i0h" "datatables-extensions/Responsive") - + ("https://cdn.datatables.net/rowgroup/1.1.1/js/dataTables.rowGroup.js" "0s4q7ir2d6q36g29nn9mqk7vrqrdig2mm5zbcv0sn2lixqi29pkj" "datatables-extensions/RowGroup") @@ -3424,7 +3479,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/rowreorder/1.2.6/js/rowReorder.semanticui.js" "1zjrx2rlgw3qannsqa88pcp3i4pc87pwv7rmgfw1dar8namkr9kk" "datatables-extensions/RowReorder") - + ("https://cdn.datatables.net/scroller/2.0.1/js/dataTables.scroller.js" "0zfjjdvwwlsnps24i9l4c97hmway2qs6addks1is5bxl4k1r6d16" "datatables-extensions/Scroller") @@ -3443,7 +3498,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/scroller/2.0.1/js/scroller.semanticui.js" "1dfbblbzbryjgiv31qfdjnijz19lmyijg12win3y8gsgfd4fp9zz" "datatables-extensions/Scroller") - + ("https://cdn.datatables.net/searchbuilder/1.0.0/js/dataTables.searchBuilder.js" "0n5g0j0yfzqvdpsmwb27bj1rd8zx864fsx2k7b2kpv6mqqavzpqc" "datatables-extensions/SearchBuilder") @@ -3478,7 +3533,7 @@ using the multicore functionality of the parallel package.") ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.semanticui.js" "1781d0xmx7xz0jly0wsw2zbrdmfc1crahmcdbsfbj5s66kdsnd7c" "datatables-extensions/SearchPanes") - + ("https://cdn.datatables.net/select/1.3.1/js/dataTables.select.js" "0a7bkbz1cizhiq4h417b4rcdr7998pn8q4dlyzx8449xdp0h0n0v" "datatables-extensions/Select") @@ -3499,13 +3554,13 @@ using the multicore functionality of the parallel package.") "datatables-extensions/Select")))) (package (name "r-dt") - (version "0.19") + (version "0.20") (source (origin (method url-fetch) (uri (cran-uri "DT" version)) (sha256 (base32 - "04rv1rprqlc56hycxpqkbmwmq4wjvmanq2lwxrflmf2s46pbv9ms")) + "17xs18i439p15agyk7z2xyyrwgrpn5pw09kd3jwxn7qhxi4pyvf6")) (modules '((guix build utils))) (snippet '(for-each delete-file @@ -3531,7 +3586,7 @@ using the multicore functionality of the parallel package.") ((url hash dir) (let* ((input (string-append "js:" (basename url))) (source (assoc-ref inputs input)) - (target (string-append dir "/" + (target (string-append dir "/js/" (basename url ".js") ".min.js"))) (mkdir-p dir) @@ -3553,15 +3608,15 @@ using the multicore functionality of the parallel package.") (string-append (assoc-ref inputs "js-selectize") "/share/javascript/selectize.min.js"))))))))) (propagated-inputs - `(("r-crosstalk" ,r-crosstalk) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jquerylib" ,r-jquerylib) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-promises" ,r-promises))) + (list r-crosstalk + r-htmltools + r-htmlwidgets + r-jquerylib + r-jsonlite + r-magrittr + r-promises)) (inputs - `(("js-selectize" ,js-selectize))) + (list js-selectize)) (native-inputs `(("r-knitr" ,r-knitr) ("uglifyjs" ,node-uglify-js) @@ -3628,17 +3683,17 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.3.3") + (version "2.3.5") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf")))) + "1fcv4vazg2sbsda8qqjjsjn2wagcp2bsahvznwm443j66q6qrz16")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://cran.r-project.org/web/packages/irlba") (synopsis "Methods for eigendecomposition of large matrices") (description @@ -3650,22 +3705,23 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "4.1-2") + (version "4.1-3") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "1kfd8kfhapx2cxw6qnkbs502c3kya4pd9qmf0mk76cdlq1c2paq6")))) + (base32 "0nij8v44b5dvp1vc843sfkl9ds83n6g687m2p37q1rdn82m3bg34")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-matrix" ,r-matrix) - ("r-shape" ,r-shape) - ("r-survival" ,r-survival))) + (list r-foreach + r-matrix + r-rcpp + r-rcppeigen + r-shape + r-survival)) (home-page "https://www.jstatsoft.org/article/view/v033i01") (synopsis "Lasso and elastic-net regularized generalized linear models") (description @@ -3689,13 +3745,13 @@ path-wise fashion.") "14ggsd24n5g5rvn0wl4w90ipxzmywqikh28llj89q6kpxwnv4iff")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-codetools" ,r-codetools) - ("r-digest" ,r-digest) - ("r-registry" ,r-registry) - ("r-stringr" ,r-stringr) - ("r-withr" ,r-withr) - ("r-xtable" ,r-xtable))) + (list r-assertthat + r-codetools + r-digest + r-registry + r-stringr + r-withr + r-xtable)) (home-page "https://renozao.github.io/pkgmaker") (synopsis "Package development utilities") (description @@ -3736,7 +3792,7 @@ package registries.") "0kd7x214cqw7hzpmk1iqy1bn7j6x0ady0yz2hsdbclbq9k57d33z")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest))) + (list r-digest)) (home-page "https://renozao.github.io/rngtools") (synopsis "Utility functions for working with random number generators") (description @@ -3761,7 +3817,7 @@ the way current RNG settings can be changed.") (properties `((upstream-name . "Rtsne"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/jkrijthe/Rtsne") (synopsis "T-distributed stochastic neighbor embedding") (description @@ -3784,8 +3840,7 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") "09i2hmyf1bxansqp24p9n9djlzzarclqs173gjjv3fg0giga3ycv")))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-proxy" ,r-proxy))) + (list r-class r-proxy)) (home-page "https://cran.r-project.org/web/packages/e1071") (synopsis "Miscellaneous functions for probability theory") (description @@ -3827,10 +3882,7 @@ bigmemory and synchronicity packages.") "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-bigmemory-sri" ,r-bigmemory-sri) - ("r-rcpp" ,r-rcpp) - ("r-uuid" ,r-uuid))) + (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 @@ -3852,9 +3904,7 @@ message passing.") "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-bigmemory-sri" ,r-bigmemory-sri))) + (list r-bh r-rcpp r-bigmemory-sri)) (home-page "http://www.bigmemory.org") (synopsis "Manage large matrices with shared memory or memory-mapped files") (description "This package provides methods to create, store, access, and @@ -3900,7 +3950,7 @@ want to migrate to S4.") (properties `((upstream-name . "R.oo"))) (build-system r-build-system) (propagated-inputs - `(("r-r-methodss3" ,r-r-methodss3))) + (list r-r-methodss3)) (home-page "https://github.com/HenrikBengtsson/R.oo") (synopsis "R object-oriented programming with or without references") (description @@ -3923,8 +3973,7 @@ maintenance for package developers.") (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo))) + (list r-r-methodss3 r-r-oo)) (home-page "https://github.com/HenrikBengtsson/R.utils") (synopsis "Various programming utilities") (description @@ -3950,10 +3999,7 @@ developing R packages.