diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 1311 |
1 files changed, 744 insertions, 567 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 88f833174a..7ba75cf59d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -12,7 +12,7 @@ ;;; 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, 2022 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> @@ -45,6 +45,7 @@ #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system r) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) @@ -73,6 +74,7 @@ #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) + #:use-module (gnu packages ocaml) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -83,6 +85,7 @@ #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) + #:use-module (gnu packages swig) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -204,7 +207,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -212,7 +215,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0gv4di1x835i4nsy21vqw66c0blmmmvyjkixc5a8x117dm4dnljd")))) + "1x9xjl6fyzs8r72zigirp905ki50wzyw9rxf7iqsbbsixi12pxhg")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -308,7 +311,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (("\\(2008\\)\n") "(2008) ") ((" ``Software") "``Software") (("Data Analysis:.") "Data Analysis:\n") - (("Programming with R") " Programming with R")))) + (("Programming with R") " Programming with R")) + (substitute* "src/library/tools/DESCRIPTION.in" + (("codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr") + "codetools, methods, xml2, curl, commonmark, + knitr, xfun, mathjaxr")))) (add-before 'build 'set-locales (lambda _ (setlocale LC_ALL "C") @@ -364,48 +371,48 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ ;; As the JDK is a rather large input with only very limited effects on R, ;; we decided to drop it. (native-inputs - `(("bzip2" ,bzip2) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo) ; for building HTML manuals - ("texlive" ,(texlive-updmap.cfg (list texlive-ae - texlive-inconsolata - texlive-fonts-ec - texlive-grfext - texlive-amsfonts - texlive-latex-base - texlive-fancyvrb - texlive-graphics - texlive-hyperref - texlive-oberdiek - texlive-tools - texlive-latex-upquote - texlive-url - texlive-latex-xkeyval))) - ("tzdata" ,tzdata-for-tests) - ("xz" ,xz))) + (list bzip2 + perl + pkg-config + texinfo ; for building HTML manuals + (texlive-updmap.cfg (list texlive-ae + texlive-inconsolata + texlive-fonts-ec + texlive-grfext + texlive-amsfonts + texlive-latex-base + texlive-latex-fancyvrb + texlive-latex-graphics + texlive-hyperref + texlive-oberdiek + texlive-latex-tools + texlive-latex-upquote + texlive-url + texlive-latex-xkeyval)) + tzdata-for-tests + xz)) (inputs - `(;; We need not only cairo here, but pango to ensure that tests for the - ;; "cairo" bitmapType plotting backend succeed. - ("pango" ,pango) - ("coreutils" ,coreutils) - ("curl" ,curl) - ("openblas" ,openblas) - ("gfortran" ,gfortran) - ("icu4c" ,icu4c) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxt" ,libxt) - ("pcre2" ,pcre2) - ("readline" ,readline) - ;; This avoids a reference to the ungraftable static bash. R uses the - ;; detected shell for the "system" procedure. - ("bash" ,bash-minimal) - ("tcl" ,tcl) - ("tk" ,tk) - ("which" ,which) - ("zlib" ,zlib))) + (list coreutils + curl + openblas + gfortran + icu4c + libjpeg-turbo + libpng + libtiff + libxt + ;; We need not only cairo here, but pango to ensure that tests for the + ;; "cairo" bitmapType plotting backend succeed. + pango + pcre2 + readline + tcl + tk + which + zlib + ;; This avoids a reference to the ungraftable static bash. R uses the + ;; detected shell for the "system" procedure. + bash-minimal)) (native-search-paths (list (search-path-specification (variable "R_LIBS_SITE") @@ -446,29 +453,23 @@ available, greatly increasing its breadth and scope.") (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" + "~a/[^-]+-(~{~a~^|~})-[^/]+" + (%store-directory) + '("bzip2" + "file" + "glibc-utf8-locales" + "graphite2" "libselinux" "libsepol" - "file" + "perl" + "texinfo" "texlive-bin" "util-macros" - "graphite2")) + "xz")) "|" - "/gnu/store/[^-]+-glibc-[^-]+-static" + (format #false "~a/[^-]+-glibc-[^-]+-static" + (%store-directory)) ")/lib")) "")))))))))))) (define-public rmath-standalone @@ -486,14 +487,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-28") + (version "1.3-28.1") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "0cjafhqv1c1mrjjcasqr767vs96wjcc6am9r1icryr8l4zymhwcz")))) + "0lzz08fpn80qzm197s4806hr6skanr3r3rlx6bx7zk4cripygkfl")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") @@ -591,14 +592,14 @@ code for possible problems.") (define-public r-foreign (package (name "r-foreign") - (version "0.8-82") + (version "0.8-84") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "1yw07yqzfm4w1h92ijyamrmf7rmkqxgamqfd74x7zv4vsn20dvgq")))) + "0jc5r5wiqqbkni2xjdd24hic1xvfi151m9lnqhni52jnqw1g7v8p")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") @@ -655,14 +656,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.5-1") + (version "1.5-3") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0pap6pb0is2s02l43y982p7banwi844bjpgbcgf6fb8pb01vlzam")))) + "03g0zqkbaa1k52i0d0yyn7vclmg93hdqaid48sbc1ccpvi70ywjf")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -677,13 +678,13 @@ and