diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 1057 |
1 files changed, 837 insertions, 220 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fb14526f98..d0166cae1d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -12,6 +12,8 @@ ;;; Copyright © 2017 Alex Kost <[email protected]> ;;; Copyright © 2018 Alex Branham <[email protected]> ;;; Copyright © 2020 Tim Howes <[email protected]> +;;; Copyright © 2021 Bonface Munyoki Kilyungi <[email protected]> +;;; Copyright © 2021 Lars-Dominik Braun <[email protected]> ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,6 +38,7 @@ #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system ant) + #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (guix build-system python) @@ -59,6 +62,7 @@ #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages java) + #:use-module (gnu packages javascript) #:use-module (gnu packages libffi) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) @@ -78,11 +82,13 @@ #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages base) + #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) - #:use-module (srfi srfi-1)) + #:use-module (srfi srfi-1) + #:use-module (ice-9 match)) (define-public pspp @@ -184,7 +190,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.0.4") + (version "4.1.1") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -192,7 +198,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0bl098xcv8v316kqnf43v6gb4kcsv31ydqfm1f7qr824jzb2fgsj")))) + "0r6kpnxjbvb7gdfg4m1z8zc6xd225vw81wrnf05ps9ajawk06pji")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -211,12 +217,15 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (substitute* "src/library/base/makebasedb.R" (("compress = TRUE") "compress = FALSE")) #t)) - (add-before 'configure 'patch-uname + (add-before 'configure 'patch-coreutils-paths (lambda* (#:key inputs #:allow-other-keys) - (let ((uname-bin (string-append (assoc-ref inputs "coreutils") - "/bin/uname"))) + (let* ((coreutils (assoc-ref inputs "coreutils")) + (uname-bin (string-append coreutils "/bin/uname")) + (rm-bin (string-append coreutils "/bin/rm"))) (substitute* "src/scripts/R.sh.in" - (("uname") uname-bin))) + (("uname") uname-bin)) + (substitute* "src/unix/sys-std.c" + (("rm -Rf ") (string-append rm-bin " -Rf ")))) #t)) (add-after 'unpack 'build-reproducibly (lambda _ @@ -339,7 +348,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ("texlive" ,(texlive-union (list texlive-ae texlive-inconsolata texlive-fonts-ec - texlive-amsfonts + texlive-amsfonts/patched texlive-latex-base texlive-latex-fancyvrb texlive-latex-graphics @@ -416,14 +425,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-27") + (version "1.3-28") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "1v9anpxj4p83kd40gyfy8a454b2jmn11incrzym7wdvh8mdxpcil")))) + "0cjafhqv1c1mrjjcasqr767vs96wjcc6am9r1icryr8l4zymhwcz")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -437,14 +446,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-53.1") + (version "7.3-54") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "0ra46441y4iwcpd8px7j7vcjfj09fawl5khilaivjbg3gswiwnz4")))) + "08g8ashbcas3ac98kxvchbwc8da9dq9anpngb4arnw62npawq05q")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") @@ -458,14 +467,14 @@ Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") (define-public r-class (package (name "r-class") - (version "7.3-18") + (version "7.3-19") (source (origin (method url-fetch) (uri (cran-uri "class" version)) (sha256 (base32 - "148k47k354k6wygpmwg79p2jwni0glpi6z7q8n0lp2w9d8p75fnj")))) + "0dxyxk59fs90713qisanlvk4p0d3l8n8n7zdd4d5c290naaaw83q")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) @@ -480,14 +489,14 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") (define-public r-cluster (package (name "r-cluster") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "cluster" version)) (sha256 (base32 - "0qw06n1f7771mszc9y1f1c9zngd82zlf2s2z30p9514vxh4wgf5x")))) + "168l653ygkg21fwrqrf7lsqi5p6jzhgmcvhrwv7lznkdzdhag2jw")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -541,14 +550,14 @@ for reading and writing some dBase files.") (define-public r-kernsmooth (package (name "r-kernsmooth") - (version "2.23-18") + (version "2.23-20") (source (origin (method url-fetch) (uri (cran-uri "KernSmooth" version)) (sha256 (base32 - "14640ddvxmczd5xjg1xsd51gll2glfg946vks8wmac6jb8680d43")))) + "0fgclmzk3ksjsh3j47jqzm3jhqrwn12rkp7f84yr6wr43q2pbsr0")))) (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) (native-inputs @@ -565,13 +574,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (define-public r-lattice (package (name "r-lattice") - (version "0.20-41") + (version "0.20-45") (source (origin (method url-fetch) (uri (cran-uri "lattice" version)) (sha256 (base32 - "1dapkmh4jlb9sxfrpvapvlfhczl4s8p3r20bn47gcgdk1izmbjjl")))) + "1b87fmyjzbg854vpi03my1p25n3d0bchhwsdm2frblxppn98sf12")))) (build-system r-build-system) (home-page "http://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") @@ -585,14 +594,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.3-2") + (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0ccmmfd0lbvrhzjzr28k4yfawiywa1m4ics34zyi3rqq23csa2wm")))) + "0fbcbysp3vaivmp1yasmp8mdsldhr826vfs4vyxrjpjl8jfifhmb")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -607,13 +616,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-152") + (version "3.1-153") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "0pji9vvmjqyk8b7lhxsixnagsrz2hmnwy6ilc2gg5ji1y6qx2rav")))) + (base32 "1qw0sq64iybyidj0s8m76z4i1gxb1fn27s29i63fw5hvvy7aj9rx")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) @@ -629,13 +638,13 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-34") + (version "1.8-37") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "1pkky9xb3wsinqd75gkfbgw270vx8zh52id6bf1xj9njnzrkmc8m")))) + (base32 "14gw714xcyvgrbajijmyd4v8zs84i701g7gyld6z8p7677dgc8w8")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) @@ -652,14 +661,14 @@ distributions beyond the exponential family.") (define-public r-nnet (package (name "r-nnet") - (version "7.3-15") + (version "7.3-16") (source (origin (method url-fetch) (uri (cran-uri "nnet" version)) (sha256 (base32 - "068yxmx165r9gk4s267iczrzwbwbbg3a8qi0cgncqn78892yvsdc")))) + "0smmyx4vhlz99vy4w238y913gq74845v0l1p0g1kgydsp9lijlcr")))) (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") @@ -690,14 +699,14 @@ classification, regression and survival trees.") (define-public r-spatial (package (name "r-spatial") - (version "7.3-13") + (version "7.3-14") (source (origin (method url-fetch) (uri (cran-uri "spatial" version)) (sha256 (base32 - "0ciqa8y2gd1gb2yzmmn4ga6z9b00fjf49bd5qn8wmxwm2fs36w64")))) + "0dlafq744mahxpb13llmsrg54fzww8ld1nbxmr7m851gff11kk2j")))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") (synopsis "Functions for kriging and point pattern analysis") @@ -710,14 +719,14 @@ analysis.") (define-public r-survival (package (name "r-survival") - (version "3.2-10") + (version "3.2-13") (source (origin (method url-fetch) (uri (cran-uri "survival" version)) (sha256 (base32 - "19fg7mrrr6chbixq10kwwl5clry2y57v6zl24jlmxx2ylis0vjzd")))) + "0zrikancm9shixvgng89f1610sphlwljczi0fnjbdqn4l85rrarz")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -823,13 +832,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.27") + (version "0.6.28") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "0gr503pinailfglpfbzxprqw7w1jla8jr9nl856a4zch498zg1gl")))) + (base32 "006vqwfrry84xn51lxlfalzn9yqr1k81s39r0zy251azx5sqqcja")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1038,14 +1047,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.5.3") + (version "1.7.4") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "0420f7zn5knyyvd3a3xa7059l4kadw0m67rfpivacqn9xn6iwkr2")))) + "1mda4612sc573zabsvygnla3vpnf3mql58fc9j450540h6hlwfv2")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -1111,13 +1120,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.3") + (version "3.3.5") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1k136k1sr6dq1xvx6gs6gzji6hbnnwnsb5qivsxrblfv90irxhj5")))) + (base32 "1si46bf9p09qzs208hqffwcb40305p361whmwhc1pwrsmx7jjxdh")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -1329,13 +1338,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.8") + (version "1.11") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "04q6y53ji7ll131khbwiz584wl8sinhh3z82p6r8dqa9f618ay6z")))) + "0353aj975mj0yjc91z76bbfy86y7d5cvlqqyfr93cdng14nnd0dx")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -1351,14 +1360,21 @@ There is also a Shiny app as a user interface in this package.") (define-public r-highr (package (name "r-highr") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "highr" version)) (sha256 (base32 - "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b")))) + "0kgdv2vf1lz3b5kbal9s83gg6812nw7fvrq0rkyr0v4k1lwi3zxy")))) (build-system r-build-system) + (propagated-inputs + `(("r-xfun" ,r-xfun))) + ;; We cannot add knitr to the inputs, because highr depends on xfun, which + ;; is an input to knitr. + #; + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yihui/highr") (synopsis "Syntax highlighting for R source code") (description @@ -1370,13 +1386,13 @@ supported via Andre Simon's highlight package.") (define-public r-mime (package (name "r-mime") - (version "0.10") + (version "0.11") (source (origin (method url-fetch) (uri (cran-uri "mime" version)) (sha256 (base32 - "1xz37fizlx4w3g8kbim7vr5slqd6cmaq5sa0s4q7ayl1bahk6ckq")))) + "1h7fz0rqnp970r9q0d95qcxpxm9mb98rqhcdncx0w2qdkyj2fm11")))) (build-system r-build-system) (home-page "https://github.com/yihui/mime") (synopsis "R package to map filenames to MIME types") @@ -1433,18 +1449,17 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.31") + (version "1.34") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1s87py0km76l72lbwx714cn5903lsdxs237k35p26d5bmyvqv39c")))) + "0p6jdicyqknrqilcjm2h4r6vza5lpzccnsdirj92jb3ljg10b0by")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) ("r-highr" ,r-highr) - ("r-markdown" ,r-markdown) ("r-stringr" ,r-stringr) ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml))) @@ -1503,19 +1518,19 @@ the execution time of R expressions.") (define-public r-pryr (package (name "r-pryr") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "pryr" version)) (sha256 (base32 - "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k")))) + "02vp1y7zhv22id43j5c0gdcgn9171dyypqp8rqrlc3w5a7n565kv")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr) - ("r-codetools" ,r-codetools))) - (native-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-codetools" ,r-codetools) + ("r-lobstr" ,r-lobstr) + ("r-rcpp" ,r-rcpp) + ("r-stringr" ,r-stringr))) (home-page "https://github.com/hadley/pryr") (synopsis "Tools for computing on the R language") (description @@ -1587,13 +1602,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.0.2") + (version "3.0.4") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "03sbk36vrjhzfap6a9czxw93r7h06rh3mb01inbrhrh5r2pd00qq")))) + "0iqizv2gpv9fg766qv8hbkmc6c5i9xcfrmq9k5m2550p28zff2w3")))) (build-system r-build-system) (propagated-inputs `(("r-brio" ,r-brio) @@ -1627,13 +1642,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.5.0") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "00ifi2kwa7kn67xf0z1w6jfdicjczygbyi5mhfw2qlzc4sbazhdf")))) + "0j5z0b0myzjyyykk310xsa9n2mcm9bz8yqbq4xgz2yzdq8lvv4ld")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") @@ -1649,13 +1664,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "0.4.10") + (version "0.4.11") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "0ximv89f6zymnwms121k1jfvvflrdm3pmmf5xyvz56f1qiq04lq7")))) + "1pfm24jjkxzdb5qcbc05dcjxyk69zpfr5jv4xakqh1xh41mr43kl")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1667,14 +1682,14 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "3.1.0") + (version "3.1.4") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "0khmypf49la8n5gx72n7gr6dl6r6ja404i578g6sg0ail3g2i7lm")))) + "0zqpg2haph0qi1x5r6wr083xckab9gw21jbr9spcr8xdf43hx1vk")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -1697,13 +1712,13 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "1.0.5") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0w3fr6sn0mw5mjs27669czpc8vpjj6ayrjavw8v0gd7ccsfa0hbm")))) + "0g8jsxclj9cgm7a2lyazy78sj62rbzw812lsw3fdsbz0pknkmznj")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -1711,6 +1726,7 @@ and printing capabilities than traditional data frames.") ("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) @@ -2014,19 +2030,18 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-16") + (version "1.7-18") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "142m70im8yd4q01q7z02y3ia0f66yh4ikdznv0ps6c7yyigs5mwv")))) + "09f5kh2mwygqpnvf53k0r54k0cvaafxm9x4nm819gwv05k2g9dpc")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) ("r-pixmap" ,r-pixmap) - ("r-progress" ,r-progress) ("r-sp" ,r-sp))) (home-page "http://pbil.univ-lyon1.fr/ADE-4") (synopsis "Multivariate data analysis and graphical display") @@ -2089,13 +2104,13 @@ jackknifed confidence intervals are available for most estimates.") (define-public r-rversions (package (name "r-rversions") - (version "2.0.2") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "rversions" version)) (sha256 (base32 - "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm")))) + "1cbwwbz8lqx2n33xr4q904whvld22s63rpyy1nn93395l7ssrakr")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) @@ -2316,24 +2331,24 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.1.1") + (version "7.1.2") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx")))) + "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-rcpp" ,r-rcpp) ("r-rlang" ,r-rlang) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) @@ -2350,14 +2365,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "1.4.3") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "0sc2skh1nz7jj65p0pq4a6bl8jza6lyi4zvmvwndzxfgivgh281l")))) + "1xy1w0rljzsgvsg91fh9hs6h9rx58mza1vg6rig9ykp9m2ml3hag")))) (build-system r-build-system) (inputs `(("libressl" ,libressl))) @@ -2456,23 +2471,22 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "2.3.2") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "0vcqs4c5dfjs2ddkclv3z7zzix2zrnrxvzax8hjvjszgp8362275")))) + "01cg2ykg0av6z7bgl41njcxcii8vjj8ipch26xazp4yjai8abw3i")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) ("r-cli" ,r-cli) - ("r-covr" ,r-covr) ("r-desc" ,r-desc) - ("r-dt" ,r-dt) ("r-ellipsis" ,r-ellipsis) + ("r-fs" ,r-fs) ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) + ("r-lifecycle" ,r-lifecycle) ("r-memoise" ,r-memoise) ("r-pkgbuild" ,r-pkgbuild) ("r-pkgload" ,r-pkgload) @@ -2497,13 +2511,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.4.1") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "13qpcx7vjnqchvbbdwiqw286gkiajp02pcvhn7w7ddjiil2xjpjz")))) + "1j5srffi748yxphwli56lkbh4cga0kmz38dyzganzkw0nx66mya8")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -2518,14 +2532,14 @@ were originally a part of the r-devtools package.") (define-public r-hms (package (name "r-hms") - (version "1.0.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "hms" version)) (sha256 (base32 - "0qn9lvpkqrpxck88nf0zbff43vd7d6s1ibg58qfr3w14sw1yj14p")))) + "0qlh4s1g9rbm6c3s906dhw3xsz28m8fg6cyynlkhvis533dk0pvb")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -2543,13 +2557,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.4.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82")))) + "0cj5k3ykkhixgdsqm1gnmpc0d8z04l3fhvm2dr5xp7cpmhgsrpfr")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -2561,7 +2575,8 @@ time-of-day values, based on the @code{difftime} class.") ("r-tibble" ,r-tibble) ("r-r6" ,r-r6) ("r-rlang" ,r-rlang) - ("r-bh" ,r-bh))) + ("r-tzdb" ,r-tzdb) + ("r-vroom" ,r-vroom))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hadley/readr") @@ -2574,13 +2589,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.8-1") + (version "3.8-2") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "0pxfaalwwmnpv19nff0cg6b871m6gjhhmx63fpxm7730z75qh663")))) + "07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") @@ -2635,13 +2650,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.10.2.2.0") + (version "0.10.6.