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (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 @@ -3981,11 +4027,7 @@ persistent (on the file system).") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-r-cache" ,r-r-cache) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (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 @@ -4003,16 +4045,16 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.1-2") + (version "1.1-3") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "05wh7mprf2sim2kxh3d72pdcmml6vbikzxavws1dq6mxwlsy2p7j")))) + "0j14q2bkc14v35s5k03sw44zsssrd2qjljlwzj014qxs74hk0kpz")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://mvtnorm.R-forge.R-project.org") (synopsis "Package for multivariate normal and t-distributions") (description "This package can compute multivariate normal and @@ -4037,7 +4079,7 @@ t-probabilities, quantiles, random deviates and densities.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes + (list r-r-rsp)) ;used to build vignettes (home-page "https://github.com/HenrikBengtsson/matrixStats") (synopsis "Methods applying to vectors and matrix rows and columns") (description @@ -4051,20 +4093,18 @@ memory usage.") (define-public r-viridis (package (name "r-viridis") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "viridis" version)) (sha256 (base32 - "1fyax36ycjiypcnxhrv58pq67qv03vfg4lx822d38jpjly54q128")))) + "048kwhbhd49g86cq11fl7vm0whwhjl5gs9xjn040lwcjv78qrdb9")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-viridislite" ,r-viridislite))) + (list r-ggplot2 r-gridextra r-viridislite)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/sjmgarnier/viridis") (synopsis "Matplotlib default color map") (description @@ -4116,13 +4156,9 @@ more complete @code{viridis} package.") "0ss8mq05mwif64cj8zmrfx0ljgy3n0fvyv7f37782shr8rknmsqq")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs))) + (list r-ellipsis r-glue r-purrr r-rlang r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tidyselect") (synopsis "Select from a set of strings") (description @@ -4135,29 +4171,29 @@ selection.") (define-public r-tidyr (package (name "r-tidyr") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "0cpbrvr759z8p7r9lpkjhj2dcdymsbnaib0rma9b4jb7i3qzmh2a")))) + "0h8jfsmn4r7zgfyjmg2qkjd54n0sncq07xjh4mdf2cx4k2z9h30b")))) (build-system r-build-system) (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-magrittr" ,r-magrittr) - ("r-glue" ,r-glue) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-cpp11 + r-dplyr + r-ellipsis + r-magrittr + r-glue + r-lifecycle + r-purrr + r-rlang + r-tidyselect + r-tibble + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/tidyr") (synopsis "Tidy data with `spread()` and `gather()` functions") (description @@ -4182,10 +4218,9 @@ and tidyr provides no margins or aggregation.") "0bbhs5pwxh474w62sq6gqvih7habancxng9wd4f2rgn6lv9zhhb2")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) ; for vignettes + (list gfortran r-knitr)) ; for vignettes (home-page "https://github.com/edzer/hexbin") (synopsis "Hexagonal binning routines") (description @@ -4206,10 +4241,9 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3")))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang))) + (list r-magrittr r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description @@ -4220,36 +4254,36 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.9.4.1") + (version "4.10.0") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "1q711c0lg0jmzrmcc2fhjy70ms49as7cakdbgbh2ij9s149fa7iq")))) + "16iqj7sv49mva6siibsci7iijsbnk7pqvfns9al0k35w9mjmr6dx")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-crosstalk" ,r-crosstalk) - ("r-digest" ,r-digest) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lazyeval" ,r-lazyeval) - ("r-magrittr" ,r-magrittr) - ("r-promises" ,r-promises) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs) - ("r-viridislite" ,r-viridislite))) + (list r-base64enc + r-crosstalk + r-digest + r-data-table + r-dplyr + r-ggplot2 + r-htmltools + r-htmlwidgets + r-httr + r-jsonlite + r-lazyeval + r-magrittr + r-promises + r-purrr + r-rcolorbrewer + r-rlang + r-scales + r-tibble + r-tidyr + r-vctrs + r-viridislite)) (home-page "https://plot.ly/r") (synopsis "Create interactive web graphics") (description @@ -4315,8 +4349,7 @@ character vector.") "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x")))) (build-system r-build-system) (propagated-inputs - `(("r-rematch" ,r-rematch) - ("r-tibble" ,r-tibble))) + (list r-rematch r-tibble)) (home-page "https://github.com/rsheets/cellranger") (synopsis "Translate spreadsheet cell ranges to rows and columns") (description @@ -4337,16 +4370,16 @@ character vector.") "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8")))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) + (list r-cellranger + r-dplyr + r-httr + r-jsonlite + r-purrr + r-readr + r-stringr + r-tibble + r-tidyr + r-xml2)) (home-page "https://github.com/jennybc/googlesheets") (synopsis "Manage Google spreadsheets from R") (description "This package provides tools to interact with Google Sheets @@ -4379,8 +4412,7 @@ from within R.") (("-mtune=native") "")) #t))))) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix))) + (list