operations on them using LAPACK and SuiteSparse.") (define-public r-nlme (package (name "r-nlme") - (version "3.1-159") + (version "3.1-161") (source (origin (method url-fetch) (uri (cran-uri "nlme" version)) (sha256 - (base32 "1gqrv4skfgcny4pdpmymdwjcmsd3hla84s76g18dgqj665f5zc4v")))) + (base32 "0pw9kwhac6a01zcchl4xxy2rk3ghzc9kxxn6kjkh2z4iq41a1z9a")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -699,13 +700,13 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-40") + (version "1.8-41") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 - (base32 "19g4lzxjw931s68ni7ii81jwi25sf19qs8nlw8r94crvdhk2grnv")))) + (base32 "14769zs1sh1bz3c87hs4vhy2y9n28vglfqfrdgpysxdyw87h6yig")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-nlme)) @@ -721,14 +722,14 @@ distributions beyond the exponential family.") (define-public r-nnet (package (name "r-nnet") - (version "7.3-17") + (version "7.3-18") (source (origin (method url-fetch) (uri (cran-uri "nnet" version)) (sha256 (base32 - "0rws3rkd7dz1maz2mkld29jfrixjgacay8rqz7nmi82a2sw0nxgf")))) + "1l73v6l9ma0vsg4za3c6i3d6yjj7bpdmakbmrzp7205hbkxyp6nj")))) (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") @@ -740,14 +741,14 @@ single hidden layer, and for multinomial log-linear models.") (define-public r-rpart (package (name "r-rpart") - (version "4.1.16") + (version "4.1.19") (source (origin (method url-fetch) (uri (cran-uri "rpart" version)) (sha256 (base32 - "0p22657j6ps6z1dn0ja2fhq4k5xd1rv3cpwzk6nmjd2si8jpbv17")))) + "0rcm4hk2k0ag9qmb0f933yqrq8jpnclwrzp6825swgsqnp83wwpy")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rpart") (synopsis "Recursive partitioning and regression trees") @@ -825,14 +826,14 @@ curves, Cox models, and parametric accelerated failure time models.") (define-public r-bit (package (name "r-bit") - (version "4.0.4") + (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "bit" version)) (sha256 (base32 - "0s7isadibxp2wr62r5cpbyh9z31sczzfz4j3rm7gxgjfpqgq8174")))) + "1g5zakrzkhrqh3d7p1zka6zzzw11rdlbrvxsh05s7dkli1m57wph")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -944,13 +945,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.29") + (version "0.6.31") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "1ncwc5fwsylwlcp9vhkhszw8m5sifg74apig2m2pf168lha1yb3r")))) + (base32 "1f9isi4i2502f88c2sh4l461hgyary2aa02zd47pb9mc1r4lya2s")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. @@ -1078,13 +1079,13 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (define-public r-plyr (package (name "r-plyr") - (version "1.8.7") + (version "1.8.8") (source (origin (method url-fetch) (uri (cran-uri "plyr" version)) (sha256 - (base32 "0zz88q055c38b9xqzfg1mwm7ikxzlyx3pnk16sfa8dbh2pqxm7vx")))) + (base32 "030706kwgqa2s5jd93ck271iqb0pj3fshrj9frg4wgp1pfs12cm7")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (home-page "http://had.co.nz/plyr") @@ -1137,14 +1138,14 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org") (define-public r-sendmailr (package (name "r-sendmailr") - (version "1.2-1.1") + (version "1.3-2") (source (origin (method url-fetch) (uri (cran-uri "sendmailR" version)) (sha256 (base32 - "1dgxl6wnadlw5b3m4has5zalpk3pd5j70hfps92b9lbx4i7xbmr0")))) + "0yyxxzhm88xipk68vzqxcckcpjgl9lajnqyxxbkp1i29jcpfgdfa")))) (properties `((upstream-name . "sendmailR"))) (build-system r-build-system) (propagated-inputs @@ -1186,16 +1187,16 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (define-public r-stringr (package (name "r-stringr") - (version "1.4.1") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "stringr" version)) (sha256 - (base32 "1cfw1lv64lzg16zb04c0fcmd3gx8vq9x73hqikqhgqd3ra88w3gc")))) + (base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj")))) (build-system r-build-system) (propagated-inputs - (list r-glue r-magrittr r-stringi)) + (list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs)) ;; We can't add r-knitr here, because this package ends up being an input ;; to r-knitr. #; @@ -1234,25 +1235,28 @@ using just two functions: melt and dcast (or acast).") (define-public r-ggplot2 (package (name "r-ggplot2") - (version "3.3.6") + (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "ggplot2" version)) (sha256 - (base32 "1aa377jdfajj8ld2fh159y8havlibsr4pjisf6mkzk8g5awlxjxz")))) + (base32 "0gj7n2y8msnmhk3x4r481biknvn2dqhahwazfqwr8f3lz599wbx8")))) (build-system r-build-system) (propagated-inputs - (list r-digest + (list r-cli + r-digest r-glue r-gtable r-isoband + r-lifecycle r-mass r-mgcv r-tibble r-rlang r-scales r-svglite ; Needed for 'ggsave' + r-vctrs r-withr)) (native-inputs (list r-knitr)) @@ -1426,13 +1430,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.16") + (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "009861l805z4c10cz0pyym5qd2b2wsiignjkz74vl25718k0mz0h")))) + "1k36mpb12nvcr5bv3n6591shhr38d6zpfwgj643cgprd8l0kvk39")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") @@ -1446,13 +1450,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.12") + (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "12wch1774113nlrc0lihfn5rbh4hln9sg6dv6zc2bvyb8fzyyllb")))) + "09z5wvbhrr2s2d196cxwzvjn0qr6pf4czrfqwdzqgqrdpwrxq1xj")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -1468,13 +1472,13 @@ There is also a Shiny app as a user interface in this package.") (define-public r-highr (package (name "r-highr") - (version "0.9") + (version "0.10") (source (origin (method url-fetch) (uri (cran-uri "highr" version)) (sha256 (base32 - "0kgdv2vf1lz3b5kbal9s83gg6812nw7fvrq0rkyr0v4k1lwi3zxy")))) + "0yrlpjs8qzq1d7iy4gypnf4x1gvxq6vaghkdh1kfv433yqgvqmgc")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -1512,13 +1516,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "1.1") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d")))) + "0ziwirplzjcci2km6wln035qfd2irjl58r77kl98r8s257kavqz0")))) (build-system r-build-system) ;; Skip check phase because the tests require the r-knitr package to be ;; installed. This prevents installation failures. Knitr normally @@ -1526,7 +1530,7 @@ data derived from /etc/mime.types in UNIX-type systems.") ;; package. (arguments `(#:tests? #f)) (propagated-inputs - (list r-mime r-xfun)) + (list r-commonmark r-mime r-xfun)) (home-page "https://github.com/rstudio/markdown") (synopsis "Markdown rendering for R") (description @@ -1538,13 +1542,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.3.5") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "0h2ixd95ww12ir13fdzbvjq4lsz6l8hmgv4bbsi89qd0ah2nrpry")))) + "09msw6k0hsazjna53ya3c6p8alfajs7cw5k2rm62xvslcs6rvlax")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") @@ -1556,13 +1560,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.40") + (version "1.41") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1g1mhnkyxd2sv6p1l6iph9dnmpbwxhah78xx4kq543ks6vzrb3wv")))) + "1izv1m56ngc20wx4da9mmr5ll6ah14ka8dqn9i3pd7ah70lmya81")))) (build-system r-build-system) (propagated-inputs (list r-evaluate r-highr r-stringr r-xfun r-yaml)) @@ -1659,13 +1663,13 @@ you call it again with the same arguments it returns the pre-computed value.") (define-public r-crayon (package (name "r-crayon") - (version "1.5.1") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "crayon" version)) (sha256 (base32 - "1yaxwkmvjaillngfafgapakqjl6s86ly3j338f78xs58g0xwf9f0")))) + "0yjsnhifr3nipaid0q11jjglvqmp51g9d2xdh9kfxh5knl2sbabh")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/crayon") (synopsis "Colored terminal output for R") @@ -1699,19 +1703,18 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.1.4") + (version "3.1.6") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "02cwdix7v8zsvcmcl3h5hfi66w1ln9qi60risf5nl62f3c1yqzm4")))) + "1bndjkwv6f9x3a0wklwnf7bymn655yhw6cmazb285hbmci0qrjx7")))) (build-system r-build-system) (propagated-inputs (list r-brio r-callr r-cli - r-crayon r-desc r-digest r-ellipsis @@ -1761,13 +1764,13 @@ defined in different packages.") (define-public r-rlang (package (name "r-rlang") - (version "1.0.5") + (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "rlang" version)) (sha256 (base32 - "1argj8pvf8b19693r6j7rw1fl4bd99b39h5y52qrm1wpcvjkba9d")))) + "0q372q8cdc3c5pf8pmjyp7qc7lb5krg47apfl46iqc7al2c3v5z6")))) (build-system r-build-system) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") @@ -1927,14 +1930,14 @@ side.") (define-public r-locfit (package (name "r-locfit") - (version "1.5-9.6") + (version "1.5-9.7") (source (origin (method url-fetch) (uri (cran-uri "locfit" version)) (sha256 (base32 - "0xilf6gp3m8xla2fvxr491j31pvim707mnhswvm9yxnb0d09xs0y")))) + "1zvsa7hvnp0pvjyy0nnrg8bdv8gv4l23jb66wkc0kipvi78grra8")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -1948,13 +1951,13 @@ and density estimation.") (define-public r-chron (package (name "r-chron") - (version "2.3-57") + (version "2.3-58") (source (origin (method url-fetch) (uri (cran-uri "chron" version)) (sha256 (base32 - "0cn2367mw27qf2nj8d1i182ns3nlzlkgix6c18mc3byihimdhicn")))) + "1l36yy9jq6hxkg9rfbsggwhjsb33scb56di0klmw4c73rllcczq5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/chron") (synopsis "Chronological R objects which can handle dates and times") @@ -1966,13 +1969,14 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.14.2") + (version "1.14.6") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "0arx5wna0sh0vf5q8rjhh8nqdmnvg2pdpbhljl9l0x4kwm8vjhgp")))) + "05h99rk2s1ds9igrqw2nhnk6yahgssszqlnw0y0p9p83lsndp30x")))) + (properties `((upstream-name . "data.table"))) (build-system r-build-system) (inputs (list zlib)) @@ -2007,6 +2011,36 @@ and fast file reading.") "This package provides tools to export R data as LaTeX and HTML tables.") (license license:gpl2+))) +(define-public python-hdmedians + (package + (name "python-hdmedians") + (version "0.14.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "hdmedians" version)) + (sha256 + (base32 + "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs (list python-cython python-numpy)) + (native-inputs (list python-nose)) + (home-page "http://github.com/daleroberts/hdmedians") + (synopsis "High-dimensional medians") + (description "Various definitions for a high-dimensional median exist and +this Python package provides a number of fast implementations of these +definitions. Medians are extremely useful due to their high breakdown +point (up to 50% contamination) and have a number of nice applications in +machine learning, computer vision, and high-dimensional statistics.") + (license license:asl2.0))) + (define-public python-patsy (package (name "python-patsy") @@ -2108,14 +2142,14 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-19") + (version "1.7-20") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "1vv5y6badksnpjb3bcphhjdzzh6i2grmwnsalcf2cfpr3y412lf8")))) + "0yxd9dgci3rzz807wsb76wis12ipgjv9w86smdyz20jrnn45giyx")))) (build-system r-build-system) (propagated-inputs (list r-mass r-pixmap r-sp)) @@ -2199,13 +2233,13 @@ previous R versions and their release dates.") (define-public r-whisker (package (name "r-whisker") - (version "0.4") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "whisker" version)) (sha256 (base32 - "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks")))) + "1g7jy6dnc5igs7yqy1n7cmy0ia8dm2yi3qj1mil2y0q88m4m2ldz")))) (build-system r-build-system) (home-page "https://github.com/edwindj/whisker") (synopsis "Logicless mustache templating for R") @@ -2264,14 +2298,14 @@ worries about execution time overhead.") (define-public r-bbmisc (package (name "r-bbmisc") - (version "1.12") + (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "BBmisc" version)) (sha256 (base32 - "0gh5f342rwra79i7imv50x8vrhd2zkifm7khb0yv3ndpd4zn62lh")))) + "01a43raxj374cg6khs14r0bxvfm8v1sp0p2ambp7npnizvwxqi8i")))) (properties `((upstream-name . "BBmisc"))) (build-system r-build-system) (propagated-inputs @@ -2339,13 +2373,13 @@ SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") (define-public r-brew (package (name "r-brew") - (version "1.0-7") + (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "brew" version)) (sha256 (base32 - "0vp7d628j6zzxhh6xfw5jlkv7wh6z2l3snbwjgv7jd56vk0mkf1q")))) + "09kq14nbaw0mmpb2vbfklz786q6lyizzkyg5bg64bmj2f1d2sr8i")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/brew") (synopsis "Templating framework for report generation") @@ -2380,14 +2414,14 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "0s765c650id19ygx57bsjsw93fwxywmp50zid671bkxi6wlyf1vx")))) + "1gjwpmcxv15y1jg9f7kzp49s68kj1skjsh5g264f9lp37l4wpbcn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") @@ -2403,13 +2437,13 @@ tables, autolinks and strikethrough text.") (define-public r-roxygen2 (package (name "r-roxygen2") - (version "7.2.1") + (version "7.2.3") (source (origin (method url-fetch) (uri (cran-uri "roxygen2" version)) (sha256 (base32 - "08fs5jw6npriqsr8pribs2yy1r8163xzcv4gmlgmcaywj4jk9w6j")))) + "1nhn0jhnxzlyqx0qnpd7k7q3azzngyn0j4zs8awmlmyjfywzli6q")))) (build-system r-build-system) (propagated-inputs (list r-brew @@ -2417,7 +2451,6 @@ tables, autolinks and strikethrough text.") r-commonmark r-cpp11 r-desc - r-digest r-knitr r-pkgload r-purrr @@ -2439,14 +2472,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "2.0.3") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1al6cb0qwafa32dxr2hhhv6hvbp26hiykamn7w27z1gc1d99ipkw")))) + "1lw60yq20r42l7y1wbp79s3mk3dwg62v0dh7jx1cdd7rb46i9hla")))) (build-system r-build-system) (arguments (list @@ -2548,13 +2581,13 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "2.4.4") + (version "2.4.5") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "0kckjr12qi8nw498x3iw648pllz63j5p6fhpv8z8jc4z4sfpbmmc")))) + "0jwh14clyj5flygpmifk01avs7mbnj2s1686pxzfrkcshfyhw5iq")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -2631,13 +2664,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "2.1.2") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "06qcw57yz0fhh3ni41d5w68cbmwmb6zkp47chllwzax43wxd1bwl")))) + "0qw2c51421zzfwpy1nkmxs9ai1r9m4yxrz0ig0wg2z78h1gda3fp")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -2726,13 +2759,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.11.2.4.0") + (version "0.11.4.2.1") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1y499idmci72x6gpj855vf4rlzh1r2qqpxyzs53r59ay8f4g0jar")))) + "172vz9j1hck6iwk56hgsrg91n4f11df1n6hy1crbv3cb53rkyjgn")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2818,13 +2851,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.16") + (version "2.19") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "0wgsc5ax4wynviasyxr240fkjk0g1wm9aq7b42mx66f43424xlyk")))) + (base32 "14lvvdq3n95qbl7nrqlym1lp05i17m6f9mx3ly35iip83p2s9hir")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2935,13 +2968,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "2.2.17") + (version "2.2.20") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "16l64ganvdlaldmqryz2c95id2m8vchlj9x5rz9kppbmhy122vjw")))) + "1km7rg2yg3lmjz7lplypw61sx78mykyksgbdq3j5kjpcvirdbdaj")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2965,13 +2998,13 @@ engine (version 3.8.8.2) is included.") (define-public r-rcurl (package (name "r-rcurl") - (version "1.98-1.8") + (version "1.98-1.9") (source (origin (method url-fetch) (uri (cran-uri "RCurl" version)) (sha256 (base32 - "0a4gr264ycy6am4849y79h3vc9vg7cgpizb88v4xw076pyn52fqy")))) + "1iff8cbfrz94mp1m82ai448zhipm8xv6zlxmbysd5hsycxqli3gj")))) (properties `((upstream-name . "RCurl"))) (build-system r-build-system) (arguments @@ -3007,13 +3040,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.99-0.10") + (version "3.99-0.13") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "0nzkgylnqnnvsh27007np8klwv2xi9wqxhw05mzczhxdxnsr2nf4")))) + "0fppx0jnqxx3l7y8ivb56sq0fjcqv3fn226i4s03mi7hwak6iic5")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) @@ -3128,14 +3161,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "1.6-0") + (version "1.6-2") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "0sg59j59kz3zrwl3mi4ps1qw3hvwljygqa1d652vjdsx9w57zbvb")))) + "0livckkhci3w1x9xai2m0a30fj06qsks2qds7y5jr9vwx03jqg21")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -3284,303 +3317,339 @@ using the multicore functionality of the parallel package.") 