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "193smj6vp3cn3qjhrx2llgi5c7hs069crhvi85xj2vzx80fx6r9q")))) + "1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2663,13 +2678,13 @@ the header files from the templated Armadillo library.") (define-public r-bitops (package (name "r-bitops") - (version "1.0-6") + (version "1.0-7") (source (origin (method url-fetch) (uri (cran-uri "bitops" version)) (sha256 (base32 - "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv")))) + "1i0phmq5yynla5x0frqll1gbf5ww59p3sgz1s06a354zqf9grdg9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bitops") (synopsis "Bitwise operations") @@ -2727,18 +2742,19 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.7") + (version "2.11") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0shj637qhpcf30il3lhl3k5bxi5l3x3gf612hbqlakp1qrgrf8lm")))) + (base32 "0xcpg9d009a71p5i6jczw02qcp907p5d52lp6vclrsp7019jawck")))) (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) @@ -2820,13 +2836,13 @@ that package, other packages are unaffected.") (define-public r-blob (package (name "r-blob") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "blob" version)) (sha256 (base32 - "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g")))) + "1yn7f13icaix0apxp4drnciwdn8bx8xmbd129jd7ck4rcly0axj9")))) (build-system r-build-system) (propagated-inputs `(("r-rlang" ,r-rlang) @@ -2842,18 +2858,17 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.5") + (version "2.2.8") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "14cxqh8j5v2rqs6yiargy1miycvx7xj47lppvpnnchi5plimlvyy")))) + "1hscgi11px9hq0sx78c2lkfzq121rlvmhxmqf305xg6lgqdxr2hv")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs `(("r-dbi" ,r-dbi) - ("r-bh" ,r-bh) ("r-memoise" ,r-memoise) ("r-plogr" ,r-plogr) ("r-rcpp" ,r-rcpp) @@ -2916,13 +2931,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.6") + (version "3.99-0.8") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "0qibvacbfm7gl41ylway3vdyi1qbpa211d48rg3k5i30d48rbf58")))) + "0l3bsgqw4bicv3sl2bfag7p4rh1y2pcyg0ajr73kkbg85qf6j7q8")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -3039,14 +3054,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.3-3") + (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "16036lp0dq7qqzy8wc4qsgv58zksz6hmgw51v88gl6xclryc670y")))) + "0bchqcy308kbywavgyg9kb4543rbkfn753q9c6d7l7aw7sxvyxl2")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") @@ -3197,43 +3212,400 @@ using the multicore functionality of the parallel package.") (license license:gpl2+))) (define-public r-dt - (package - (name "r-dt") - (version "0.17") - (source (origin - (method url-fetch) - (uri (cran-uri "DT" version)) - (sha256 - (base32 - "0mpvyfmi2viyhdqx11hznd7dl0q6kxrdmppjsmm2pk0x8a904hz3")))) - (properties - `((upstream-name . 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"datatables-extensions/Scroller") + + ("https://cdn.datatables.net/searchbuilder/1.0.0/js/dataTables.searchBuilder.js" + "0n5g0j0yfzqvdpsmwb27bj1rd8zx864fsx2k7b2kpv6mqqavzpqc" + "datatables-extensions/SearchBuilder") + ("https://cdn.datatables.net/searchbuilder/1.0.0/js/searchBuilder.bootstrap.js" + "1gnd8rjcg9c96xayshn9rwinzgmlwzddczjlpfmf2j33npmyka2y" + "datatables-extensions/SearchBuilder") + ("https://cdn.datatables.net/searchbuilder/1.0.0/js/searchBuilder.bootstrap4.js" + "0vdv5mi6zbp2dspmj0lw2vaqxvfadcydlmc6frqv4a68rms7wz05" + "datatables-extensions/SearchBuilder") + ("https://cdn.datatables.net/searchbuilder/1.0.0/js/searchBuilder.dataTables.js" + "0fbzfnaqswb2xq7m1vdzcg7l7qi0wmyz64ml6k4002kp0dm4xnlx" + "datatables-extensions/SearchBuilder") + + ("https://cdn.datatables.net/searchpanes/1.1.1/js/dataTables.searchPanes.js" + "1s697avk42h24fsaq79d1kkw66dqig7xgpx9bvmhwncv8amkmz6i" + "datatables-extensions/SearchPanes") + 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"1781d0xmx7xz0jly0wsw2zbrdmfc1crahmcdbsfbj5s66kdsnd7c" + "datatables-extensions/SearchPanes") + + ("https://cdn.datatables.net/select/1.3.1/js/dataTables.select.js" + "0a7bkbz1cizhiq4h417b4rcdr7998pn8q4dlyzx8449xdp0h0n0v" + "datatables-extensions/Select") + ("https://cdn.datatables.net/select/1.3.1/js/select.bootstrap.js" + "0mm5ly3p2iprlfi8ajz548rjqx8lz1sbjj5ysgqmwqg14gw7l9k7" + "datatables-extensions/Select") + ("https://cdn.datatables.net/select/1.3.1/js/select.bootstrap4.js" + "1hv6d9lwgflmxhy7mdfb9rvli2wa2cbkdhqjz64zkf1a1a7wlb5q" + "datatables-extensions/Select") + ("https://cdn.datatables.net/select/1.3.1/js/select.foundation.js" + "1zzygcbngvrqh7m22x0s23k8m5xj5fv1p466pzjs23p94qq24a2r" + "datatables-extensions/Select") + ("https://cdn.datatables.net/select/1.3.1/js/select.jqueryui.js" + "1hv5zlmfifd27hylfqsji09y2hbp3m2hnb7j41418sjrxs63f6x6" + "datatables-extensions/Select") + ("https://cdn.datatables.net/select/1.3.1/js/select.semanticui.js" + "0q6q3vb6pa5nmkxy7zcnjs0bkn4ldw8ykdcfrc04bf1d2hjjaw47" + "datatables-extensions/Select")))) + (package + (name "r-dt") + (version "0.19") + (source (origin + (method url-fetch) + (uri (cran-uri "DT" version)) + (sha256 + (base32 + "04rv1rprqlc56hycxpqkbmwmq4wjvmanq2lwxrflmf2s46pbv9ms")) + (modules '((guix build utils))) + (snippet + '(for-each delete-file + (find-files "inst/htmlwidgets/lib" "\\.min\\.js$"))))) + (properties + `((upstream-name . "DT"))) + (build-system r-build-system) + (arguments + `(#:modules + ((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules + (,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + (modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (for-each (match-lambda + ((url hash dir) + (let* ((input (string-append "js:" (basename url))) + (source (assoc-ref inputs input)) + (target (string-append dir "/" + (basename url ".js") + ".min.js"))) + (mkdir-p dir) + (minify source #:target target)))) + ',javascript-sources) + (minify (string-append (assoc-ref inputs "datatables-plugins") + "/features/scrollResize/dataTables.scrollResize.js") + #:target "datatables-plugins/features/scrollResize/source.min.js") + (minify (string-append (assoc-ref inputs "datatables-plugins") + "/features/searchHighlight/dataTables.searchHighlight.js") + #:target "datatables-plugins/features/searchHighlight/source.min.js") + (minify (assoc-ref inputs "js-nouislider") + #:target "nouislider/jquery.nouislider.min.js") + + (let ((replace-file (lambda (old new) + (format #t "replacing ~a with ~a\n" old new) + (symlink new old)))) + (replace-file "selectize/selectize.min.js" + (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))) + (inputs + `(("js-selectize" ,js-selectize))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("uglifyjs" ,node-uglify-js) + ("datatables-plugins" + ,(let ((version "1.10.20")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DataTables/Plugins.git") + (commit version))) + (file-name (git-file-name "datatables-plugins" version)) + (sha256 + (base32 + "05zni20863ml1711lfllljdfkb3k05h0kpqhkijkbp0bp7q0ak94"))))) + ("js-nouislider" + ,(let ((version "7.0.10")) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/leongersen/noUiSlider/" + version "/distribute/jquery.nouislider.js")) + (sha256 + (base32 + "1f7vsfcn7wwzngib6j0wpl0psd6qriiaa6kv728ynfn5da73zfxm"))))) + ,@(map (match-lambda + ((url hash dir) + `(,(string-append "js:" (basename url)) + ,(origin (method url-fetch) + (uri url) + (sha256 (base32 hash)))))) + javascript-sources))) + (home-page "https://rstudio.github.io/DT") + (synopsis "R wrapper of the DataTables JavaScript library") + (description + "This package allows for data objects in R to be rendered as HTML tables using the JavaScript library @code{DataTables} (typically via R Markdown or Shiny). The @code{DataTables} library has been included in this R package.") - ;; The DT package as a whole is distributed under GPLv3. The DT package - ;; inludes other software components under different licenses: - ;; - ;; * Expat: jQuery, jquery.highlight.js, DataTables - ;; * ASL2.0: selectize.js - ;; * WTFPL: noUiSlider - (license (list license:gpl3 - license:expat - license:asl2.0 - license:wtfpl2)))) + ;; The DT package as a whole is distributed under GPLv3. The DT package + ;; inludes other software components under different licenses: + ;; + ;; * Expat: jquery.highlight.js, DataTables + ;; * WTFPL: noUiSlider + (license (list license:gpl3 + license:expat + license:wtfpl2))))) (define-public r-base64enc (package @@ -3278,13 +3650,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "4.1-1") + (version "4.1-2") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "0zpfq0m1y5zks5p9r28553ykywwrhrb3ds8m6b7sm6hj4n1c4csd")))) + (base32 "1kfd8kfhapx2cxw6qnkbs502c3kya4pd9qmf0mk76cdlq1c2paq6")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -3354,14 +3726,14 @@ package registries.") (define-public r-rngtools (package (name "r-rngtools") - (version "1.5") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "rngtools" version)) (sha256 (base32 - "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42")))) + "0kd7x214cqw7hzpmk1iqy1bn7j6x0ady0yz2hsdbclbq9k57d33z")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest))) @@ -3402,14 +3774,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-6") + (version "1.7-9") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "0blfnv3m5k5xm9bfx1v5awvagqlhqaqpabrvzplf4244c3j259qa")))) + "09i2hmyf1bxansqp24p9n9djlzzarclqs173gjjv3fg0giga3ycv")))) (build-system r-build-system) (propagated-inputs `(("r-class" ,r-class) @@ -3541,13 +3913,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.10.1") + (version "2.11.0") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "1gssnk73nhisc20by9kvfl4byfsmwrk6597na0x40ycck58lyylm")))) + "1n7y4dzls7dc8fdkm9zncq4cpiblb2a9vwirwjkf72zpjpwn0a32")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -3563,15 +3935,20 @@ developing R packages.") (define-public r-r-cache (package (name "r-r-cache") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "R.cache" version)) (sha256 (base32 - "1n8n5ihkryrbxv630dwhz4r048nyv676qd3i9f5z5fa04hvlxbqq")))) + "09pipn1974ivjh4sm3n5fjlh31rilf87p30qwq7y25vriyqd7d5d")))) (properties `((upstream-name . "R.cache"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-digest" ,r-digest) ("r-r-methodss3" ,r-r-methodss3) @@ -3598,6 +3975,11 @@ persistent (on the file system).") "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-digest" ,r-digest) ("r-r-cache" ,r-r-cache) @@ -3621,13 +4003,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.1-1") + (version "1.1-2") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "1pj51mi0g6ip7a2nhzc93yv9289kaayvspjvsbgbgarvx7axlrg9")))) + "05wh7mprf2sim2kxh3d72pdcmml6vbikzxavws1dq6mxwlsy2p7j")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -3640,15 +4022,20 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.58.0") + (version "0.61.