r-lattice r-matrix)) (home-page "https://spams-devel.gforge.inria.fr") (synopsis "Toolbox for solving sparse estimation problems") (description "SPAMS (SPArse Modeling Software) is an optimization toolbox @@ -4411,7 +4443,7 @@ following problems: "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf")))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl))) + (list r-openssl)) (home-page "https://cran.r-project.org/web/packages/base64") (synopsis "Base64 encoder and decoder") (description @@ -4423,34 +4455,34 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.5-0") + (version "4.6-0") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "11qj73zj16p113jpwn2vv06l99kqlcxcmrldbpyi5s7pwing9jnx")))) + (base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-cluster" ,r-cluster) - ("r-data-table" ,r-data-table) - ("r-foreign" ,r-foreign) - ("r-formula" ,r-formula) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-htmltable" ,r-htmltable) - ("r-htmltools" ,r-htmltools) - ("r-nnet" ,r-nnet) - ("r-rpart" ,r-rpart) - ("r-survival" ,r-survival) - ("r-viridis" ,r-viridis))) + (list r-base64enc + r-cluster + r-data-table + r-foreign + r-formula + r-ggplot2 + r-gridextra + r-gtable + r-lattice + r-latticeextra + r-htmltable + r-htmltools + r-nnet + r-rpart + r-survival + r-viridis)) (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") (synopsis "Miscellaneous data analysis and graphics functions") (description @@ -4581,9 +4613,9 @@ tests for whether a value is missing, empty or contains only @code{NA} and "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b")))) (build-system r-build-system) (inputs - `(("perl" ,perl))) + (list perl)) (propagated-inputs - `(("r-gtools" ,r-gtools))) + (list r-gtools)) (home-page "https://cran.r-project.org/web/packages/gdata") (synopsis "Various R programming tools for data manipulation") (description @@ -4621,11 +4653,9 @@ including: "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr")))) (build-system r-build-system) (propagated-inputs - `(("r-catools" ,r-catools) - ("r-gtools" ,r-gtools) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-catools r-gtools r-kernsmooth)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gplots") (synopsis "Various R programming tools for plotting data") (description @@ -4663,9 +4693,9 @@ including: (properties `((upstream-name . "ROCR"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots))) + (list r-gplots)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rocr.bioinf.mpi-sb.mpg.de/") (synopsis "Visualizing the performance of scoring classifiers") (description @@ -4684,24 +4714,24 @@ mechanism.") (define-public r-ztable (package (name "r-ztable") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "ztable" version)) (sha256 (base32 - "0wxcdb7yp2r6w5iznz1k49npp5sn4jiybfcj30s3198hkcnv0r8y")))) + "1ps7ix0hc84s0p0ra6bkjxky3cffs1rvdcagqzj78lbdq22dk5j8")))) (build-system r-build-system) (propagated-inputs - `(("r-flextable" ,r-flextable) - ("r-magrittr" ,r-magrittr) - ("r-officer" ,r-officer) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rstudioapi" ,r-rstudioapi) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + (list r-flextable + r-magrittr + r-officer + r-rcolorbrewer + r-rstudioapi + r-scales + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ztable") (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") (description @@ -4782,9 +4812,7 @@ representation of R code.") "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v")))) (build-system r-build-system) (propagated-inputs - `(("r-beeswarm" ,r-beeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-vipor" ,r-vipor))) + (list r-beeswarm r-ggplot2 r-vipor)) (home-page "https://github.com/eclarke/ggbeeswarm") (synopsis "Categorical scatter (violin point) plots") (description @@ -4805,11 +4833,7 @@ data at that region, and avoids over-plotting.") "0rw5f6axyz1pqn6qx9jwm38hjzn8bqs1nfjkvm96z3xnyn61cdbv")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-purrr" ,r-purrr) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) + (list r-ggplot2 r-purrr r-scales r-stringr r-tibble)) (home-page "https://cran.rstudio.com/web/packages/ggthemes") (synopsis "Extra themes, scales and geoms for @code{ggplot2}") (description "This package provides extra themes and scales for @@ -4832,7 +4856,7 @@ Wall Street Journal, among others. This package also provides (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/statmod") (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (synopsis "Statistical modeling") (description "This package provides a collection of algorithms and functions to aid @@ -4880,13 +4904,13 @@ approximate, exact searches, fixed radius searches, bd and kb trees.") "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl")))) (build-system r-build-system) (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-dplyr" ,r-dplyr) - ("r-readr" ,r-readr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-stringr" ,r-stringr))) + (list r-knitr + r-rmarkdown + r-dplyr + r-readr + r-ggplot2 + r-magrittr + r-stringr)) (home-page "https://mran.microsoft.com/package/fivethirtyeight/") (synopsis "Data and code behind the stories at FiveThirtyEight") (description "This R package provides access to the code and data sets @@ -4927,12 +4951,9 @@ Farebrother's algorithm or Liu et al.'s algorithm.") "0j7d5vhzdxn1blrsfafx5z8lhq122rp8230hp9czrpsnnhjydp67")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-gtable r-rlang r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/wilkelab/cowplot") (synopsis "Streamlined plot theme and plot annotations for ggplot2") (description @@ -4954,10 +4975,7 @@ letters, as is often required for scientific publications.") "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-kernlab" ,r-kernlab) - ("r-segmented" ,r-segmented) - ("r-survival" ,r-survival))) + (list