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"DT"))) (build-system r-build-system) @@ -3637,7 +3706,7 @@ using the multicore functionality of the parallel package.") `(("r-knitr" ,r-knitr) ("uglifyjs" ,node-uglify-js) ("datatables-plugins" - ,(let ((version "1.10.20")) + ,(let ((version "1.12.0")) (origin (method git-fetch) (uri (git-reference @@ -3646,7 +3715,7 @@ using the multicore functionality of the parallel package.") (file-name (git-file-name "datatables-plugins" version)) (sha256 (base32 - "05zni20863ml1711lfllljdfkb3k05h0kpqhkijkbp0bp7q0ak94"))))) + "15kiqjy0ssd2ksvrqv8jyg9gc92ga3kn542vp1mij5hnfcbj6hf8"))))) ("js-nouislider" ,(let ((version "7.0.10")) (origin @@ -3699,14 +3768,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.3.5") + (version "2.3.5.1") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "1fcv4vazg2sbsda8qqjjsjn2wagcp2bsahvznwm443j66q6qrz16")))) + "1ky5nlmyrnwz6121wwqd8p8r1ycnjkl5r290k4x2477rzs267zic")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) @@ -3721,13 +3790,13 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "4.1-4") + (version "4.1-6") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 - (base32 "1y80a3b5s24ywhlil3r7b3a0vs9j59d7jkxrqa8zz09x1c5ggc7n")))) + (base32 "0c3y9g3k0f0yclcffxzgfhfylb3py0iydhyspcjdrl44lb7cdi5y")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -3846,14 +3915,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-11") + (version "1.7-12") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "0byr92csnydycdarxdkq4cghddnx5qp6fqxm6wnp9g6aww88xha8")))) + "1ksxbkf2zb1hs353vc1qr8n2l7v0vcldn2prdnk79nr1lp855q4i")))) (build-system r-build-system) (propagated-inputs (list r-class r-proxy)) @@ -3868,13 +3937,13 @@ computation, bagged clustering, naive Bayes classifier, and more.") (define-public r-bigmemory-sri (package (name "r-bigmemory-sri") - (version "0.1.3") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "bigmemory.sri" version)) (sha256 - (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m")))) + (base32 "03468ak0lgd9m0f7synxms2zzr8f7n2nm1gmhcraj3nfcv4nmyiv")))) (properties `((upstream-name . "bigmemory.sri"))) (build-system r-build-system) @@ -3981,13 +4050,13 @@ maintenance for package developers.") (define-public r-r-utils (package (name "r-r-utils") - (version "2.12.0") + (version "2.12.2") (source (origin (method url-fetch) (uri (cran-uri "R.utils" version)) (sha256 (base32 - "00v5hpdid6h1yiwpf631xf1dk1z6dcx7dx83qn56a7pa4194bpkl")))) + "0dl8rc7s7vg4g2pkmrwwqx7dkm02096jk439x4s0cm21hsmg2g7y")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) (propagated-inputs @@ -4082,13 +4151,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.62.0") + (version "0.63.0") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "1jjfsi5vzx6js7phlnd3v64fd05fg0jyz8iq5pivy36jdmmh3ql5")))) + "0pqz6mn5l7inh464yj45i6rf8ycab0zdvvjczwsv0bkl442bc060")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments @@ -4164,17 +4233,17 @@ more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "1.1.2") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "0w423pmg9wjx6q2rnp2ap66323rxvpmzd4nnsqq4m58pajqs7283")))) + "0fwy4qp3j0ksy15rkrh3588h7wa8c21h0fzx5s762zg34yvjd3ak")))) (build-system r-build-system) (propagated-inputs - (list r-ellipsis r-glue r-purrr r-rlang r-vctrs)) + (list r-cli r-glue r-lifecycle r-rlang r-vctrs r-withr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tidyselect") @@ -4249,17 +4318,17 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.3.4") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3")))) + "1hm6lylx05s43rdk9q7xqdcydz495aim16c7xlw94lyw7v5l81kz")))) (build-system r-build-system) (propagated-inputs - (list r-magrittr r-rlang)) + (list r-cli r-lifecycle r-magrittr r-rlang r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/hadley/purrr") @@ -4272,14 +4341,53 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.10.0") + (version "4.10.1") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "16iqj7sv49mva6siibsci7iijsbnk7pqvfns9al0k35w9mjmr6dx")))) + "0yin1kid3a69fcwrrajwzqbhx4xc81x8p8m0yfh1fkm2rfhj22dc")) + (modules '((guix build utils))) + (snippet + '(with-directory-excursion "inst/htmlwidgets/lib/" + (for-each delete-file + '("plotlyjs/plotly-latest.min.js" + "colourpicker/colourpicker.min.js" + "typedarray/typedarray.min.js" + "selectize/selectize.min.js")))))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (symlink (string-append (assoc-ref inputs "js-selectize") + "/share/javascript/selectize.min.js") + "selectize/selectize.min.js") + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-plotly") + "plotlyjs/plotly-latest.min.js") + (,(string-append (assoc-ref inputs "js-colourpicker") + "/js/colourpicker.js") + "colourpicker/colourpicker.min.js") + (,(string-append (assoc-ref inputs "js-typedarray") + "/typedarray.js") + "typedarray/typedarray.