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "0jab3xk56vqqzgz8jbsvxvsvr83sj0gb3cic0906wjyjijwv8rw3")))) + "16pxsba5i51ifbbgvxln2w6nigbwd3290b2ckgzn5bmib7nc1lyv")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes (home-page "https://github.com/HenrikBengtsson/matrixStats") @@ -3664,13 +4051,13 @@ memory usage.") (define-public r-viridis (package (name "r-viridis") - (version "0.5.1") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "viridis" version)) (sha256 (base32 - "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx")))) + "1fyax36ycjiypcnxhrv58pq67qv03vfg4lx822d38jpjly54q128")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -3693,14 +4080,14 @@ most common form of color blindness.") (define-public r-viridislite (package (name "r-viridislite") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "viridisLite" version)) (sha256 (base32 - "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq")))) + "0siwr0vq80gs3sbyd542zjb0cl9av5zqdm0fqnym5g6ribf5b6c4")))) (properties `((upstream-name . "viridisLite"))) (build-system r-build-system) (home-page "https://github.com/sjmgarnier/viridisLite") @@ -3719,14 +4106,14 @@ more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "14rqx4dq574hilmdwrr34wyjg8rlw4rvndpsqd9plgxm3wwfsdg6")))) + "0ss8mq05mwif64cj8zmrfx0ljgy3n0fvyv7f37782shr8rknmsqq")))) (build-system r-build-system) (propagated-inputs `(("r-ellipsis" ,r-ellipsis) @@ -3833,13 +4220,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.9.3") + (version "4.9.4.1") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "0801i2q7sw62x734d58h9p2fwpi1hirqj73gsg18pqkdv4b1lkfl")))) + "1q711c0lg0jmzrmcc2fhjy70ms49as7cakdbgbh2ij9s149fa7iq")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) @@ -4118,14 +4505,14 @@ hierarchical clustering dendrograms.") (define-public r-fastcluster (package (name "r-fastcluster") - (version "1.1.25") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "fastcluster" version)) (sha256 (base32 - "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk")))) + "009amz7i5yndqw2008fgd3p11n4fsb291k2ypg3pip6dw4lr28hz")))) (build-system r-build-system) (home-page "http://danifold.net/fastcluster.html") (synopsis "Fast hierarchical clustering routines") @@ -4143,14 +4530,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-10") + (version "1.1-12") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "1skxahq5jgqdsllpsavzrcpz8l0yj3mfzcf70as8d33jxbiaa4s4")))) + "10h76pgzcxv1y5pkmba9607lvjrsyq62sq63s2n7ry7z5151h4lv")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4162,23 +4549,15 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.8.2") + (version "3.9.2") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "1pnwy412wvhhvnnx8qg6s9hrgcnsfhnfcpf2560ipipk845acfsh")))) + "0lx97yafrms2mjym8rhcq5586z7s1iqgy8qfm4px3xl1yn5qkc83")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'make-deterministic - (lambda _ - (substitute* "R/checkReverseDependencies.R" - (("tempdir\\(\\)") "\"/tmp\"")) - #t))))) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") (description @@ -4355,13 +4734,13 @@ within a category based on their density using quasirandom noise.") (define-public r-beeswarm (package (name "r-beeswarm") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "beeswarm" version)) (sha256 (base32 - "1jsggypyww77hkcic03kdb3fp8h938qs142xi0lapzh62bkn2pjj")))) + "016mqcbdksialkmap56rprzna9b6cd6896ml9gl2n2h8yjdk7x2i")))) (build-system r-build-system) (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/") (synopsis "Implementation of bee swarm plots") @@ -4443,13 +4822,13 @@ Wall Street Journal, among others. This package also provides (define-public r-statmod (package (name "r-statmod") - (version "1.4.35") + (version "1.4.36") (source (origin (method url-fetch) (uri (cran-uri "statmod" version)) (sha256 (base32 - "1zpqnfslq5gi6hvqjqnsn5kf2m986s1yb6kvyjd881n3h67l4pny")))) + "1hkvklcav6gj4zib4g3b4xwsdsbsmnzdblr0v6jaqv227p49gs0l")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/statmod") (native-inputs @@ -4615,14 +4994,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-2") + (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij")))) + "0l49cmxm1n4dzrv8q3q3mq4drcjgby4f1dmpwfdb8jxn9ij85vz9")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/fastICA") @@ -4658,14 +5037,14 @@ forest of trees using random inputs, for classification and regression.") (define-public r-diptest (package (name "r-diptest") - (version "0.75-7") + (version "0.76-0") (source (origin (method url-fetch) (uri (cran-uri "diptest" version)) (sha256 (base32 - "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6")))) + "10629vwn6r2949jjrmj5slbb5v0vnm3w0v8mrl7ws68m2sxmx2jh")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/diptest") (synopsis "Hartigan's dip test statistic for unimodality") @@ -4772,14 +5151,14 @@ data for species delimitation, nearest neighbor based noise detection.") (define-public r-deoptimr (package (name "r-deoptimr") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 - "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4")))) + "04k5gi0a5hbm6znzvjaipbmkacp694krkqs38dkbxx1gymsallb1")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") @@ -4795,14 +5174,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.93-7") + (version "0.93-8") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "0mh9d114p3jdrjf8yn4dx5ff41niz5wn411y0ckjcpnazp8d44c9")))) + "16fmnk3p32mi70rkx89l1v4pry3gnrpy9jicnlfnk6lg1pwz5j8w")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -4818,14 +5197,14 @@ regression methodology including model selections and