r-mass r-kernlab r-segmented r-survival)) (home-page "https://cran.r-project.org/web/packages/mixtools") (synopsis "Tools for analyzing finite mixture models") (description @@ -4978,7 +4996,7 @@ mixture models.") "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34")))) (build-system r-build-system) (inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://web.stanford.edu/~hastie/Papers/LARS/") (synopsis "Least angle regression software") (description @@ -5027,7 +5045,7 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.") (build-system r-build-system) (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/") (native-inputs - `(("gfortran" ,gfortran))) + (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 @@ -5087,9 +5105,7 @@ to change in the future.") "0jangf89174p0idh9afbicfiln2sz8jxc3bjc6n0j9036dw9n09n")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-modeltools" ,r-modeltools) - ("r-nnet" ,r-nnet))) + (list r-lattice r-modeltools r-nnet)) (home-page "https://cran.r-project.org/web/packages/flexmix") (synopsis "Flexible mixture modeling") (description @@ -5103,18 +5119,17 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.7") + (version "5.4.9") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "08scl72llpinfijiyx14yqvmx8lma9jvh8h92v9ynnzfr9kadxa5")))) + "0s4mva0n04f3pl41msmzhlh7pnk0zbmf06n826smxkw6mz327wb5")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://www.stat.washington.edu/mclust/") (synopsis "Gaussian mixture modelling for model-based clustering etc.") (description @@ -5137,8 +5152,7 @@ and resampling-based inference.") "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-mclust" ,r-mclust))) + (list r-mass r-mclust)) (home-page "https://cran.r-project.org/web/packages/prabclus") (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") (description @@ -5151,14 +5165,14 @@ data for species delimitation, nearest neighbor based noise detection.") (define-public r-deoptimr (package (name "r-deoptimr") - (version "1.0-9") + (version "1.0-10") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 - "04k5gi0a5hbm6znzvjaipbmkacp694krkqs38dkbxx1gymsallb1")))) + "1m9ag073i7pbxsy74vkj0n4hjn6vmyc4n0k78nmslwwwmjh7nkvp")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") @@ -5174,19 +5188,19 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-8") + (version "0.93-9") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "16fmnk3p32mi70rkx89l1v4pry3gnrpy9jicnlfnk6lg1pwz5j8w")))) + "0i9wf4aq8zpn2np6z2rjja21ks9n740dgkiv0qfwdzk3ah3vapyp")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-deoptimr" ,r-deoptimr))) + (list r-deoptimr)) (home-page "http://robustbase.r-forge.r-project.org/") (synopsis "Basic robust statistics") (description @@ -5208,7 +5222,7 @@ regression methodology including model selections and multivariate statistics.") (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm))) + (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/pcaPP") (synopsis "Robust PCA by projection pursuit") (description @@ -5229,12 +5243,9 @@ analysis} (PCA) by projection pursuit.") "0i69gv55c86gkclwhch0jzdfyb20l20mx1nx1xp9qz71nd4klpvr")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mvtnorm" ,r-mvtnorm) - ("r-pcapp" ,r-pcapp) - ("r-robustbase" ,r-robustbase))) + (list r-lattice r-mvtnorm r-pcapp r-robustbase)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rrcov") (synopsis "Scalable robust estimators with high breakdown Point") (description @@ -5256,7 +5267,7 @@ estimation and robust multivariate analysis with high breakdown point.") (properties `((upstream-name . "fit.models"))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/fit.models") (synopsis "Compare fitted models") (description @@ -5273,23 +5284,19 @@ generally.") (define-public r-robust (package (name "r-robust") - (version "0.5-0.0") + (version "0.6-1") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 - "1ks5scp8bnicl9j1r8yrmz668fjs6ifdmi540zw6d2ck500bbw42")))) + "0z8i0qqlsa6vpl457qir3dlsynhjfn2g22436d776vxwyqjx4vs9")))) (build-system r-build-system) (propagated-inputs - `(("r-fit-models" ,r-fit-models) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-robustbase" ,r-robustbase) - ("r-rrcov" ,r-rrcov))) + (list r-fit-models r-lattice r-mass r-robustbase r-rrcov)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/robust") (synopsis "Port of the S+ \"Robust Library\"") (description @@ -5332,15 +5339,15 @@ of the points.") "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19")))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-cluster" ,r-cluster) - ("r-diptest" ,r-diptest) - ("r-flexmix" ,r-flexmix) - ("r-kernlab" ,r-kernlab) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-prabclus" ,r-prabclus) - ("r-robustbase" ,r-robustbase))) + (list r-class + r-cluster + r-diptest + r-flexmix + r-kernlab + r-mass + r-mclust + r-prabclus + r-robustbase)) (home-page "https://cran.r-project.org/web/packages/fpc") (synopsis "Flexible procedures for clustering") (description @@ -5364,7 +5371,7 @@ groupings.") (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM") (synopsis "Vector generalized linear and additive models") (description @@ -5408,9 +5415,9 @@ showing the progress is useful e.g. bootstrap.") "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://optimizer.r-forge.r-project.org") (synopsis "Derivative-free optimization algorithms by quadratic approximation") (description @@ -5432,8 +5439,7 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-matrix" ,r-matrix))) + (list r-rcpp r-matrix)) (home-page "http://eigen.tuxfamily.org") (synopsis "Rcpp integration for the Eigen templated linear algebra library") (description @@ -5457,8 +5463,7 @@ decompositions of such matrices, and solutions of linear systems.") (properties `((upstream-name . "ModelMetrics"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-data-table" ,r-data-table))) + (list r-rcpp r-data-table)) (home-page "https://cran.r-project.org/web/packages/ModelMetrics") (synopsis "Rapid calculation of model metrics") (description @@ -5480,7 +5485,7 @@ metrics for evaluating models.") (properties `((upstream-name . "MatrixModels"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://cran.r-project.org/web/packages/MatrixModels") (synopsis "Modelling with sparse and dense matrices") (description @@ -5500,12 +5505,9 @@ using modular prediction and response module classes.") (base32 "01fnp6ndh7npxj76xlynndacsgmcfr9kgh2waw0clx3mmwlwilbi")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-conquer" ,r-conquer) - ("r-matrix" ,r-matrix) - ("r-matrixmodels" ,r-matrixmodels) - ("r-sparsem" ,r-sparsem))) + (list r-conquer r-matrix r-matrixmodels r-sparsem)) (home-page "https://www.r-project.org") (synopsis "Quantile regression") (description @@ -5519,21 +5521,20 @@ expected shortfall risk are also included.") (define-public r-nloptr (package (name "r-nloptr") - (version "1.2.2.2") + (version "1.2.2.3") (source (origin (method url-fetch) (uri (cran-uri "nloptr" version)) (sha256 (base32 - "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8")))) + "1zznk9f2w2g02zqzay21k8xqzfvc6icxfzp6bx2wpd77sm7vf25g")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) ; for building vignettes - ("pkg-config" ,pkg-config) - ("gfortran" ,gfortran))) + (list r-knitr ; for building vignettes + pkg-config gfortran)) (inputs - `(("nlopt" ,nlopt))) + (list nlopt)) (home-page "https://cran.r-project.org/web/packages/nloptr") (synopsis "R interface to NLopt") (description @@ -5557,17 +5558,17 @@ algorithms.") "1i9f8kl2qj48j75dbn1vmwxz1xlbikdr7v2yq542w6dq74z8gyi5")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-minqa" ,r-minqa) - ("r-nloptr" ,r-nloptr) - ("r-nlme" ,r-nlme) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-boot + r-lattice + r-mass + r-matrix + r-minqa + r-nloptr + r-nlme + r-rcpp + r-rcppeigen)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/lme4") (synopsis "Linear mixed-effects models using eigen and S4") (description @@ -5590,15 +5591,15 @@ C++ library for numerical linear algebra and RcppEigen glue.") "1if7msv9i7jhg1as1f7m81a95dnwhwj3yfs24bqr0f6r0ch4b8xj")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-lme4" ,r-lme4) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-numderiv" ,r-numderiv))) + (list r-broom + r-dplyr + r-lme4 + r-magrittr + r-mass + r-matrix + r-numderiv)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/pbkrtest/") (synopsis "Methods for linear mixed model comparison") (description @@ -5610,13 +5611,13 @@ bootstrap test for generalized linear mixed models.") (define-public r-cardata (package (name "r-cardata") - (version "3.0-4") + (version "3.0-5") (source (origin (method url-fetch) (uri (cran-uri "carData" version)) (sha256 - (base32 "09270j39n4jpswxqps20b12zaj8dz4rrqpk2l2j5bnf1xzizb9nd")))) + (base32 "06j52rpbqi6fj7chfjwjbwbr6slrbb7i3aygv66gnfiyndcp3rq2")))) (properties `((upstream-name . "carData"))) (build-system r-build-system) (home-page "https://r-forge.r-project.org/projects/car/") @@ -5629,28 +5630,27 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-11") + (version "3.0-12") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "0b2l35656bi75hfvnjhzhlnrnbpjn0vv7nvny8gn65gm0rr94b5k")))) + (base32 "00kk8l71508f73kyn21is1mx6kjbrzdq3ls94c5ajhiqmvpsd6dq")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-cardata" ,r-cardata) - ("r-lme4" ,r-lme4) - ("r-maptools" ,r-maptools) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-nlme" ,r-nlme) - ("r-nnet" ,r-nnet) - ("r-pbkrtest" ,r-pbkrtest) - ("r-quantreg" ,r-quantreg) - ("r-rio" ,r-rio))) + (list r-abind + r-cardata + r-lme4 + r-maptools + r-mass + r-mgcv + r-nlme + r-nnet + r-pbkrtest + r-quantreg)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://r-forge.r-project.org/projects/car/") (synopsis "Companion to applied regression") (description @@ -5692,7 +5692,7 @@ even in multithreaded code, typically using OpenMP.") "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp")))) (properties `((upstream-name . "tmvnsim"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://www.r-project.org") (synopsis "Truncated multivariate normal simulation") (description @@ -5721,9 +5721,9 @@ normals.") "0d7ka4l4fl1wi77r2r81dc91n6cbj2xrb3lsizz5y0ziscva0sjw")))) (build-system r-build-system) (propagated-inputs - `(("r-tmvnsim" ,r-tmvnsim))) + (list r-tmvnsim)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt") (synopsis "Multivariate normal and \"t\" distributions") (description @@ -5756,19 +5756,17 @@ first and second order derivatives.") (define-public r-sn (package (name "r-sn") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "sn" version)) (sha256 (base32 - "0sl8qzy9isy5fq8qxh1fg5285jzgy895nbgz8gdq5d0r6zdwrmmb")))) + "1z58kwvq8igjm3biyyjdlhs2qq8hfjq5d9x0lzy80yk5hw08kcw6")))) (build-system r-build-system) (propagated-inputs - `(("r-mnormt" ,r-mnormt) - ("r-numderiv" ,r-numderiv) - ("r-quantreg" ,r-quantreg))) + (list r-mnormt r-numderiv r-quantreg)) (home-page "http://azzalini.stat.unipd.it/SN") (synopsis "The skew-normal and skew-t distributions") (description @@ -5793,10 +5791,7 @@ multivariate case.") (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-mclust" ,r-mclust) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sn" ,r-sn))) + (list r-cluster r-mclust r-mvtnorm r-sn)) (home-page "https://cran.r-project.org/web/packages/tclust") (synopsis "Robust trimmed clustering") (description @@ -5818,9 +5813,7 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") "02idcc6zbdz4wsi1mcwh7qyhmlbwvnzxwkdvvppxw7n2rh54z4v0")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-matrix" ,r-matrix) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-rcpp