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #t "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) (propagated-inputs (list r-base64enc r-crosstalk @@ -4302,6 +4410,48 @@ features present in other programming languages.") r-tidyr r-vctrs r-viridislite)) + (native-inputs + `(("esbuild" ,esbuild) + ("js-colourpicker" + ,(let ((commit "27c2a266d51e18a9fe6d7542264152b27c7d34e0") + (version "1.1") + (revision "0")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daattali/jquery-colourpicker") + (commit commit))) + (file-name (git-file-name "jquery-colourpicker" + (git-version version revision commit))) + (sha256 + (base32 + "0lg8amh8xh6p246j38rqghrljd7v5z34i169ra6403z8ga33wiqb"))))) + ("js-plotly" + ,(let ((version "2.11.1")) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/v" + version "/dist/plotly.js")) + (sha256 + (base32 + "1mxd8s4v3i885w5i02cyzqsrvqfr9w0svdclvqxbd05dly4bdkbj"))))) + ("js-selectize" ,js-selectize) + ;; This is not quite the same as the bundled minified script from 2016, + ;; but it seems to be the original with fixes from late 2017. + ("js-typedarray" + ,(let ((commit "9f7d4168657e2c164d647a6959f402f2c33eb5b4") + (version "0") + (revision "0")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/inexorabletash/polyfill/") + (commit commit))) + (file-name (git-file-name "typedarray-polyfill" + (git-version version revision commit))) + (sha256 + (base32 + "0f9np4mmyhny03n3xpwzs07rld30lnfqsnh97x1v7xm0qy0zjanf"))))))) (home-page "https://plot.ly/r") (synopsis "Create interactive web graphics") (description @@ -4314,14 +4464,14 @@ data behind them) can be viewed and modified in a web browser.") (define-public r-biased-urn (package (name "r-biased-urn") - (version "1.07") + (version "2.0.8") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) + "0mmq8zf52p6y76nqm0fcvvg8bdlrfl12mlfr9fznz9zvm26pypi0")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://www.agner.org/random/") @@ -4407,31 +4557,55 @@ from within R.") (define-public r-spams (package (name "r-spams") - (version "2.6-2017-03-22") - (source - (origin - (method url-fetch) - ;; Use the ‘Latest version’ link for a stable URI across releases. - (uri (string-append "https://gforge.inria.fr/frs/download.php/" - "latestfile/4531/spams-R-v" version ".tar.gz")) - (sha256 - (base32 - "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx")))) + (version "2.6.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.inria.fr/thoth/spams-devel") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qvj87fw4sm54c7dvhxjgmgvnyyrrz9fk6dqp3ak0gwgb42gqh60")))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "spams") #t)) - ;; Don't tune for the building machine. - (add-after 'chdir 'no-mtune - (lambda _ - (substitute* "src/Makevars" - (("-mtune=native") "")) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'patch-generated-file-shebangs 'patch-paths + (lambda _ + (substitute* (cons* "swig/setRelease" + "swig/R/docmatlab2R" + "swig/R/mkdist" + (find-files "." "(^mk|\\.sh$)")) + (("/bin/pwd") "pwd") + (("/bin/rm") "rm")))) + (add-after 'patch-paths 'mkdist + (lambda _ + (chdir "swig/R") + (setenv "TEXINPUTS" (string-append (getcwd) "/../../doc:")) + (substitute* "mkdist" + (("^SWIG=.*") + (string-append "SWIG=" (which "swig"))) + (("^../mkdoc") "")) ;requires texlive-aeguill + (invoke "./mkdist") + (chdir "dist/spams-R/spams"))) + ;; Don't tune for the building machine. + (add-after 'mkdist 'no-mtune + (lambda _ + (substitute* "src/Makevars" + (("-mtune=native") ""))))))) + (native-inputs + (list hevea + perl + swig + ;;texlive-aeguill ;;FIXME: package me! + texlive-base + texlive-jknappen)) (propagated-inputs - (list r-lattice r-matrix)) - (home-page "https://spams-devel.gforge.inria.fr") + (list r-lattice + r-matrix)) + (home-page "https://gitlab.inria.fr/thoth/spams-devel/") (synopsis "Toolbox for solving sparse estimation problems") (description "SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. It includes tools for the @@ -4473,13 +4647,13 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.7-1") + (version "4.7-2") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "0zrfi2mmi6wfl6440iqflzzmkina8dhxia2qsamqw6djd0d5fp9j")))) + (base32 "0lyacs5q6mdg9lirixl9r2dqs9ljxyn5d53mmb04ci0jam3vk0wc")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs @@ -4580,14 +4754,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-13") + (version "1.1-14") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0622yf4fl1b1zm988dfwdrhq7pg0rllhm8wz1pqdmp72glsi05x8")))) + "1vxkziprndrzc5sdz36i20qdqfcyw8m87vpxm3jccf6pqbc45adw")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -4599,14 +4773,14 @@ Zurich, including many that are related to graphics.") (define-public r-gtools (package (name "r-gtools") - (version "3.9.3") + (version "3.9.4") (source (origin (method url-fetch) (uri (cran-uri "gtools" version)) (sha256 (base32 - "0criwc0jmbrgaslh2kdjirgdzbf0ycry8yjryi95fb9qgckm7yvs")))) + "04gihp78x2caahqvf0mlv1cqy1m121l6hkdvbp01r2z99wcqpksr")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") @@ -4821,16 +4995,16 @@ representation of R code.") (define-public r-ggbeeswarm (package (name "r-ggbeeswarm") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "ggbeeswarm" version)) (sha256 (base32 - "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v")))) + "14mc00i107rww3al5q3rrqmd1v0ck06jipfhzqi23g29a4rm05gl")))) (build-system r-build-system) (propagated-inputs - (list r-beeswarm r-ggplot2 r-vipor)) + (list r-beeswarm r-ggplot2 r-lifecycle r-vipor)) (home-page "https://github.com/eclarke/ggbeeswarm") (synopsis "Categorical scatter (violin point) plots") (description @@ -4864,13 +5038,13 @@ Wall Street Journal, among others. This package also provides (define-public r-statmod (package (name "r-statmod") - (version "1.4.37") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "statmod" version)) (sha256 (base32 - "04v9nynv3lakhnd7b17v5syrlnscrxml71jnd3r93chckskwillh")))) + "1jbf07h0mnncn2qp4wcw5bnbvsw3lizpd3cg0cpb8mcxn3wkw76n")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/statmod") (native-inputs @@ -4983,17 +5157,17 @@ letters, as is often required for scientific publications.") (define-public r-mixtools (package (name "r-mixtools") - (version "1.2.