multivariate statistics.") (define-public r-pcapp (package (name "r-pcapp") - (version "1.9-73") + (version "1.9-74") (source (origin (method url-fetch) (uri (cran-uri "pcaPP" version)) (sha256 (base32 - "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa")))) + "1dlrz5plb8b89vr3j6sn9jwryyhcwflqkiilxkybbr379m1pp0sh")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs @@ -4840,14 +5219,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.5-5") + (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0ag6q16ajkqwj28dk9vp4xkvqw26fqqqdxnz38gpszilirahfzqz")))) + "0i69gv55c86gkclwhch0jzdfyb20l20mx1nx1xp9qz71nd4klpvr")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -4999,14 +5378,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.4-3") + (version "1.5-0") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "08gb6c8p1r9z8wrfidj2dfn6irm43k6f4448d1d6nxmy6msjirlg")))) + "0m8a0ygwl98cs0vcha5gs9f7z8whcplwxhravhs9bfp5hvigxzgg")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") @@ -5112,13 +5491,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.85") + (version "5.86") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "1y8sgl16yby1k7g23y6bdnfllwnxj3iik3fqp96iwm5jd8blb7q4")))) + (base32 "01fnp6ndh7npxj76xlynndacsgmcfr9kgh2waw0clx3mmwlwilbi")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -5168,14 +5547,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-26") + (version "1.1-27.1") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "0ls2krph4pfjn45vf9fn3ln3x98s85wxrkvm5pnxyx55n1pnsjrn")))) + "1i9f8kl2qj48j75dbn1vmwxz1xlbikdr7v2yq542w6dq74z8gyi5")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -5186,8 +5565,7 @@ algorithms.") ("r-nloptr" ,r-nloptr) ("r-nlme" ,r-nlme) ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-statmod" ,r-statmod))) + ("r-rcppeigen" ,r-rcppeigen))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/lme4") @@ -5251,13 +5629,13 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.0-10") + (version "3.0-11") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "1w95b7xm0bna3qm637pwyv4s7294ffz9dl153naprd79zv91dqqw")))) + (base32 "0b2l35656bi75hfvnjhzhlnrnbpjn0vv7nvny8gn65gm0rr94b5k")))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) @@ -5430,14 +5808,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.12.1") + (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w")))) + "02idcc6zbdz4wsi1mcwh7qyhmlbwvnzxwkdvvppxw7n2rh54z4v0")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -5710,31 +6088,14 @@ to any arbitrary string. In this case, it is up to you to set valid values.") (define-public python-rpy2 (package (name "python-rpy2") - (version "3.3.5") + (version "3.4.5") (source (origin (method url-fetch) (uri (pypi-uri "rpy2" version)) (sha256 (base32 - "1bs36rds5fq8821l5q85q2b25161rs9ppw5c26x0hjwj487gpcfj")) - ;; These patches should be removed with the next release. - (patches - (list - (origin - (method url-fetch) - (uri "https://github.com/rpy2/rpy2/commit/04c57598f00145d868ea8da31ac1b1e7c49f7570.patch") - (file-name "python-rpy2-fix-test-failure.patch") - (sha256 - (base32 - "1lqd3yxjfx1rxrybcmnapy0r6ambg9myrb98q4nlfhpxanwfdbbh"))) - (origin - (method url-fetch) - (uri "https://github.com/rpy2/rpy2/commit/685f67d0a6b47ea80e718116a10755019446aef7.patch") - (file-name "python-rpy2-r-console-test-fix.patch") - (sha256 - (base32 - "18wpvfaa4c13d44cb4sw88c3c7403xdy5m8h82wfq8fjmcq3cmzn"))))))) + "1cysswxr5glrdblyl2zsmywcj7xhxn3wmyihxinrz9gm8gmaacax")))) (build-system python-build-system) (arguments '(#:modules ((ice-9 ftw) @@ -5907,6 +6268,33 @@ is designed to support editing of scripts and interaction with various statistical analysis programs such as R, Julia, and JAGS.") (license license:gpl3+)))) +(define-public emacs-poly-r + (package + (name "emacs-poly-r") + (version "0.2.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/polymode/poly-R") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0a4wx73jkngw5nbq1fa4jfhba6bsmyn6vnsf887x3xhb5v3ykhsg")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-ess" ,emacs-ess) + ("emacs-poly-noweb" ,emacs-poly-noweb) + ("emacs-polymode-markdown" ,emacs-polymode-markdown) + ("emacs-polymode" ,emacs-polymode))) + (properties '((upstream-name . "poly-R"))) + (home-page "https://github.com/polymode/poly-markdown") + (synopsis "Polymodes for the R language") + (description + "This package provides a number of polymodes for working with mixed R +files, including Rmarkdown files.") + (license license:gpl3+))) + (define-public readstat (package (name "readstat") @@ -6086,3 +6474,232 @@ input, the effect size can be returned as standardized mean difference, Cohen's f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds, or eta squared effect size.") (license license:gpl3))) + +(define-public r-kknn + (package + (name "r-kknn") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "kknn" version)) + (sha256 + (base32 + "1nzkg3dxaiqp87p56wm895qx5xn86hv5hjr73qvl1yiaxiq0x112")))) + (properties `((upstream-name . "kknn"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix))) + (home-page "https://github.com/KlausVigo/kknn") + (synopsis "Weighted k-Nearest Neighbors") + (description + "Weighted k-Nearest Neighbors for Classification, Regression and Clustering.") + (license license:gpl2+))) + +(define-public r-logspline + (package + (name "r-logspline") + (version "2.1.