r-matrix r-rcppeigen)) (home-page "https://github.com/imbs-hl/ranger") (synopsis "Fast implementation of random forests") (description @@ -5851,22 +5844,20 @@ genome-wide association studies can be analyzed efficiently.") (define-public r-cairo (package (name "r-cairo") - (version "1.5-12.2") + (version "1.5-14") (source (origin (method url-fetch) (uri (cran-uri "Cairo" version)) (sha256 (base32 - "14hgz5wmnhlbqkd1g662n1agmjnlj3pq69gfng1vb0ivr02l2lnx")))) + "0ysc40smkjwk8fmp5dk0q3nbp9xkxzz9pd4z5zkp2mrvrvx52xq6")))) (properties `((upstream-name . "Cairo"))) (build-system r-build-system) (inputs - `(("cairo" ,cairo) - ("libxt" ,libxt) - ("zlib" ,zlib))) + (list cairo libxt zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.rforge.net/Cairo/") (synopsis "R graphics device using Cairo graphics library") (description @@ -5887,20 +5878,19 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.10") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "1s653d6rnpf9bkynxmbq4fdjdcz7r9ma19aph8f5y9ck70his4hm")))) + "199b00cql07gf3rf4hh5ba34amnk0ai40zhx73dq1mpkn7ynxml7")))) (build-system r-build-system) (propagated-inputs - `(("r-generics" ,r-generics) - ("r-rcpp" ,r-rcpp))) + (list r-generics r-cpp11)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/lubridate/") (synopsis "Make dealing with dates a little easier") (description @@ -5915,14 +5905,14 @@ easy and fun.") (define-public r-fdrtool (package (name "r-fdrtool") - (version "1.2.16") + (version "1.2.17") (source (origin (method url-fetch) (uri (cran-uri "fdrtool" version)) (sha256 (base32 - "1aap4k1l3a9m43374xq688mqnzkgqx8l021li262r3h1xr4adpp7")))) + "1pf554vb902vavgqc4c0kgghywbgcvr3lkkr414bxngavcd60lil")))) (build-system r-build-system) (home-page "http://strimmerlab.org/software/fdrtool/") (synopsis "Estimation of false discovery rates and higher criticism") @@ -5953,12 +5943,9 @@ and the corresponding decision threshold.") "12d2nv2w15085jscgidmjdnr1ryymciflcmal6ldmgp2fkl9dyy4")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-magrittr" ,r-magrittr) - ("r-tibble" ,r-tibble) - ("r-rlang" ,r-rlang))) + (list r-ellipsis r-magrittr r-tibble r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://forcats.tidyverse.org") (synopsis "Tools for working with factors") (description "This package provides helpers for reordering factor @@ -5995,7 +5982,7 @@ manually \"recoding\").") "#define isnan std::isnan")) #t))))) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://bitbucket.org/tanaylab/tgstat/") (synopsis "Tanay's group statistical utilities") (description @@ -6021,7 +6008,7 @@ tools.") "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj")))) (build-system r-build-system) (propagated-inputs - `(("r-yaml" ,r-yaml))) + (list r-yaml)) (home-page "https://bitbucket.org/tanaylab/tgconfig/") (synopsis "Infrastructure for managing package parameters") (description @@ -6046,7 +6033,7 @@ parameters.") "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg")))) (build-system r-build-system) (propagated-inputs - `(("r-png" ,r-png))) + (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 @@ -6098,48 +6085,37 @@ to any arbitrary string. In this case, it is up to you to set valid values.") "1cysswxr5glrdblyl2zsmywcj7xhxn3wmyihxinrz9gm8gmaacax")))) (build-system python-build-system) (arguments - '(#:modules ((ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26) - (guix build utils) - (guix build python-build-system)) - #:phases + '(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key outputs inputs #:allow-other-keys) (let ((cwd (getcwd))) - (setenv "TZ" "UTC") - (setenv "PYTHONPATH" - (string-append cwd "/build/" - (find (cut string-prefix? "lib" <>) - (scandir (string-append cwd "/build"))) - ":" - (getenv "PYTHONPATH")))) + (setenv "TZ" "UTC")) ;; test_vector_complex has issues when run in our environment. - (invoke "pytest" "-v" "rpy2/tests/" "-k" "not test_vector_complex")))))) + (invoke "pytest" "-v" "rpy2/tests/" + "-k" "not test_vector_complex")))))) (propagated-inputs - `(("python-cffi" ,python-cffi) - ("python-six" ,python-six) - ("python-jinja2" ,python-jinja2) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pytz" ,python-pytz) - ("python-ipython" ,python-ipython) - ("python-tzlocal" ,python-tzlocal))) + (list python-cffi + python-six + python-jinja2 + python-numpy + python-pandas + python-pytz + python-ipython + python-tzlocal)) (inputs - `(("readline" ,readline) - ("icu4c" ,icu4c) - ("pcre" ,pcre) - ("r-minimal" ,r-minimal) - ("r-survival" ,r-survival) - ("r-ggplot2" ,r-ggplot2) - ("r-rsqlite" ,r-rsqlite) - ("r-dplyr" ,r-dplyr) - ("r-dbplyr" ,r-dbplyr) - ("python-numpy" ,python-numpy))) + (list readline + icu4c + pcre + r-minimal + r-survival + r-ggplot2 + r-rsqlite + r-dplyr + r-dbplyr + python-numpy)) (native-inputs - `(("zlib" ,zlib) - ("python-pytest" ,python-pytest))) + (list zlib python-pytest)) (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 @@ -6176,9 +6152,9 @@ functions.") (("Scheff.