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "mixtools" version)) (sha256 (base32 - "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg")))) + "03by64xi7yka0hzc1qyz1jdqzah6isvr3cdsc7g5v6hb4f178kl5")))) (build-system r-build-system) (propagated-inputs - (list r-mass r-kernlab r-segmented r-survival)) + (list r-mass r-kernlab r-plotly r-scales r-segmented r-survival)) (home-page "https://cran.r-project.org/web/packages/mixtools") (synopsis "Tools for analyzing finite mixture models") (description @@ -5137,14 +5311,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.4.10") + (version "6.0.0") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0wh6nsbma4b0wsmqm2ynbznl2wlwdly4vg583f6z0zd1qkrvn6ra")))) + "0ahj5161lmid0gxyw6vidd4ig50l1374iisn9970zvx1rdp30z6y")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -5229,14 +5403,14 @@ regression methodology including model selections and multivariate statistics.") (define-public r-pcapp (package (name "r-pcapp") - (version "2.0-2") + (version "2.0-3") (source (origin (method url-fetch) (uri (cran-uri "pcaPP" version)) (sha256 (base32 - "0jxm1cl48bzfi0s0f2b0y0r5nq7x0iypgkasa3v5myhb9sbnd2x1")))) + "00ynanxpngzsvq5fsyalyzqz6axqcryy94300afvylwp0d7mbb0s")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) (propagated-inputs @@ -5251,14 +5425,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.7-1") + (version "1.7-2") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "1rd4r4acgpr25x2iy7v2mnahmmf76a378zq16gnpwv5ljycs05g1")))) + "1bpc401515ig5i3rka7dhvxv4zr3f8zhl117pby5vrf9rc3ys08g")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) @@ -5347,14 +5521,14 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-9") + (version "2.2-10") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19")))) + "1lj7j74yx747iic1hcngzbym0sqxppja8bxw64m0j6na5s7m9d4r")))) (build-system r-build-system) (propagated-inputs (list r-class @@ -5403,14 +5577,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.5-0") + (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "0m8a0ygwl98cs0vcha5gs9f7z8whcplwxhravhs9bfp5hvigxzgg")))) + "0qbzqgxz3lm97y0k9v2radqblzb4r5zkfrjw5wj1a91dvxz3xhg8")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") @@ -5423,14 +5597,14 @@ showing the progress is useful e.g. bootstrap.") (define-public r-minqa (package (name "r-minqa") - (version "1.2.4") + (version "1.2.5") (source (origin (method url-fetch) (uri (cran-uri "minqa" version)) (sha256 (base32 - "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg")))) + "1gpli7f3piz3jqjj63a6bk9v1jlygjdaqqqvqsr083crj0imd0wv")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -5446,14 +5620,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.3.9.2") + (version "0.3.3.9.3") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "14ylrq7mmylmi513zkwyqqy43kqbz95fc6fzpagqvyx6snaffir5")))) + "0xhwgn77166ir7qnzl25mj0byskkqr0b36hihrpr2zaqsrzs8wsq")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs @@ -5573,14 +5747,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-30") + (version "1.1-31") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "03rhg6cnsvdk06a1yxkivfvfwlx9934nd9q6jnp0bzscnv2dzazx")))) + "1zgdfbzc8lv4rrsjdacagwa693ij2bmn6xkc1bnfbv1z7pix3zss")))) (build-system r-build-system) (propagated-inputs (list r-boot @@ -5655,25 +5829,25 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "08ga187qqnl7cih7kzzzw9jx5sq63lq4ad6rrj7q5kj6xbmb8lmx")))) + (base32 "1g6jdcxl2aig6zirdn3k5l48sjmpljzy1aadnlr6mr6pxqamiicg")))) (build-system r-build-system) (propagated-inputs (list r-abind r-cardata r-lme4 - r-maptools r-mass r-mgcv r-nlme r-nnet r-pbkrtest - r-quantreg)) + r-quantreg + r-scales)) (native-inputs (list r-knitr)) (home-page "https://r-forge.r-project.org/projects/car/") @@ -5736,14 +5910,14 @@ normals.") (define-public r-mnormt (package (name "r-mnormt") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "mnormt" version)) (sha256 (base32 - "1f07ngi89px437az030anbh8afmf6n635ax1akxak2idwc2qaj9d")))) + "020ka48jsxm9l109ksvy2l17xcpm51avm0l971dgs2mgg01sgz4m")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -5803,14 +5977,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.5-1") + (version "1.5-2") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "09zk38gih67a8lk72k46mfgv21jpnxh2nzrxc5ypdc2bfwq8nckk")))) + "12vg9q35srddjidrn3q955xybn6ldraya35s4955ypj61arp89j9")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs @@ -5901,17 +6075,17 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.8.0") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "199b00cql07gf3rf4hh5ba34amnk0ai40zhx73dq1mpkn7ynxml7")))) + "0flh3arja7al9xznj5jvicadvq1kb2s63zyg63wlx2bii8gh8dmr")))) (build-system r-build-system) (propagated-inputs - (list r-generics r-cpp11)) + (list r-generics