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "logspline" version)) + (sha256 + (base32 + "12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l")))) + (properties `((upstream-name . "logspline"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page + "https://cran.r-project.org/web/packages/logspline/") + (synopsis + "Routines for Logspline Density Estimation") + (description + "Contains routines for logspline density estimation. The function +@code{oldlogspline()} uses the same algorithm as the logspline package version +1.0.x; i.e. the Kooperberg and Stone (1992) algorithm (with an improved +interface). The recommended routine @code{logspline()} uses an algorithm from +@url{doi:10.1214/aos/1031594728,Stone et al (1997)}.") + (license license:asl2.0))) + +(define-public r-effects + (package + (name "r-effects") + (version "4.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "effects" version)) + (sha256 + (base32 + "0iks79rd4knrd81x4kvcpgpclr69l0m0v6sfla8k3wzkcnydycv8")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr) + ("r-car", r-car))) + (home-page "https://www.r-project.org") + (synopsis + "Effect Displays for Linear, Generalized Linear, and Other Models") + (description + "Graphical and tabular effect displays, e.g., of interactions, for +various statistical models with linear predictors.") + (license license:gpl2+))) + +(define-public r-bayesfactor + (package + (name "r-bayesfactor") + (version "0.9.12-4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "BayesFactor" version)) + (sha256 + (base32 + "1z083v7is21gm0a458jm5ph3xfdm7mh29a6sg2r1njq82f8x3s3g")))) + (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))) + (home-page + "https://richarddmorey.github.io/BayesFactor/") + (synopsis + "Computation of Bayes Factors for Common Designs") + (description + "This package provides a suite of functions for computing various Bayes +factors for simple designs, including contingency tables, one- and two-sample +designs, one-way designs, general ANOVA designs, and linear regression.") + (license license:gpl2))) + +(define-public r-norm + (package + (name "r-norm") + (version "1.0-9.5") + (source (origin + (method url-fetch) + (uri (cran-uri "norm" version)) + (sha256 + (base32 + "01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,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 +normal model.") + ;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE. + (license (license:non-copyleft "file://LICENSE")))) + +(define-public r-naniar + (package + (name "r-naniar") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (cran-uri "naniar" version)) + (sha256 + (base32 + "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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/njtierney/naniar") + (synopsis + "Data structures, summaries, and visualisations for missing data") + (description + "Missing values are ubiquitous in data and need to be explored and +handled in the initial stages of analysis. The package provides data structures +and functions that facilitate the plotting of missing values and examination of +imputations. This allows missing data dependencies to be explored with minimal +deviation from the common work patterns of @code{ggplot2} and tidy data.") + (license license:expat))) + +(define-public r-glinternet + (package + (name "r-glinternet") + (version "1.0.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "glinternet" version)) + (sha256 + (base32 + "0aphdscj0s6kqxlkgqkw2d6snrylz6hiis6307pl8ldh7q5cvm33")))) + (build-system r-build-system) + (home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf") + (synopsis "Learning interactions via hierarchical group-lasso regularization") + (description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction +models that satisfy strong hierarchy: if an interaction coefficient is estimated +to be nonzero, then its two associated main effects also have nonzero estimated +coefficients. Accommodates categorical variables (factors) with arbitrary +numbers of levels, continuous variables, and combinations thereof. Implements +the machinery described in the paper \"Learning interactions via hierarchical +group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3). +Michael Lim & Trevor Hastie (2015)") + (license license:gpl2))) + +(define-public r-datasaurus + (package + (name "r-datasaurus") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "datasauRus" version)) + (sha256 + (base32 + "1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl")))) + (properties `((upstream-name . "datasauRus"))) + (build-system r-build-system) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/lockedata/datasauRus") + (synopsis "Datasets from the Datasaurus Dozen") + (description + "The Datasaurus Dozen is a set of datasets with the same summary +statistics. They retain the same summary statistics despite having radically +different distributions. The datasets represent a larger and quirkier object +lesson that is typically taught via Anscombe's Quartet (available in the +'datasets' package). Anscombe's Quartet contains four very different +distributions with the same summary statistics and as such highlights the value +of visualisation in understanding data, over and above summary statistics. As +well as being an engaging variant on the Quartet, the data is generated in a +novel way. The simulated annealing process used to derive datasets from the +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))) |