+-Tukey") "Scheffe-Tukey"))) #t))))) (propagated-inputs - `(("java-jtransforms" ,java-jtransforms))) + (list java-jtransforms)) (native-inputs - `(("java-junit" ,java-junit))) + (list java-junit)) (home-page "http://jdistlib.sourceforge.net/") (synopsis "Java library of statistical distributions") (description "JDistlib is the Java Statistical Distribution Library, a @@ -6252,14 +6228,12 @@ Java package that provides routines for various statistical distributions.") (replace 'check (lambda _ (invoke "make" "test"))))))) (native-inputs - `(("perl" ,perl) - ("r-roxygen2" ,r-roxygen2) - ("texinfo" ,texinfo))) + (list perl r-roxygen2 texinfo)) (inputs `(("emacs" ,emacs-minimal) ("r-minimal" ,r-minimal))) (propagated-inputs - `(("emacs-julia-mode" ,emacs-julia-mode))) + (list emacs-julia-mode)) (home-page "https://ess.r-project.org/") (synopsis "Emacs mode for statistical analysis programs") (description @@ -6283,10 +6257,8 @@ statistical analysis programs such as R, Julia, and JAGS.") (base32 "0a4wx73jkngw5nbq1fa4jfhba6bsmyn6vnsf887x3xhb5v3ykhsg")))) (build-system emacs-build-system) (propagated-inputs - `(("emacs-ess" ,emacs-ess) - ("emacs-poly-noweb" ,emacs-poly-noweb) - ("emacs-polymode-markdown" ,emacs-polymode-markdown) - ("emacs-polymode" ,emacs-polymode))) + (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") @@ -6310,12 +6282,9 @@ files, including Rmarkdown files.") (base32 "00sdmaq0qzp6kyv53fpfi6jf3iv4pd0ap0gmw3mbfip52bbnl55w")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("gettext" ,gnu-gettext) - ("libtool" ,libtool))) + (list autoconf automake gnu-gettext libtool)) (inputs - `(("zlib" ,zlib))) ; libz + (list zlib)) ; libz (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.") @@ -6336,7 +6305,7 @@ popular stats packages like SAS, Stata and SPSS.") (properties `((upstream-name . "QuantPsyc"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) ("r-mass" ,r-mass))) + (list r-boot r-mass)) (home-page "https://cran.r-project.org/web/packages/QuantPsyc/") (synopsis "Quantitative Psychology Tools") (description @@ -6347,19 +6316,19 @@ mediation and estimating power.") (define-public r-clubsandwich (package (name "r-clubsandwich") - (version "0.5.3") + (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "clubSandwich" version)) (sha256 (base32 - "0jazgka18bb5n58d5sn94q7rc9sac82qrpl2i5b4rkx9q2pb39cn")))) + "1ifnc2rg5agf7lpilmm27iq0af7ghfhkvwykajhvykgf6h4clvhf")))) (properties `((upstream-name . "clubSandwich"))) (build-system r-build-system) (propagated-inputs - `(("r-sandwich" ,r-sandwich))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-sandwich)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jepusto/clubSandwich") (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections") @@ -6396,10 +6365,7 @@ Methods are provided for a variety of fitted models, including @code{lm()} and (properties `((upstream-name . "puniform"))) (build-system r-build-system) (propagated-inputs - `(("r-adgoftest" ,r-adgoftest) - ("r-metafor" ,r-metafor) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-adgoftest r-metafor r-rcpp r-rcpparmadillo)) (home-page "https://github.com/RobbievanAert/puniform") (synopsis @@ -6489,7 +6455,7 @@ or eta squared effect size.") (properties `((upstream-name . "kknn"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix))) + (list r-igraph r-matrix)) (home-page "https://github.com/KlausVigo/kknn") (synopsis "Weighted k-Nearest Neighbors") (description @@ -6509,7 +6475,7 @@ or eta squared effect size.") "12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l")))) (properties `((upstream-name . "logspline"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/logspline/") (synopsis @@ -6525,28 +6491,27 @@ interface). The recommended routine @code{logspline()} uses an algorithm from (define-public r-effects (package (name "r-effects") - (version "4.2-0") + (version "4.2-1") (source (origin (method url-fetch) (uri (cran-uri "effects" version)) (sha256 (base32 - "0iks79rd4knrd81x4kvcpgpclr69l0m0v6sfla8k3wzkcnydycv8")))) + "0h3n2kd43fddy29hlv1nckw3wglykwrgk1hp8khb0pnm2i12b5sk")))) (properties `((upstream-name . "effects"))) (build-system r-build-system) (propagated-inputs - `(("r-cardata" ,r-cardata) - ("r-colorspace" ,r-colorspace) - ("r-estimability" ,r-estimability) - ("r-insight" ,r-insight) - ("r-lattice" ,r-lattice) - ("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-survey" ,r-survey))) + (list r-cardata + r-colorspace + r-estimability + r-insight + r-lattice + r-lme4 + r-nnet + r-survey)) (native-inputs - `(("r-knitr" ,r-knitr) - ("r-car", r-car))) + (list r-knitr r-car)) (home-page "https://www.r-project.org") (synopsis "Effect Displays for Linear, Generalized Linear, and Other Models") @@ -6558,28 +6523,28 @@ various statistical models with linear predictors.") (define-public r-bayesfactor (package (name "r-bayesfactor") - (version "0.9.12-4.2") + (version "0.9.12-4.3") (source (origin (method url-fetch) (uri (cran-uri "BayesFactor" version)) (sha256 (base32 - "1z083v7is21gm0a458jm5ph3xfdm7mh29a6sg2r1njq82f8x3s3g")))) + "171hbr445v8mq4hqi1k8q3h8zqsccwjv0a2mj98h9b77667ziyfw")))) (properties `((upstream-name . "BayesFactor"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda) - ("r-gtools" ,r-gtools) - ("r-hypergeo" ,r-hypergeo) - ("r-matrix" ,r-matrix) - ("r-matrixmodels" ,r-matrixmodels) - ("r-mvtnorm" ,r-mvtnorm) - ("r-pbapply" ,r-pbapply) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-stringr" ,r-stringr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-coda + r-gtools + r-hypergeo + r-matrix + r-matrixmodels + r-mvtnorm + r-pbapply + r-rcpp + r-rcppeigen + r-stringr)) + (native-inputs (list r-knitr)) (home-page "https://richarddmorey.github.io/BayesFactor/") (synopsis @@ -6602,7 +6567,7 @@ designs, one-way designs, general ANOVA designs, and linear regression.") "01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/norm/") (synopsis "Analysis of multivariate normal datasets with missing values") (description "Multiple imputation of multivariate continuous data under a @@ -6622,21 +6587,21 @@ normal model.") "0l3l2x85v3srilww483kpgp4zlwixyml257b0cqly8kcpwawlinm")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-norm" ,r-norm) - ("r-forcats" ,r-forcats) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-upsetr" ,r-upsetr) - ("r-viridis" ,r-viridis) - ("r-visdat" ,r-visdat))) + (list r-dplyr + r-norm + r-forcats + r-ggplot2 + r-glue + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-upsetr + r-viridis + r-visdat)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/njtierney/naniar") (synopsis "Data structures, summaries, and visualisations for missing data") @@ -6685,7 +6650,7 @@ Michael Lim & Trevor Hastie (2015)") "1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl")))) (properties `((upstream-name . "datasauRus"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/lockedata/datasauRus") (synopsis "Datasets from the Datasaurus Dozen") @@ -6703,3 +6668,186 @@ original Datasaurus is detailed in \"Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing\" @url{doi:10.1145/3025453.3025912}.") (license license:expat))) + +(define-public r-lmom + (package + (name "r-lmom") + (version "2.