r-timechange)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/lubridate/") @@ -6229,25 +6403,23 @@ completion.") (define-public python-rpy2 (package (name "python-rpy2") - (version "3.4.5") + (version "3.5.5") (source (origin (method url-fetch) (uri (pypi-uri "rpy2" version)) (sha256 (base32 - "1cysswxr5glrdblyl2zsmywcj7xhxn3wmyihxinrz9gm8gmaacax")))) + "0dyhb3xn2p6s67yxhgh4qd4hp45mhb5zvgqkdsn26kyg447c8lm2")))) (build-system python-build-system) (arguments '(#:phases (modify-phases %standard-phases (replace 'check - (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((cwd (getcwd))) - (setenv "TZ" "UTC")) - ;; test_vector_complex has issues when run in our environment. - (invoke "pytest" "-v" "rpy2/tests/" - "-k" "not test_vector_complex")))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "TZ" "UTC") + (invoke "pytest" "-v" "rpy2/tests/"))))))) (propagated-inputs (list python-cffi python-six @@ -6624,14 +6796,14 @@ or eta squared effect size.") (define-public r-logspline (package (name "r-logspline") - (version "2.1.17") + (version "2.1.19") (source (origin (method url-fetch) (uri (cran-uri "logspline" version)) (sha256 (base32 - "05c8l22zcvb086909h9vw7icphww703vkcxp2h881y4n1232pdq3")))) + "1527cnnn5qdjp8gr4yls0jp0aachjz5s2v79vs79vrfyvxp9w89p")))) (properties `((upstream-name . "logspline"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -6852,13 +7024,13 @@ extreme-value distribution.") (define-public r-gld (package (name "r-gld") - (version "2.6.5") + (version "2.6.6") (source (origin (method url-fetch) (uri (cran-uri "gld" version)) (sha256 - (base32 "1scflrfhvf26psnh7ayi4x2j706k8sfyqlmib6ssjyhl6g0gg542")))) + (base32 "1i7xpyxd7r1fkjy9zkzd3rfsnb35v5c5fkafs1zd9d8729wfj8za")))) (properties `((upstream-name . "gld"))) (build-system r-build-system) (propagated-inputs (list r-e1071 r-lmom)) @@ -6885,13 +7057,13 @@ L-Moments and Distributional Least Absolutes.") (define-public r-exact (package (name "r-exact") - (version "3.1") + (version "3.2") (source (origin (method url-fetch) (uri (cran-uri "Exact" version)) (sha256 - (base32 "1kz3hw11sl142mai4ly2r85rwdbjz8q7b38ybmjym6r0n5qmqzyn")))) + (base32 "0a33gbhzd580i31xxsjxigg0nl8ag1x4xz3jqmq5jqappc6f5d2k")))) (properties `((upstream-name . "Exact"))) (build-system r-build-system) (propagated-inputs (list r-rootsolve)) @@ -6914,13 +7086,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.46") + (version "0.99.47") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "1f6jhvwgzv8mw5vmy7nqh8bpmrrzl36x1bq1ggnk3va24fcd01jq")))) + (base32 "0dd1n2dwyh8sdsmmsqj670hmawffqck35qdanrgb4yfcc0zzmd1j")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (propagated-inputs @@ -7089,34 +7261,39 @@ models, using simulation. It was designed to work with models fit using the (license license:gpl2+))) (define-public r-mixedpower - (package - (name "r-mixedpower") - (version "2.0") - (source - (origin - ;; Not available on CRAN. - (method git-fetch) - (uri (git-reference - (url "https://github.com/DejanDraschkow/mixedpower") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1dy1i8lijbq59xl7482j17a0r4rsdy61smzddk8jsr8nygp2gqy8")))) - (properties `((upstream-name . "mixedpower"))) - (build-system r-build-system) - (propagated-inputs - (list r-doparallel r-foreach r-ggplot2 r-lme4 r-reshape2)) - (home-page "https://github.com/DejanDraschkow/mixedpower") - (synopsis - "Pilotdata based simulations for estimating power in linear mixed models") - (description - "Implementation of a simulation based aproach to power analysis. Mixedpower uses -lotdata and a linear mixed model fitted with lme4 to simulate new data sets. -wer is computed seperate for every effect in the model output as the relation -significant simulations to all simulations. More conservative simulations as -protection against a bias in the pilotdata are available aswell as methods for -otting the results.") - (license license:gpl3))) + ;; This commit contains fixes for R>=4.2. A newer release does not exist. + (let ((commit "6520195481bca3ce01862ef80a28c53b0a35d0f5") + (revision "1")) + (package + (name "r-mixedpower") + (version (git-version "2.0" revision commit)) + (source + (origin + ;; Not available on CRAN. + (method git-fetch) + (uri (git-reference + (url "https://github.com/DejanDraschkow/mixedpower") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "114z9pvya2jg10y804ga41gq00r7zcw4a7c7234ybhmv3jqw78q1")) + (patches + (search-patches "r-mixedpower-r2power.patch")))) + (properties `((upstream-name . "mixedpower"))) + (build-system r-build-system) + (propagated-inputs + (list r-doparallel r-foreach r-ggplot2 r-lme4 r-reshape2)) + (home-page "https://github.com/DejanDraschkow/mixedpower") + (synopsis + "Pilotdata based simulations for estimating power in linear mixed models") + (description + "Implementation of a simulation based aproach to power analysis. +Mixedpower uses lotdata and a linear mixed model fitted with lme4 to +simulate new data sets. wer is computed separate for every effect in the +model output as the relation significant simulations to all simulations. +More conservative simulations as protection against a bias in the +pilotdata are available aswell as methods for otting the results.") + (license license:gpl3)))) (define-public r-colorway (let ((commit "8ba8f0026aba37752c6770de45bf53b1b0f48afc") |