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "lmom" version)) + (sha256 + (base32 "1lnj41gynaar5isyijg5nbll64qdxa12dnqvz7lxhaclqcjskqna")))) + (properties `((upstream-name . "lmom"))) + (build-system r-build-system) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=lmom") + (synopsis "L-Moments for R") + (description + "This package provides functions related to L-moments: computation +of L-moments and trimmed L-moments of distributions and data samples; +parameter estimation; L-moment ratio diagram; plot vs. quantiles of an +extreme-value distribution.") + (license license:cpl1.0))) + +(define-public r-gld + (package + (name "r-gld") + (version "2.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "gld" version)) + (sha256 + (base32 "08rkv7g6ci969vh9fbyg3lrpfmjhbiwzdhcjs9j6s9bf3gpdmdhd")))) + (properties `((upstream-name . "gld"))) + (build-system r-build-system) + (propagated-inputs (list r-e1071 r-lmom)) + (home-page + "https://cran.r-project.org/package=gld") + (synopsis + "Estimation and Use of the Generalised (Tukey) Lambda Distribution") + (description + "The generalised lambda distribution, or Tukey lambda distribution, +provides a wide variety of shapes with one functional form. This package +provides random numbers, quantiles, probabilities, densities and +density quantiles for four different types of the distribution, the FKML +(Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden +and Loots 2009) and FM5 - see documentation for details. It provides the +density function, distribution function, and Quantile-Quantile plots. +It implements a variety of estimation methods for the distribution, +including diagnostic plots. Estimation methods include the starship (all +4 types), method of L-Moments for the GPD and FKML types, and a number +of methods for only the FKML type. These include maximum likelihood, +maximum product of spacings, Titterington's method, Moments, Trimmed +L-Moments and Distributional Least Absolutes.") + (license license:gpl2+))) + +(define-public r-exact + (package + (name "r-exact") + (version "3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Exact" version)) + (sha256 + (base32 "1kz3hw11sl142mai4ly2r85rwdbjz8q7b38ybmjym6r0n5qmqzyn")))) + (properties `((upstream-name . "Exact"))) + (build-system r-build-system) + (propagated-inputs (list r-rootsolve)) + (home-page "https://cran.r-project.org/package=Exact") + (synopsis "Unconditional Exact Test") + (description + "Performs unconditional exact tests and power calculations for 2x2 +contingency tables. For comparing two independent proportions, performs +@url{doi:10.1038/156177a0, Barnard's test (1945)} using the original CSM +test (@url{doi:10.1093/biomet/34.1-2.123, Barnard (1947)}), using Fisher's +p-value referred to as @url{doi:10.1111/j.1467-9574.1970.tb00104.x, +Boschloo's test (1970)}, or using a Z-statistic (@url{doi:10.2307/2981892, +Suissa and Shuster (1985)}). For comparing two binary proportions, +performs unconditional exact test using McNemar's Z-statistic +(@url{doi:10.1191/0962280203sm312ra, Berger and Sidik (2003)}), using +McNemar's Z-statistic with continuity correction, or using CSM test. +Calculates confidence intervals for the difference in proportion.") + (license license:gpl2))) + +(define-public r-desctools + (package + (name "r-desctools") + (version "0.99.44") + (source + (origin + (method url-fetch) + (uri (cran-uri "DescTools" version)) + (sha256 + (base32 "04wp3sp6sahgq167465y38y13h1ia5a4zqazysacpjxd1if0578j")))) + (properties `((upstream-name . "DescTools"))) + (build-system r-build-system) + (propagated-inputs + (list r-bh + r-boot + r-data-table + r-exact + r-expm + r-gld + r-mass + r-mvtnorm + r-rcpp + r-rstudioapi)) + (native-inputs (list gfortran)) + (home-page "https://andrisignorell.github.io/DescTools/") + (synopsis "Tools for Descriptive Statistics") + (description + "This package provides a collection of miscellaneous basic statistic +functions and convenience wrappers for efficiently describing data. +The author's intention was to create a toolbox, which facilitates the +(notoriously time consuming) first descriptive tasks in data analysis, +consisting of calculating descriptive statistics, drawing graphical +summaries and reporting the results. The package contains furthermore +functions to produce documents using MS Word (or PowerPoint) and functions +to import data from Excel. Many of the included functions can be found +scattered in other packages and other sources written partly by Titans +of R. The reason for collecting them here, was primarily to have them +consolidated in ONE instead of dozens of packages (which themselves might +depend on other packages which are not needed at all), and to provide a +common and consistent interface as far as function and arguments naming, +NA handling, recycling rules etc. are concerned. Google style guides +were used as naming rules (in absence of convincing alternatives). +The BigCamelCase style was consequently applied to functions borrowed +from contributed R packages as well.") + (license license:gpl2+))) + +(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 "http://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/") + (license license:expat)))) |